This document summarizes research on the chloroplast gene organization and phylogenetic relationships of green algae. It finds that the chloroplast genomes of green algae like Chlamydomonas have undergone extensive rearrangements compared to land plants. A phylogenetic analysis of rRNA gene sequences from green algae places Chlamydomonas in two major lineages, with greater diversity than all land plants. Mapping of over 70 genes in C. reinhardtii and C. moewusii found they share a similar gene complement but with rearrangements. However, 40 genes were found in 13 conserved clusters, suggesting these were present in their common ancestor.
This document summarizes a study that probed the conformation of 18S rRNA in yeast 40S ribosomal subunits using kethoxal. Kethoxal reacts with unpaired guanine bases. Over 130 oligonucleotides were isolated from kethoxal-treated subunits and sequenced, identifying 48 kethoxal-reactive sites in the 18S rRNA. The results support the proposed secondary structure model for 18S rRNA derived from comparative sequence analysis. Reactivity at specific positions also argues for extensive structural homology between bacterial 30S and eukaryotic 40S subunits, particularly in regions involved in translation.
Molecular and cytogenetic phylogeography of h. malabaricuscmvolcker
Claudio Michael Völcker
Jorge A. Dergam
Molecular and karyotypic phylogeography in the Neotropical Hoplias malabaricus (Erythrinidae) fish in eastern Brazil
This document describes a thesis submitted by Alvaro Eugenio Rodríguez Mendoza to the University of Texas at Austin in partial fulfillment of the requirements for a Master of Arts degree. The thesis aimed to identify mutations that could enhance the evolutionary stability of green fluorescent protein expression from a plasmid in Escherichia coli. An evolution experiment was performed where a mutagenized E. coli population expressing GFP was periodically sorted by flow cytometry to select for cells with stable GFP expression over hundreds of generations. Genome sequencing of evolved strains with more stable GFP expression identified mutations in DNA polymerase genes PolA and PolB, which may enhance stability by lowering the mutation rate in the host.
The document discusses various biology concepts. It provides answers to 22 multiple choice questions related to topics like nucleolus function, T cell receptor engagement, amino acid roles in protein glycosylation, neurotransmitters, translation product molecular weight, protein separation techniques, membrane protein structure, epigenetics, plant hormones, genetic variation, primary production, electron microscope resolution, gene mapping, enzyme function, Mendel's experiments, speciation modes, niche competition, and vaccine success factors.
1. The document discusses biological classification and taxonomy. It contains 60 multiple choice questions related to topics like kingdoms, phyla, taxonomic ranks, binomial nomenclature, evolution, and key figures in the development of biological classification systems.
2. Some questions test understanding of taxonomic categories and their hierarchical relationships. Others ask about important classification systems developed by scientists like Linnaeus, Whittaker, and characteristics used to classify different groups of organisms.
3. The document serves as a review of core concepts in taxonomy and aims to assess understanding of biological classification through multiple choice questions.
pold ts mutant NAR00065-0214 (dragged)Hyunsun Park
This study characterized temperature-sensitive mutants of the DNA polymerase gene polb in the fission yeast Schizosaccharomyces pombe. The researchers generated three conditional lethal polb mutant alleles through random mutagenesis. At the restrictive temperature, all three mutants arrested in S phase of the cell cycle and exhibited a typical cell division cycle terminal phenotype. Sequencing revealed that the temperature-sensitive mutations were missense mutations altering amino acids uniquely conserved among known polymerase 6 sequences.
Genetic variability among the chloroplast genomes of sugarcane (Saccharum spp...Jianrong Zhu
This document describes a study analyzing genetic variability among the chloroplast genomes of sugarcane cultivars and Saccharum spontaneum. Nineteen primer pairs were designed to target polymorphic chloroplast DNA segments. Sequencing of the amplified regions revealed 14 mutation sites, including indels and SNPs. The chloroplast genomes of three Saccharum hybrids containing S. spontaneum cytoplasm were maternally inherited from S. spontaneum. Comparative analyses clustered sugarcane cultivars separately from S. spontaneum. Three species-specific mutation sites were identified. The genetic variability data can help determine maternal origins in the Saccharum genus.
This document summarizes a study that probed the conformation of 18S rRNA in yeast 40S ribosomal subunits using kethoxal. Kethoxal reacts with unpaired guanine bases. Over 130 oligonucleotides were isolated from kethoxal-treated subunits and sequenced, identifying 48 kethoxal-reactive sites in the 18S rRNA. The results support the proposed secondary structure model for 18S rRNA derived from comparative sequence analysis. Reactivity at specific positions also argues for extensive structural homology between bacterial 30S and eukaryotic 40S subunits, particularly in regions involved in translation.
Molecular and cytogenetic phylogeography of h. malabaricuscmvolcker
Claudio Michael Völcker
Jorge A. Dergam
Molecular and karyotypic phylogeography in the Neotropical Hoplias malabaricus (Erythrinidae) fish in eastern Brazil
This document describes a thesis submitted by Alvaro Eugenio Rodríguez Mendoza to the University of Texas at Austin in partial fulfillment of the requirements for a Master of Arts degree. The thesis aimed to identify mutations that could enhance the evolutionary stability of green fluorescent protein expression from a plasmid in Escherichia coli. An evolution experiment was performed where a mutagenized E. coli population expressing GFP was periodically sorted by flow cytometry to select for cells with stable GFP expression over hundreds of generations. Genome sequencing of evolved strains with more stable GFP expression identified mutations in DNA polymerase genes PolA and PolB, which may enhance stability by lowering the mutation rate in the host.
The document discusses various biology concepts. It provides answers to 22 multiple choice questions related to topics like nucleolus function, T cell receptor engagement, amino acid roles in protein glycosylation, neurotransmitters, translation product molecular weight, protein separation techniques, membrane protein structure, epigenetics, plant hormones, genetic variation, primary production, electron microscope resolution, gene mapping, enzyme function, Mendel's experiments, speciation modes, niche competition, and vaccine success factors.
1. The document discusses biological classification and taxonomy. It contains 60 multiple choice questions related to topics like kingdoms, phyla, taxonomic ranks, binomial nomenclature, evolution, and key figures in the development of biological classification systems.
2. Some questions test understanding of taxonomic categories and their hierarchical relationships. Others ask about important classification systems developed by scientists like Linnaeus, Whittaker, and characteristics used to classify different groups of organisms.
3. The document serves as a review of core concepts in taxonomy and aims to assess understanding of biological classification through multiple choice questions.
pold ts mutant NAR00065-0214 (dragged)Hyunsun Park
This study characterized temperature-sensitive mutants of the DNA polymerase gene polb in the fission yeast Schizosaccharomyces pombe. The researchers generated three conditional lethal polb mutant alleles through random mutagenesis. At the restrictive temperature, all three mutants arrested in S phase of the cell cycle and exhibited a typical cell division cycle terminal phenotype. Sequencing revealed that the temperature-sensitive mutations were missense mutations altering amino acids uniquely conserved among known polymerase 6 sequences.
Genetic variability among the chloroplast genomes of sugarcane (Saccharum spp...Jianrong Zhu
This document describes a study analyzing genetic variability among the chloroplast genomes of sugarcane cultivars and Saccharum spontaneum. Nineteen primer pairs were designed to target polymorphic chloroplast DNA segments. Sequencing of the amplified regions revealed 14 mutation sites, including indels and SNPs. The chloroplast genomes of three Saccharum hybrids containing S. spontaneum cytoplasm were maternally inherited from S. spontaneum. Comparative analyses clustered sugarcane cultivars separately from S. spontaneum. Three species-specific mutation sites were identified. The genetic variability data can help determine maternal origins in the Saccharum genus.
This document discusses the use of genetic markers to characterize livestock breeds for conservation purposes. It explains that livestock breeds represent a valuable genetic resource but many are at risk of extinction. Molecular genetic characterization using DNA markers provides a precise way to measure genetic diversity and relationships between breeds. This can help prioritize breeds for conservation in order to maintain maximum genetic diversity.
This document contains a biology exam with 44 multiple choice questions covering topics like biological organization, elements that make up living organisms, cell structures, plant and animal classification, evolution, and plant physiology. The questions test fundamental concepts in these subject areas and each question is followed by the correct multiple choice answer.
The document discusses a study investigating SVP, a gene involved in floral transition timing, in the Arabidopsis thaliana accession Dja-1. SVP is hypermethylated in Dja-1, which flowers early, whereas it is not methylated in other accessions. The study aimed to determine if DNA methylation of SVP (SVPepi) in Dja-1 causes its early flowering phenotype. Results showed SVPepi has the lowest expression in Dja-1. Treatment with demethylating agents reduced genomic methylation but did not significantly alter SVP expression or flowering time. However, the presence of a transposable element in SVPepi's promoter region suggests it may not be a
A complementation test (sometimes called a "cis-trans" test) can be used to test whether the mutations in two strains are in different genes. By taking an example of Benzer's work, complementation has been explained.
This document provides instructions for a Grade 12 Life Sciences exam. It consists of 14 pages and students have 2.5 hours to complete it. The exam contains 3 sections. Section A has 10 multiple choice questions worth 1 or 2 marks each, and short answer questions worth 1-8 marks. Section B contains diagram and graph interpretation questions worth 1-14 marks. Section C involves investigating the resistance of mosquitoes to DDT over time, with associated graphing and analysis questions worth 1-6 marks. Students are instructed to show all working, use scientific terms correctly, and answer all questions in full sentences in the answer book provided.
The study examines DNA double-strand break repair in Drosophila melanogaster mutants lacking both the Pif1 and Pol32 genes. PCR analysis confirms the generation of homozygous pif1 pol32 double mutant fly stocks, unlike in yeast where such double mutants are lethal. The pif1 pol32 double mutants are viable and fertile. Using a P-element excision assay to assess DNA repair, the study finds the double mutants exhibit significant defects in somatic repair of excised P-elements, compared to single mutants and wildtype flies.
This document provides information about a genetics course, including contact information for the professor and teaching assistants, grading policies, textbook and chapter information, homework assignments, and lecture topics. The lecture topics include principles of genetics, DNA structure and function, gene expression, protein structure and function, mutations, mitosis, meiosis, Mendelian inheritance patterns from monohybrid crosses, and the molecular basis of Mendel's experiments.
Gene loci that are located on the same chromosome are said to be linked, and will be inherited together. Unlinked genes on different chromosomes assort independently during meiosis. The document discusses inheritance of two traits controlled by unlinked genes in the fruit fly Drosophila melanogaster. It provides examples of setting up and solving Punnett squares for dihybrid crosses to determine expected genotypic and phenotypic ratios.
The document summarizes research on the Magdalena River turtle (Podocnemis lewyana) in northern Colombia. It includes:
1) Studies of the reproductive ecology, nesting biology, incubation temperatures, hatchling sex ratios and growth under field and laboratory conditions. Temperature-dependent sex determination was confirmed in this species.
2) Analysis of genetic variation between two populations that found low genetic differentiation.
3) Research on hatchling performance, such as running speed, righting response, and swimming ability, and how it relates to egg and hatchling measurements.
4) A discussion of potential impacts of climate change, including a potential expansion of the species' geographic range but negative consequences for
info-chemiclas inhance the efficacy of natural enemies in biological control. Infochemicals are chemicals that convey information in an interaction between two individuals evoking in receiver a behavioural or physiological response that is adaptive to one of interactants or both.
This study examines genetic variation in the Alabama hog sucker (Hypentelium etowanum) across river drainages in the southeastern United States using DNA sequencing of the mitochondrial cytochrome b gene. Tissue samples were collected from seven locations and DNA was extracted and amplified via PCR. Approximately 1150 base pairs of the cyt b gene were sequenced. Preliminary results found genetic variations between populations that are consistent with a previous study. The sequences from a new location in the Little Tallapoosa drainage were most closely related to those from the Chattahoochee drainage. This ongoing study aims to increase sampling to further resolve the genetic structure of H. etowanum across its range.
Detection of Genetic variation in tissue culture clones of date palm using IS...IJSRD
Date palm is a plant having high nutritional value and long life (yielding up to 100 years). Phoenix dactylifera requires 2-5 males for pollination of 100 females’ plant depending up on genetic and environment factors. Therefore paternity variation expected to very low according to PCR based techniques, Even though we have tried to find out genetic variation among tissue culture cloned plant. Tissue culture technique can be used for genetic improvement of date palm. The main purpose of this study was to evaluate the genetic variation in the tissue culture clones of date palm by using ISSR primers among mother and it’s two clones. The plant DNA was extracted and subjected to detection of genetic variation in two groups of date palm using ISSR primers. In this study ISSR primers produced monomorphic bands within group-1 and group-2. Genetic variation in tissue culture clones of date palm was not detecte by UBC primer series.
"Phylogeny-Driven Approaches to Genomics and Metagenomics" talk by Jonathan E...Jonathan Eisen
This document summarizes a talk given by Jonathan Eisen on October 23, 2013 at the University of Washington. The talk discussed four eras of sequencing and microbes, beginning with the establishment of the tree of life in the late 1970s/early 1980s based on rRNA sequencing. It then covered the use of rRNA sequencing in environmental samples in the 1990s to characterize microbial communities. Finally, it discussed how next generation sequencing revolutionized rRNA PCR and allowed for deeper sequencing of more samples and finer-scale spatial sampling of microbial communities.
This ppt contains few solved questions of GATE 2009 examination along with explanations. This will be helpful for all those who are preparing for GATE, CSIR, UGC NET, etc. Complete set of questions along with answers and explanations can be viewed at http://purnasrinivas.weebly.com
1) The document describes a study identifying new genes involved in gliding motility in Flavobacterium johnsoniae.
2) Transposon mutagenesis of an F. johnsoniae sprB mutant identified 8 mutants with increased phage resistance and reduced motility. 4 mutants had transposon insertions in remA, which encodes a cell surface protein with a lectin domain.
3) RemA was shown to localize to the cell surface and move rapidly along the cell surface, suggesting it acts as a mobile adhesin involved in gliding motility.
This document describes a study that developed a new method called amplified functional DNA restriction analysis (AFDRA) to analyze the diversity of catechol 2,3-dioxygenase (C23O) genes in soil bacteria. C23O genes code for enzymes important for degrading aromatic pollutants. The researchers used AFDRA to analyze C23O genes from reference strains and soil isolates. They found that AFDRA generated distinct restriction patterns that clustered the isolates into four groups, consistent with sequence analysis. AFDRA also allowed them to determine the predominant C23O gene variants present in environmental DNA extracts from soil samples. The study demonstrates that AFDRA provides a rapid way to assess functional gene diversity in cultures and
This study aims to determine if differences in alleles of the APETALA1 (AP1) gene are responsible for phenotypic differences between varieties of Brassica oleracea, specifically cauliflower and Rbo. The researchers generated F1 and F2 crosses between cauliflower and Rbo, which showed segregating phenotypes. They are determining the genotypes of the AP1a and AP1c alleles in the F2 plants to test if there is a correlation between genotype and phenotype. Preliminary results found the AP1c sequence from cauliflower is identical to sequences from broccoli and kale, suggesting AP1 may not be responsible for phenotypic differences as hypothesized.
cp genome of C. fruticosum: comparative and phlogenetic analysisFMSafiulAzam
The document describes the sequencing and analysis of the chloroplast genome of Corethrodendron fruticosum. Key findings include:
1) The C. fruticosum chloroplast genome is 123,100 bp in length and encodes 105 genes, including 74 protein-coding genes and 4 rRNA and 27 tRNA genes.
2) Comparative analysis with C. multijugum and four Hedysarum species revealed highly conserved genomes, with variation primarily in non-coding regions. The accD and clpP genes also exhibited high variability.
3) Phylogenetic analysis showed that C. fruticosum and C. multijugum formed separate clades from the four Hedysarum species,
This document describes a study comparing the phylogenetic relationships of green algal taxa from the order Chlamydomonadales based on analysis of sequences from the small subunit ribosomal RNA gene in the nucleus and the large subunit ribosomal RNA gene in the chloroplast. The results from both data sets show considerable congruence and support six distinct lineages within Chlamydomonadales that include taxa from the biflagellate genus Chlamydomonas as well as a basal lineage containing quadriflagellate Carteria taxa. Both data sets support the conclusion that Chlamydomonas is not monophyletic. The chloroplast data were ambiguous regarding Carteria monophyly while the nuclear data did not support it.
This document discusses the use of genetic markers to characterize livestock breeds for conservation purposes. It explains that livestock breeds represent a valuable genetic resource but many are at risk of extinction. Molecular genetic characterization using DNA markers provides a precise way to measure genetic diversity and relationships between breeds. This can help prioritize breeds for conservation in order to maintain maximum genetic diversity.
This document contains a biology exam with 44 multiple choice questions covering topics like biological organization, elements that make up living organisms, cell structures, plant and animal classification, evolution, and plant physiology. The questions test fundamental concepts in these subject areas and each question is followed by the correct multiple choice answer.
The document discusses a study investigating SVP, a gene involved in floral transition timing, in the Arabidopsis thaliana accession Dja-1. SVP is hypermethylated in Dja-1, which flowers early, whereas it is not methylated in other accessions. The study aimed to determine if DNA methylation of SVP (SVPepi) in Dja-1 causes its early flowering phenotype. Results showed SVPepi has the lowest expression in Dja-1. Treatment with demethylating agents reduced genomic methylation but did not significantly alter SVP expression or flowering time. However, the presence of a transposable element in SVPepi's promoter region suggests it may not be a
A complementation test (sometimes called a "cis-trans" test) can be used to test whether the mutations in two strains are in different genes. By taking an example of Benzer's work, complementation has been explained.
This document provides instructions for a Grade 12 Life Sciences exam. It consists of 14 pages and students have 2.5 hours to complete it. The exam contains 3 sections. Section A has 10 multiple choice questions worth 1 or 2 marks each, and short answer questions worth 1-8 marks. Section B contains diagram and graph interpretation questions worth 1-14 marks. Section C involves investigating the resistance of mosquitoes to DDT over time, with associated graphing and analysis questions worth 1-6 marks. Students are instructed to show all working, use scientific terms correctly, and answer all questions in full sentences in the answer book provided.
The study examines DNA double-strand break repair in Drosophila melanogaster mutants lacking both the Pif1 and Pol32 genes. PCR analysis confirms the generation of homozygous pif1 pol32 double mutant fly stocks, unlike in yeast where such double mutants are lethal. The pif1 pol32 double mutants are viable and fertile. Using a P-element excision assay to assess DNA repair, the study finds the double mutants exhibit significant defects in somatic repair of excised P-elements, compared to single mutants and wildtype flies.
This document provides information about a genetics course, including contact information for the professor and teaching assistants, grading policies, textbook and chapter information, homework assignments, and lecture topics. The lecture topics include principles of genetics, DNA structure and function, gene expression, protein structure and function, mutations, mitosis, meiosis, Mendelian inheritance patterns from monohybrid crosses, and the molecular basis of Mendel's experiments.
Gene loci that are located on the same chromosome are said to be linked, and will be inherited together. Unlinked genes on different chromosomes assort independently during meiosis. The document discusses inheritance of two traits controlled by unlinked genes in the fruit fly Drosophila melanogaster. It provides examples of setting up and solving Punnett squares for dihybrid crosses to determine expected genotypic and phenotypic ratios.
The document summarizes research on the Magdalena River turtle (Podocnemis lewyana) in northern Colombia. It includes:
1) Studies of the reproductive ecology, nesting biology, incubation temperatures, hatchling sex ratios and growth under field and laboratory conditions. Temperature-dependent sex determination was confirmed in this species.
2) Analysis of genetic variation between two populations that found low genetic differentiation.
3) Research on hatchling performance, such as running speed, righting response, and swimming ability, and how it relates to egg and hatchling measurements.
4) A discussion of potential impacts of climate change, including a potential expansion of the species' geographic range but negative consequences for
info-chemiclas inhance the efficacy of natural enemies in biological control. Infochemicals are chemicals that convey information in an interaction between two individuals evoking in receiver a behavioural or physiological response that is adaptive to one of interactants or both.
This study examines genetic variation in the Alabama hog sucker (Hypentelium etowanum) across river drainages in the southeastern United States using DNA sequencing of the mitochondrial cytochrome b gene. Tissue samples were collected from seven locations and DNA was extracted and amplified via PCR. Approximately 1150 base pairs of the cyt b gene were sequenced. Preliminary results found genetic variations between populations that are consistent with a previous study. The sequences from a new location in the Little Tallapoosa drainage were most closely related to those from the Chattahoochee drainage. This ongoing study aims to increase sampling to further resolve the genetic structure of H. etowanum across its range.
Detection of Genetic variation in tissue culture clones of date palm using IS...IJSRD
Date palm is a plant having high nutritional value and long life (yielding up to 100 years). Phoenix dactylifera requires 2-5 males for pollination of 100 females’ plant depending up on genetic and environment factors. Therefore paternity variation expected to very low according to PCR based techniques, Even though we have tried to find out genetic variation among tissue culture cloned plant. Tissue culture technique can be used for genetic improvement of date palm. The main purpose of this study was to evaluate the genetic variation in the tissue culture clones of date palm by using ISSR primers among mother and it’s two clones. The plant DNA was extracted and subjected to detection of genetic variation in two groups of date palm using ISSR primers. In this study ISSR primers produced monomorphic bands within group-1 and group-2. Genetic variation in tissue culture clones of date palm was not detecte by UBC primer series.
"Phylogeny-Driven Approaches to Genomics and Metagenomics" talk by Jonathan E...Jonathan Eisen
This document summarizes a talk given by Jonathan Eisen on October 23, 2013 at the University of Washington. The talk discussed four eras of sequencing and microbes, beginning with the establishment of the tree of life in the late 1970s/early 1980s based on rRNA sequencing. It then covered the use of rRNA sequencing in environmental samples in the 1990s to characterize microbial communities. Finally, it discussed how next generation sequencing revolutionized rRNA PCR and allowed for deeper sequencing of more samples and finer-scale spatial sampling of microbial communities.
This ppt contains few solved questions of GATE 2009 examination along with explanations. This will be helpful for all those who are preparing for GATE, CSIR, UGC NET, etc. Complete set of questions along with answers and explanations can be viewed at http://purnasrinivas.weebly.com
1) The document describes a study identifying new genes involved in gliding motility in Flavobacterium johnsoniae.
2) Transposon mutagenesis of an F. johnsoniae sprB mutant identified 8 mutants with increased phage resistance and reduced motility. 4 mutants had transposon insertions in remA, which encodes a cell surface protein with a lectin domain.
3) RemA was shown to localize to the cell surface and move rapidly along the cell surface, suggesting it acts as a mobile adhesin involved in gliding motility.
This document describes a study that developed a new method called amplified functional DNA restriction analysis (AFDRA) to analyze the diversity of catechol 2,3-dioxygenase (C23O) genes in soil bacteria. C23O genes code for enzymes important for degrading aromatic pollutants. The researchers used AFDRA to analyze C23O genes from reference strains and soil isolates. They found that AFDRA generated distinct restriction patterns that clustered the isolates into four groups, consistent with sequence analysis. AFDRA also allowed them to determine the predominant C23O gene variants present in environmental DNA extracts from soil samples. The study demonstrates that AFDRA provides a rapid way to assess functional gene diversity in cultures and
This study aims to determine if differences in alleles of the APETALA1 (AP1) gene are responsible for phenotypic differences between varieties of Brassica oleracea, specifically cauliflower and Rbo. The researchers generated F1 and F2 crosses between cauliflower and Rbo, which showed segregating phenotypes. They are determining the genotypes of the AP1a and AP1c alleles in the F2 plants to test if there is a correlation between genotype and phenotype. Preliminary results found the AP1c sequence from cauliflower is identical to sequences from broccoli and kale, suggesting AP1 may not be responsible for phenotypic differences as hypothesized.
cp genome of C. fruticosum: comparative and phlogenetic analysisFMSafiulAzam
The document describes the sequencing and analysis of the chloroplast genome of Corethrodendron fruticosum. Key findings include:
1) The C. fruticosum chloroplast genome is 123,100 bp in length and encodes 105 genes, including 74 protein-coding genes and 4 rRNA and 27 tRNA genes.
2) Comparative analysis with C. multijugum and four Hedysarum species revealed highly conserved genomes, with variation primarily in non-coding regions. The accD and clpP genes also exhibited high variability.
3) Phylogenetic analysis showed that C. fruticosum and C. multijugum formed separate clades from the four Hedysarum species,
This document describes a study comparing the phylogenetic relationships of green algal taxa from the order Chlamydomonadales based on analysis of sequences from the small subunit ribosomal RNA gene in the nucleus and the large subunit ribosomal RNA gene in the chloroplast. The results from both data sets show considerable congruence and support six distinct lineages within Chlamydomonadales that include taxa from the biflagellate genus Chlamydomonas as well as a basal lineage containing quadriflagellate Carteria taxa. Both data sets support the conclusion that Chlamydomonas is not monophyletic. The chloroplast data were ambiguous regarding Carteria monophyly while the nuclear data did not support it.
This study aimed to determine the phylogenetic relationships between 17 species of sea cucumbers found in Malaysia using sequences of the 16S mitochondrial rRNA gene. Phylogenetic trees were constructed using neighbor joining, maximum parsimony, and maximum likelihood methods. The trees showed five main genera of sea cucumbers were present: Molpadia, Holothuria, Stichopus, Bohadschia, and Actinopyga. However, one species of Holothuria was found to be outside of the Holothuria group, making it paraphyletic. Further studies with more samples and different mitochondrial DNA genes are needed to better understand the molecular phylogeny of sea cucumbers.
This document summarizes a study on the cytogenetics of seven ornamental Chrysanthemum species. The key findings are:
1) The species showed varying chromosome numbers of 2n=18, 2n=36. Some diploid species like C. carinatum showed structural heterozygosity involving reciprocal translocations.
2) Meiosis in most species involved bivalents, with some like C. morifolium and C. carinatum also forming multivalents. This led to irregular meiotic divisions and reduced pollen fertility in some cases.
3) Chiasma frequency varied from 14-16.8 per cell across species. C. leucanthemum in particular
Chloroplasts are organelles found in plant cells and algae that conduct photosynthesis. They contain their own DNA known as the chloroplast genome, which is typically 100-200kb in size and encodes genes for photosynthesis. The chloroplast genome is highly conserved and maternally inherited. It has been used for phylogenetic studies and shows potential for genetic engineering due to high transgene expression and maternal inheritance that prevents gene flow to other species.
Chloroplasts are double-membrane organelles found in plant cells that contain chlorophyll and are the site of photosynthesis. Chloroplast DNA is circular and ranges in size from 120,000 to 170,000 base pairs. It contains approximately 120 genes, including genes that encode proteins involved in photosynthesis and the transcription and translation machinery. Chloroplast DNA replication is semi-conservative and there are typically multiple copies of the chloroplast genome within each chloroplast.
The potato genome was sequenced using a homozygous doubled-monoploid potato clone. Analysis of the genome sequence revealed:
1) The potato genome is approximately 844 megabases in size, with over 39,000 predicted protein-coding genes.
2) There is evidence of at least two whole genome duplication events in the evolutionary history of potato, consistent with paleopolyploidy.
3) Compared to other plant genomes sequenced so far, the potato genome contains over 2,600 genes that are specific to the asterid plant clade, to which potato belongs.
Science 2013-schuenemann-179-83 leprosy önemliHazal Sav
This study obtained near-complete genome sequences of Mycobacterium leprae from skeletal remains dating from the 11th to 14th centuries in Europe, as well as from recent patient biopsies. Genome comparisons revealed remarkable genomic conservation of M. leprae over the past 1000 years. The ancient genomes suggest a European origin for leprosy in the Americas and the presence of a genotype in medieval Europe now commonly associated with the Middle East. Exceptional DNA and mycolic acid preservation in the ancient skeletal remains provides insights into pathogen evolution and the disappearance of leprosy in Europe.
This document describes the development of a multiplex PCR assay targeting the cgcA gene, which encodes a diguanylate cyclase, to differentiate between species within the genus Cronobacter. Analysis of 12 Cronobacter genomes identified 7 conserved diguanylate cyclase-encoding genes, one of which, cgcA, showed species-specific divergence that matched known phylogenetic relationships between Cronobacter species. Primers were designed for this gene and tested in a multiplex PCR assay on 305 Cronobacter isolates representing 6 species. The assay correctly identified the species of all isolates tested and did not identify any of 20 non-Cronobacter species, demonstrating high specificity and sensitivity for rapid identification of Cronobacter.
Chromosomes and molecular cytogenetics of oil palm: impact for breeding and g...Pat (JS) Heslop-Harrison
See also related talk Crops, Climate Change and Super-domestication Heslop-Harrison for Oil Palm Breeders symposium on Gearing Oil Palm Breeding and Agronomy for Climate Change: Keynote opening address MPOB PIPOC and PIPOC ISOPB ISOPA
http://www.slideshare.net/PatHeslopHarrison/heslop-harrisoncrops-climatechangesuperdomestication
Molecular cytogenetic analysis of the chromosomes of oil palm allows us to understand their evolution, genetics and segregation, genetic recombination and karyotypic stability. The cytogenetic manipulation of genomes and their chromosomes is often valuable for plant breeders to introduce and exploit new variation. Cytological landmarks such as centromeres, telomeres, heterochromatin and nucleolar organizer regions are important for the integration of physical chromosomes with the DNA sequence information. This linkage of the genetic, chromosomal and physical maps is particularly useful in a long-lived tree crop where genetic mapping requires decades of preparation and the mapping crosses may not be directly relevant to DxP commercial plantings. Repetitive DNA is often the most rapidly evolving genomic component, but is poorly understood from sequence assemblies; molecular cytogenetic studies allow its organization and variation to be studied, and the exploitation of repetitive sequences as markers and, by the amplification and mobility of transposable elements or satellite repeats, in generation of new variation.
Molecular cytogenetic approaches provide tools for oil palm genomic research, comparative genomics and evolutionary studies and further facilitate understanding the inheritance of specific traits in oil palm, including DNA methylation, epigenetics, and somaclonal variation, allowing work with hybrids, haploids and polyploids. Knowledge of the structures and organization of the chromosomes of oil palm, as in many crop species, is valuable for development of new lines, making hybrids, understanding the causes of some abnormalities or infertility, and exploiting variation and biodiversity found in related species or breeding lines.
Further information and slides from the talk will be on our website www.molcyt.com.
This document reports on a study comparing the karyotypes and protein profiles of three Trifolium species: T. alexandrinum, T. refeigratum, and T. repens. The results found that T. refeigratum and T. repens both have 16 pairs of chromosomes with one pair containing satellites, while T. alexandrinum has 8 pairs of chromosomes. Analysis of the karyotypes showed differences in symmetry indices between the species. Protein profile analysis via SDS-PAGE revealed clustering of T. alexandrinum separately from the other two species, indicating polymorphic protein bands that differ. The study provides cytological and protein evidence to compare the three clover species
GENOMICS OF STAY GREEN TRAITS AND THEIR UTILITY IN CROP IMPROVEMENTKK CHANDEL
1) A rice mutant with delayed leaf senescence (stay green trait) was developed using chemical mutagen N-methyl-N-nitrosourea.
2) The stay green trait was found to be controlled by a single recessive nuclear gene (sgr(t)) located on chromosome 9.
3) The stay green mutant maintained green leaves and photosynthetic activity longer than the parental varieties after flowering, without reductions in yield.
Molecular Systematics provides a solid conceptual basis for the evolutionary history of organisms. Molecular systematics is the study of DNA and RNA sequences to infer evolutionary links across organisms. Molecular approaches/ techniques provide excellent resources for the study of evolution and phylogeny.
The potato genome sequencing consortium sequenced and assembled 86% of the 844-megabase potato genome. They predicted 39,031 protein-coding genes and found evidence of at least two genome duplication events. By also sequencing a heterozygous diploid potato clone, they showed that gene presence/absence variants and other potentially deleterious mutations occur frequently and likely cause inbreeding depression in potato. The potato genome provides insights into tuber development and a platform for genetic improvement of this important crop.
The ribosomal RNA gene unit of Tritrichomonas foetus was cloned and analyzed. Southern blot analysis showed the rDNA unit is organized as a tandem head to tail repeat of 6 kb, with 12 copies present. The small subunit rRNA is one of the shortest reported at 1571 bp, while the 5.8S rRNA is 159 bp. Northern blot analysis detected primary and precursor rRNA transcripts of 5.8 kb and 4 kb. Sequence analysis confirmed the secondary structure of the small subunit rRNA is similar to other eukaryotes, while being shorter in variable regions.
Genomics is the field of studying genomes through techniques like DNA sequencing and bioinformatics. It aims to understand genome content, organization, function, and evolution. Genomics has two main areas - structural genomics determines genome sequence and organization, while functional genomics studies gene function. A third area, comparative genomics, compares genomes across species. Genomics research has contributed to human health, agriculture and other fields by providing gene sequences. Comparing genome sequences is also improving understanding of evolution and life's history.
Rhodophyta: A cornucopia of cryptic diversityEukRef
This document summarizes research on the taxonomy and phylogeny of red algae (Rhodophyta). It finds that:
1) Molecular analysis has revealed cryptic diversity and non-monophyletic orders within the traditional morphological classification of red algae.
2) The phylum Rhodophyta is highly diverse, with over 6,000 described species classified into 7 classes that vary morphologically but share characteristics like lacking flagella.
3) Resolving the evolutionary relationships among some orders, like those in the lineage Nemaliophycidae, remains challenging despite molecular studies.
The document summarizes cytological features of green algae. It discusses nuclear structure, the cell cycle and processes of cell division including mitosis and meiosis. It describes different chromosome types observed such as long, small, polycentric and nucleolar organizing chromosomes. Karyotypes and chromosome numbers are provided for various orders of green algae. Methods used to study chromosomes including light microscopy, electron microscopy and fluorescence microscopy are mentioned. Important contributions to the field from researchers in India and abroad are also noted.
Similar to Gutell 052.book pgp.1995.c15.0147-0156 (20)
This document summarizes Carl Woese's contributions to science, particularly his discovery of the third domain of life (Archaea) through analysis of rRNA sequences. It describes how his work established the use of comparative analysis to determine rRNA secondary structure and identify structural motifs. It highlights that he envisioned comparative analysis providing details about RNA structure and energetics. The summary discusses Woese's seminal concepts regarding the need for a universal phylogenetic framework and how analysis of rRNA satisfied criteria to reconstruct evolutionary relationships across all life.
Gutell 123.app environ micro_2013_79_1803Robin Gutell
This document summarizes a study examining the host specificity of Lactobacillus bacteria associated with different hymenopteran (bee and ant) hosts. The researchers compiled nearly full-length 16S rRNA gene sequences of Lactobacillus from public databases and used these to construct phylogenetic trees. They also included shorter 16S sequences from surveys of bacteria associated with sweat bees, fungus-growing ants, and fire ants. The results showed that lactobacilli associated with honey bees and bumble bees are highly host specific, while sweat bees and ants associate with lactobacilli more closely related to those found in diverse environments or vertebrate hosts. The high host specificity seen in corbiculate bees (honey bees
Gutell R.R. (2013).
Comparative Analysis of the Higher-Order Structure of RNA.
in: Biophysics of RNA Folding. Volume editor: Rick Russell. Series title: Biophysics for the Life Sciences. Series editors: Norma Allewell, Ivan Rayment, Bertrand Garcia-Moreno, Jonathan Dinman, and Michael McCarthy. pp. 11-22. Publisher: Springer, New York, NY.
Gardner D.P., Xu W., Miranker D.P., Ozer S., Cannone J.J., and Gutell R.R. (2012).
An Accurate Scalable Template-based Alignment Algorithm.
Proceedings of 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2012), Philadelphia, PA. October 4-7, 2012. IEEE Computer Society, Washington, DC, USA. pp. 237-243.
Lee J.C. and Gutell R.R. (2012).
A Comparison of the Crystal Structures of the Eukaryotic and Bacterial SSU Ribosomal RNAs Reveals Common Structural Features in the Hypervariable Regions.
PLoS ONE, 7(5):e38203.
Gardner D.P., Ren P., Ozer S., and Gutell R.R. (2011).
Statistical Potentials for Hairpin and Internal Loops Improve the Accuracy of the Predicted RNA Structure.
Journal of Molecular Biology, 413(2):473-483.2011. pp 15-22.
Ozer S., Doshi K.J., Xu W., and Gutell R.R. (2011).
rCAD: A Novel Database Schema for the Comparative Analysis of RNA.
7th IEEE International Conference on e-Science, Stockholm, Sweden. December 5-8, 2011. pp 15-22.
Jiang Y., Xu W., Thompson L.P., Gutell R., and Miranker D. (2011).
R-PASS: A Fast Structure-based RNA Sequence Alignment Algorithm.
Proceedings of 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011), Atlanta, GA. November 12-15, 2011. IEEE Computer Society, Washington, DC, USA. pp. 618-622.
Xu W., Wongsa A., Lee J., Shang L., Cannone J.J., and Gutell R.R. (2011).
RNA2DMap: A Visual Exploration Tool of the Information in RNA's Higher-Order Structure.
Proceedings of 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011), Atlanta, GA. November 12-15, 2011. IEEE Computer Society, Washington, DC, USA. pp. 613-617.
Muralidhara C., Gross A.M., Gutell R.R., and Alter O. (2011).
Tensor Decomposition Reveals Concurrent Evolutionary Convergences and Divergences and Correlations with Structural Motifs in Ribosomal RNA.
PLoS ONE, 6(4):e18768.
Xia Z., Gardner D.P., Gutell R.R., and Ren P. (2010).
Coarse-Grained Model for Simulation of RNA Three-Dimensional Structures.
The Journal of Physical Chemistry B, 114(42):13497-13506.
The document describes research on fragmentation of the large subunit ribosomal RNA (LSU rRNA) gene in oyster mitochondrial genomes. Key findings include:
1) The LSU rRNA gene is split into two fragments separated by thousands of nucleotides in three species of oysters.
2) RT-PCR and EST analysis showed the two fragments are transcribed separately in Crassostrea virginica and are not spliced together.
3) Secondary structure models of the fragmented LSU rRNA genes were predicted for C. virginica, C. gigas, and C. hongkongensis based on comparative sequence analysis. This fragmentation represents a novel phenomenon in bilateral metazoan mitochondrial genomes.
Mueller U.G., Ishak H., Lee J.C., Sen R., and Gutell R.R. (2010).
Placement of attine ant-associated Pseudonocardia in a global phylogeny (Pseudonocardiaceae, Actinomycetales): a test of two symbiont-association models.
Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology, 98(2):195-212.
Theriot E.C., Cannone J.J., Gutell R.R., and Alverson A.J. (2009).
The limits of nuclear encoded SSU rDNA for resolving the diatom phylogeny.
European Journal of Phycology, 44(3):277-290.
Wu J.C., Gardner D.P., Ozer S., Gutell R.R. and Ren P. (2009).
Correlation of RNA Secondary Structure Statistics with Thermodynamic Stability and Applications to Folding.
Journal of Molecular Biology, 391(4):769-783.
Xu W., Ozer S., and Gutell R.R. (2009).
Covariant Evolutionary Event Analysis for Base Interaction Prediction Using a Relational Database Management System for RNA.
21st International Conference on Scientific and Statistical Database Management. June 2-4, 2009. Springer-Verlag. pp. 200-216.
Chen Y.P., Evans J.D., Murphy C., Gutell R., Zuker M., Gundersen-Rindal D., and Pettis J.S. (2009).
Morphological, Molecular, and Phylogenetic Characterization of Nosema cerenae, a Microsporidian Parasite Isolated from the European Honey Bee, Apis mellifera.
The Journal of Eukaryotic Microbiology, 56(2):142-147.
Maddison D.R., Moore W., Baker M.D., Ellis T.M., Ober K.A., Cannone J.J., and Gutell R.R. (2009).
Monophyly of terrestrial adephagan beetles as indicated by three nuclear genes (Coleoptera: Carabidae and Trachypachidae).
Zoologica Scripta, 38(1):43-62.
The document discusses the origin and evolution of the ribosome. It finds:
1) There is no single self-folding RNA segment that defines the small subunit's decoding site, while the large subunit's peptidyl transfer center is defined by one self-folding RNA segment.
2) The proteins contacting the small subunit's decoding site use universally alignable sequence blocks, while the large subunit's contact proteins use bacterial- or archaeal-specific blocks.
3) These differences support an earlier origin for the large subunit's peptidyl transfer center, with the small subunit's decoding site evolving later as an addition to the ribosome. The implications are that a single self-folding
Communications Mining Series - Zero to Hero - Session 1DianaGray10
This session provides introduction to UiPath Communication Mining, importance and platform overview. You will acquire a good understand of the phases in Communication Mining as we go over the platform with you. Topics covered:
• Communication Mining Overview
• Why is it important?
• How can it help today’s business and the benefits
• Phases in Communication Mining
• Demo on Platform overview
• Q/A
HCL Notes and Domino License Cost Reduction in the World of DLAUpanagenda
Webinar Recording: https://www.panagenda.com/webinars/hcl-notes-and-domino-license-cost-reduction-in-the-world-of-dlau/
The introduction of DLAU and the CCB & CCX licensing model caused quite a stir in the HCL community. As a Notes and Domino customer, you may have faced challenges with unexpected user counts and license costs. You probably have questions on how this new licensing approach works and how to benefit from it. Most importantly, you likely have budget constraints and want to save money where possible. Don’t worry, we can help with all of this!
We’ll show you how to fix common misconfigurations that cause higher-than-expected user counts, and how to identify accounts which you can deactivate to save money. There are also frequent patterns that can cause unnecessary cost, like using a person document instead of a mail-in for shared mailboxes. We’ll provide examples and solutions for those as well. And naturally we’ll explain the new licensing model.
Join HCL Ambassador Marc Thomas in this webinar with a special guest appearance from Franz Walder. It will give you the tools and know-how to stay on top of what is going on with Domino licensing. You will be able lower your cost through an optimized configuration and keep it low going forward.
These topics will be covered
- Reducing license cost by finding and fixing misconfigurations and superfluous accounts
- How do CCB and CCX licenses really work?
- Understanding the DLAU tool and how to best utilize it
- Tips for common problem areas, like team mailboxes, functional/test users, etc
- Practical examples and best practices to implement right away
Removing Uninteresting Bytes in Software FuzzingAftab Hussain
Imagine a world where software fuzzing, the process of mutating bytes in test seeds to uncover hidden and erroneous program behaviors, becomes faster and more effective. A lot depends on the initial seeds, which can significantly dictate the trajectory of a fuzzing campaign, particularly in terms of how long it takes to uncover interesting behaviour in your code. We introduce DIAR, a technique designed to speedup fuzzing campaigns by pinpointing and eliminating those uninteresting bytes in the seeds. Picture this: instead of wasting valuable resources on meaningless mutations in large, bloated seeds, DIAR removes the unnecessary bytes, streamlining the entire process.
In this work, we equipped AFL, a popular fuzzer, with DIAR and examined two critical Linux libraries -- Libxml's xmllint, a tool for parsing xml documents, and Binutil's readelf, an essential debugging and security analysis command-line tool used to display detailed information about ELF (Executable and Linkable Format). Our preliminary results show that AFL+DIAR does not only discover new paths more quickly but also achieves higher coverage overall. This work thus showcases how starting with lean and optimized seeds can lead to faster, more comprehensive fuzzing campaigns -- and DIAR helps you find such seeds.
- These are slides of the talk given at IEEE International Conference on Software Testing Verification and Validation Workshop, ICSTW 2022.
“An Outlook of the Ongoing and Future Relationship between Blockchain Technologies and Process-aware Information Systems.” Invited talk at the joint workshop on Blockchain for Information Systems (BC4IS) and Blockchain for Trusted Data Sharing (B4TDS), co-located with with the 36th International Conference on Advanced Information Systems Engineering (CAiSE), 3 June 2024, Limassol, Cyprus.
How to Get CNIC Information System with Paksim Ga.pptxdanishmna97
Pakdata Cf is a groundbreaking system designed to streamline and facilitate access to CNIC information. This innovative platform leverages advanced technology to provide users with efficient and secure access to their CNIC details.
Climate Impact of Software Testing at Nordic Testing DaysKari Kakkonen
My slides at Nordic Testing Days 6.6.2024
Climate impact / sustainability of software testing discussed on the talk. ICT and testing must carry their part of global responsibility to help with the climat warming. We can minimize the carbon footprint but we can also have a carbon handprint, a positive impact on the climate. Quality characteristics can be added with sustainability, and then measured continuously. Test environments can be used less, and in smaller scale and on demand. Test techniques can be used in optimizing or minimizing number of tests. Test automation can be used to speed up testing.
Essentials of Automations: The Art of Triggers and Actions in FMESafe Software
In this second installment of our Essentials of Automations webinar series, we’ll explore the landscape of triggers and actions, guiding you through the nuances of authoring and adapting workspaces for seamless automations. Gain an understanding of the full spectrum of triggers and actions available in FME, empowering you to enhance your workspaces for efficient automation.
We’ll kick things off by showcasing the most commonly used event-based triggers, introducing you to various automation workflows like manual triggers, schedules, directory watchers, and more. Plus, see how these elements play out in real scenarios.
Whether you’re tweaking your current setup or building from the ground up, this session will arm you with the tools and insights needed to transform your FME usage into a powerhouse of productivity. Join us to discover effective strategies that simplify complex processes, enhancing your productivity and transforming your data management practices with FME. Let’s turn complexity into clarity and make your workspaces work wonders!
GraphSummit Singapore | The Future of Agility: Supercharging Digital Transfor...Neo4j
Leonard Jayamohan, Partner & Generative AI Lead, Deloitte
This keynote will reveal how Deloitte leverages Neo4j’s graph power for groundbreaking digital twin solutions, achieving a staggering 100x performance boost. Discover the essential role knowledge graphs play in successful generative AI implementations. Plus, get an exclusive look at an innovative Neo4j + Generative AI solution Deloitte is developing in-house.
Programming Foundation Models with DSPy - Meetup SlidesZilliz
Prompting language models is hard, while programming language models is easy. In this talk, I will discuss the state-of-the-art framework DSPy for programming foundation models with its powerful optimizers and runtime constraint system.
HCL Notes und Domino Lizenzkostenreduzierung in der Welt von DLAUpanagenda
Webinar Recording: https://www.panagenda.com/webinars/hcl-notes-und-domino-lizenzkostenreduzierung-in-der-welt-von-dlau/
DLAU und die Lizenzen nach dem CCB- und CCX-Modell sind für viele in der HCL-Community seit letztem Jahr ein heißes Thema. Als Notes- oder Domino-Kunde haben Sie vielleicht mit unerwartet hohen Benutzerzahlen und Lizenzgebühren zu kämpfen. Sie fragen sich vielleicht, wie diese neue Art der Lizenzierung funktioniert und welchen Nutzen sie Ihnen bringt. Vor allem wollen Sie sicherlich Ihr Budget einhalten und Kosten sparen, wo immer möglich. Das verstehen wir und wir möchten Ihnen dabei helfen!
Wir erklären Ihnen, wie Sie häufige Konfigurationsprobleme lösen können, die dazu führen können, dass mehr Benutzer gezählt werden als nötig, und wie Sie überflüssige oder ungenutzte Konten identifizieren und entfernen können, um Geld zu sparen. Es gibt auch einige Ansätze, die zu unnötigen Ausgaben führen können, z. B. wenn ein Personendokument anstelle eines Mail-Ins für geteilte Mailboxen verwendet wird. Wir zeigen Ihnen solche Fälle und deren Lösungen. Und natürlich erklären wir Ihnen das neue Lizenzmodell.
Nehmen Sie an diesem Webinar teil, bei dem HCL-Ambassador Marc Thomas und Gastredner Franz Walder Ihnen diese neue Welt näherbringen. Es vermittelt Ihnen die Tools und das Know-how, um den Überblick zu bewahren. Sie werden in der Lage sein, Ihre Kosten durch eine optimierte Domino-Konfiguration zu reduzieren und auch in Zukunft gering zu halten.
Diese Themen werden behandelt
- Reduzierung der Lizenzkosten durch Auffinden und Beheben von Fehlkonfigurationen und überflüssigen Konten
- Wie funktionieren CCB- und CCX-Lizenzen wirklich?
- Verstehen des DLAU-Tools und wie man es am besten nutzt
- Tipps für häufige Problembereiche, wie z. B. Team-Postfächer, Funktions-/Testbenutzer usw.
- Praxisbeispiele und Best Practices zum sofortigen Umsetzen
Observability Concepts EVERY Developer Should Know -- DeveloperWeek Europe.pdfPaige Cruz
Monitoring and observability aren’t traditionally found in software curriculums and many of us cobble this knowledge together from whatever vendor or ecosystem we were first introduced to and whatever is a part of your current company’s observability stack.
While the dev and ops silo continues to crumble….many organizations still relegate monitoring & observability as the purview of ops, infra and SRE teams. This is a mistake - achieving a highly observable system requires collaboration up and down the stack.
I, a former op, would like to extend an invitation to all application developers to join the observability party will share these foundational concepts to build on:
GraphRAG for Life Science to increase LLM accuracyTomaz Bratanic
GraphRAG for life science domain, where you retriever information from biomedical knowledge graphs using LLMs to increase the accuracy and performance of generated answers
Full-RAG: A modern architecture for hyper-personalizationZilliz
Mike Del Balso, CEO & Co-Founder at Tecton, presents "Full RAG," a novel approach to AI recommendation systems, aiming to push beyond the limitations of traditional models through a deep integration of contextual insights and real-time data, leveraging the Retrieval-Augmented Generation architecture. This talk will outline Full RAG's potential to significantly enhance personalization, address engineering challenges such as data management and model training, and introduce data enrichment with reranking as a key solution. Attendees will gain crucial insights into the importance of hyperpersonalization in AI, the capabilities of Full RAG for advanced personalization, and strategies for managing complex data integrations for deploying cutting-edge AI solutions.
Let's Integrate MuleSoft RPA, COMPOSER, APM with AWS IDP along with Slackshyamraj55
Discover the seamless integration of RPA (Robotic Process Automation), COMPOSER, and APM with AWS IDP enhanced with Slack notifications. Explore how these technologies converge to streamline workflows, optimize performance, and ensure secure access, all while leveraging the power of AWS IDP and real-time communication via Slack notifications.
Dr. Sean Tan, Head of Data Science, Changi Airport Group
Discover how Changi Airport Group (CAG) leverages graph technologies and generative AI to revolutionize their search capabilities. This session delves into the unique search needs of CAG’s diverse passengers and customers, showcasing how graph data structures enhance the accuracy and relevance of AI-generated search results, mitigating the risk of “hallucinations” and improving the overall customer journey.
Sudheer Mechineni, Head of Application Frameworks, Standard Chartered Bank
Discover how Standard Chartered Bank harnessed the power of Neo4j to transform complex data access challenges into a dynamic, scalable graph database solution. This keynote will cover their journey from initial adoption to deploying a fully automated, enterprise-grade causal cluster, highlighting key strategies for modelling organisational changes and ensuring robust disaster recovery. Learn how these innovations have not only enhanced Standard Chartered Bank’s data infrastructure but also positioned them as pioneers in the banking sector’s adoption of graph technology.
Goodbye Windows 11: Make Way for Nitrux Linux 3.5.0!SOFTTECHHUB
As the digital landscape continually evolves, operating systems play a critical role in shaping user experiences and productivity. The launch of Nitrux Linux 3.5.0 marks a significant milestone, offering a robust alternative to traditional systems such as Windows 11. This article delves into the essence of Nitrux Linux 3.5.0, exploring its unique features, advantages, and how it stands as a compelling choice for both casual users and tech enthusiasts.
UiPath Test Automation using UiPath Test Suite series, part 5DianaGray10
Welcome to UiPath Test Automation using UiPath Test Suite series part 5. In this session, we will cover CI/CD with devops.
Topics covered:
CI/CD with in UiPath
End-to-end overview of CI/CD pipeline with Azure devops
Speaker:
Lyndsey Byblow, Test Suite Sales Engineer @ UiPath, Inc.
1. 15
Chloroplast Gene Organization and
Phylogenetic Relationships in Green Algae
M. Turmel", E. Boudreau', R.R. Gutell', C. Otis' and C. Lemieux'
Dcpartemenl de biochimie, Faculle des sciences el de genie, Universite Laval. Quebec (Quebec) GIK 7P4.
Canada
2 Departments ~r Molecular, Cellular and Developmental Biology. Campus Box 347. University oj Colorado.
Boulder. CO 80309, USA
INTRODUCTION
Although the.chloroplasts of green algae and land plants share a common endosymbiotic
origin, their genomes appear to have followed very different evolutionary pathways.
It is well known that the land plant chloroplast genome evolves very conservatively and
• All correspondence should be sent to Monique Tunnel at the above address.
147
2. • .0..1." .."".... .h' .... ' ....... o..IlIU I.'''U'''''II
is under strong constraints to retain a compact gene organization (reviewed by Palmer 1991).•
Indeed studies of over 1000 rhotosynthetic plant srecies have indicated that this circular
~~
genome is remarkably conserved in structure, size (120-160 kb), gene content, primary~, j
sequence and overall gene order. Most of the 110-1 18 chloroplast genes encoded are grouped ,
into multicistronic operons, several of which are highly similar to those found in cyano- I
bacteria, the ancestors of chloroplasts. IIn contrast, the limited data available on green algal chloroplast DNAs (cpDNAs) have
revealed great variability in structure, size (89- >400 kb) and gene organization (reviewed by •
Palmer 199 I). Low-resolution chloroplast gene 'maps have been reported for only eight I
green algae representing three of the five major classes that have been proposed by Mattox, I
and Stewart (1984) on the basis of ultrastructural characters (see Palmer 1991). These three I
classes are the Charophyceae, whose members are the closest relatives of I~nd .plants,. the :m. 'I'
Ulvophyceae and the Chlorophyceae. Although all green algal cpDNAs studied In detail so 'Jfar consist of circular DNA molecules, some of which feature the large inverted repeat ,.;;;. ,
characteristic of the land plant genome, none of them shows strong similarity with the'·' I
consensus gene order found in land plants. Extensive gene rearrangements have been Iobserved even within the genus Chlamydomonas. In this large and highly diversified group
ofgreen algae, two divergent pairs of interfertile taxa have been examined: one pair consists
of C. reinhardtii and C. smithii and the other of C. eugametos and C. moewusii. On the basis I
of heterologous hybridizations with cloned cpDNA fragments spanning the compared I
chloroplast genomes, the cpDNAs of C. reinhardtii (196 kb) and C. eugametos (243 kb) i
have been found to be extremely scrambled in their gene order (Lemieux and Lemieux 1985), I
whereas the cpDNAs within each pair of interfertile algae have been found to be essentially Icolinear (Turmel et af. 1987; Boynton et af. 1992).
To gain insight into the tempo and, mode of evolution of the chloroplast genome in i
Chlamydomonas, we have recently examined the phylogenetic relationships among representa- I
tives ofthis genus as well as of other green algal genera, and have also begun to investigate
the organization ofabau! 75 chloroplast genes in representatives ofthe various Chlamydomonas
lineages identified. We report here the preliminary results of our phylogenetic analysis
based on the chloroplast large subunit rRNA gene (rrnL) and briefly review our most recent·
studies on the structure and organization of chloroplast genes in C. eugametoslC. moewusii
and C. reinhardtii, i.e. in members of the two major lineages found in Chlamydomonas. In
the presentation ofour results, we have placed a special emphasis on the differences between
these green algal cpDNAs and their land plant counterparts.
MATERIALS AND METHODS
Sequencing ojthe chloroplast rmL gene and phylogenetic analysis
The chloroplast rrnL gene from 28 green algae (see legend ofFig.15.1) and from the
chlorarachniophyte-like species designated Pedinomonas minutissima (see Chapman and
Buchheim 1992) was partially sequenced. For each organism, three overlapping segments of
the gene were PCR-amplified from total cellular DNA preparations with pairs of primers that
are complementary to highly conserved regions (Turmel et af. 1993a). PCR-fragments were
sequenced using the dsDNA cycle sequencing system from Life Technologies, Inc. (Gaithers-
burg, MD). Alignment of all chloroplast rrnL sequences and their analysis with the neighbor-
148
joining method ofSaitou and Nei (1987) were carried Ollt as described previollsly (Tunnel ('(
til. 1993n).
RESULTS AND DISCUSSION
ChlamydomonasJorms a highly diversified group ofgreen algae within the
Chlorophyceae
To understand the evolutionary basis for the extensively rearranged cpDNAs in
Chlamydomonas, we have inferred the phylogenetic positions of C. reinhardtii and C.
moewlisii relative to those of other green algae from this genus as well as from other genera
by comparing sequences for the chloroplast rrnL gene. The phylogeny presented in
Fig. 15. I features 45 green algae from the classes Chlorophyceae, Pleurastrophyceae and
Micromonadophyceae sensu Mattox and Stewart (1984), eight land plants, two euglenophytes,
one chlorarachniophyte-like species, one brown alga and one red alga. The 25 Chlamydomonas
taxa examined represent all of the groups that were distinguished in this genus on the basis
of morphological and biochemical characters (Ettl 1976; Schiisser 1984). These taxa cluster
into two major lineages, one of which comprises C. reinhardtii and the other C. moewlisii.
Within each of these major lineages, there are additional lineages that form sister groups. As
reported previously (Buchheim et af. 1990), Chlamydomonas is clearly polyphyletic as some
taxa classified in this genus (e.g. C. applanata ) are more closely related to green algae
belonging to other genera (e.g. Chlorogonium and Dunaniella) than to other Chlamydomonas
taxa. Altogether, the Chlamydomonas lineages show at least twice the range of sequence
divergence seen in all land' plants. This molecular diversity is supported by the greater
variability in chloroplast gene organization among Chlamydomonas taxa as compared to that
observed among land plants. In the inferred phylogeny, the micromonadophycean green
algae and land plants clearly occupy basal positions relative to the pleurastrophycean and
chlorophycean green algae, a result that is consistent with a recently reported phylogenetic
analysis based on partial sequences of the nuclear small subunit rRNA (Kantz et af. 1990).
.The highly rearranged cpDNAs oJe. moewusii and C. reinhardtiifeature conserved
gene clusters
We have extended to 74 and 75 the number of genes mapped on the C. reinhardtii and
C. moewusii cpDNAs, respectively (see Fig. 15.2) (Boudreau et af. 1994). To map additional
genes on these cpDNAs, we first attempted, but with little success, to carry out Southern blot
hybridizations with gene-specific fragments from the tobacco cpDNA. Since, most of the
probes proved ineffective, we undertook the partial sequencing ofthe colinear C. eugametos
and C. moewusii cpDNAs. We have sequenced thus far about 140 kb of the genome using
both random and directed sequencing approaches. The resulting sequences along with those
reported for the C. reinhardtii cpDNA allowed us to generate gene-specific probes that proved
useful in heterologous hybridizations., The results of these hybridizations indicated that the
C. moewusii and C. reinhardtii cpDNAs share a similar gene complement. Only four of the
genes mapped, tseA and three open reading frames (ORF715, ORFA and ORFB), have not
been reported in any cpDNAs and may thus be specific to Chlamydomonas or a larger
taxonomic group. Interestingly, rpl5 resides on both the C. reinhardtii and C. moewusii
cpDNAs, but is absent from the cpDNAs ofland plants (Ohyama et al. 1986; Shinozaki et af.
1986; Hiratsuka et af. 1989). From our results, it appears that a very small fraction of the
149
3. Fig. 15.1
C. mexicana
C. peterf,;
C. gigantea
C lrankii
- C. palidostigmata
~--- C.nivalis
C. mdiata
C.mutabilis
Chlorogonvm dmglltum
C.humicola
C.lIpplanala
~ DunalitJIa paIVa
C. lIgtul(ormis
Stephanosptz.tua pllviafs
' - - - - - HaematoCDCDlS lacustris
C. pischmlJnni
C. ~ugllm.tos
C. mOflwusi
O'lbrococcum ttchnozygotum
C. species 66.72
C.geifleri
C. pstJudapettusa
C. monadna
~
Catteriacrudera
camuiatildiosa
Garteria luzsnsis
~S::::/:::,s:~~~'::tus
L-_____ Uonema btlDcae
Chlomlfa vulgaris
Prototheca widuuhami
o:T
o
a1:J
:T
'<
o
(!)
III
m
"U
m-e
OJ
!!!.
a1:J
~
o
(!)
III
m
Chlamlla elipsoidea
Tmbouxia aggre9a,a
{=====-TetJaselmiscatteriilormis
Pleur-utrum tenestra
L-___ Pedinomonas mnor
;;::
fi'
o
3
o
=>
::jJ
~
=-!OI)'U sativa
aa mays
Nicotiaflll labacum
Anusncanus
Eplagus rig'iniana
- Conopho& americm..
PIsum sativum
Uan:/lantia polymotph..
' - - - - - i'kphlOsernis OMara
f----------- M.i:mmonas pusila
1-----:-----'- Pedinomonasmnutissina
G Pyfaiela iftorais
Pamatia pamata
Astasia Jonga
Euglena gracilis
Anacystis nidulans Escherichia. col
r'<
III 0
=> m
a. III
1:J m
iii
=>
u;
==:J-~o
g
=>
D>
a.
.g
~
g
D>
m
Neighbor-joining phylogeoetic analysis ofplastid rmL sequences ftum 45 green algal taxa (Chlorophyceae,
Pleurastrophyceae and Micromonadophyceae sensu Mattox and Stewart). eight land plants. two
euglenophytes (Astaria longa and Euglena gracilis), one chlorarachniophyte-like species (Pedinomonas
minutissimo), one brown alga (Pylaiella littoralis) and one red alga (Palmoria palmata). This tree, which
includes also a cyanobacterium (Anacystis nidu/ans), is a 50% majority-rule tree derived from a Kimura
dissimilarity matrix that was computed from a data set of 2,1 02 semiconserved positions. One thousand
bootstrap replications were done in. which the Escherichia coli rmL sequence was used as an outgroup.
Branch lengths on the horizontal axis represent the evolutionary distance between the nodes. The P.
minutissima chloroplast rrnL sequence and all green algal rrnL sequences, with the exception of that
from Chlorella elJipsoidea (accession no.: M36158), were determined in our laboratories. Of these
sequences, those from 17 Chlamydomonas taxa have been reported (see Tunnel et al. 1991a, 1993a).
Accession numbers for the published non-green algal sequences are as follows: Oryza sativa, X15901; Zea
mays, X01365; Nicotiana tabacum, JOl446 and Z00044; Alnus incana, M76448 and M75722; Epifagus
virginiana, M81884; Conopholis americana, X59768; Pisum salivum, M37430; Marchantia pO(l'morpha,
XOI647 and X04465; Astasia longa, X14386; Euglena gracilis, XI331O; Pylaiella littoralis, X61179
and 536159; and Palmaria palmata, ZI8289
150
.."..
f"i~'l:,1~1 "1
-)< 1 ,
;~ili
~ ':
II
I
" I
I,
Increased size of Chlamydomonas cpDNAs relative to their land plant countcrparIs is
explained by the presence of additional genes. Most of this extra size seems 10 be due to the
presence of enlarged spacers between coding regions and also to Ihe presence of unusually
long genes (see below) (Boudreau et al. 1994).
As shown in Fig. 15.2, all gene rearrangements between the C. moewlIsii and C.
reinhardtii cpDNAs, with the exception of those accounting for the relocations of rbcL and
the apiA and psbl gene pair, occurred within corresponding regions of the genome. Despite
these numerous rearrangements, 40 genes were found to define 13 conserved clusters of
closely linked loci (see Fig. 15.2). Ten of the 13 clusters (rpsIB-rps2-trnD-psbB-ycj8-psbH-
tmEI, ycJ3-ycJ4 and petB-chlL are the exceptions) have been partially or entirely sequenced,
and interestingly, each of them features contiguous genes that are encoded by the same DNA
strand. It is very likely that these ten gene clusters were present in the common ancestor of
all Chlamydomonas species. Only 16 of the genes mapped on the C. moewusii and C.
reinhardtii cpDNAs are organized similarly to ancestral operons found in other cpDNAs (see
Fig. 15.2); they reside within five of the 13 conserved clusters identified. The rRNA gene
cluster shows exactly the same gene content as its land plant homologue, whereas segments
ofland plant operons are represented by the four remaining clusters. These results suggest
that most of the ancestral operons that characterize the chloroplast genome organization of
land plants and early-diverging photosynthetic eukaryotes have been disrupted before the
emergence of Chlamydomonas. Of the multiple sequence rearrangements that marked the
evolution of the Chlamydomonas chloroplast genome, one seems to have led to the break-up
of the ancestral region containing rp123, rpl2, rpsl9, rpll6, rpll4, rpl5, rpsB and thepsaA
exon 1. This gene cluster, which differs from the corresponding land plant operon by the
absence ofrp122, rps3 and infA and also by the presence ofrpl5 and the psaA exon 1, is found
in C. reinhardtii, while it is divided into two separate fragments, rpI23-rpI2-rps19 and rplJ6-
plJ4-rpI5-rpsB-pasA exon I, in C. moewusii (see Fig. 15.2).
The molecular mechanisms underlying the tremendous rearrangements that occurred
during the evolution of the Chlamydomonas chloroplast genome remain unknown. As
discussed previously (Boudreau et af. 1994), repeated sequences located in intergenic spacers
and/or tRNA genes might have been implicated in such rearrangements. To identify the
nature ofthe sequence elements involved ip gene reshuffling, it will be necessary to analyze
the endpoints of rearranged cpDNA segments from closely related green algae showing
specific mutations. In this regard, it would be interesting to undertake the molecular character-
ization of the few rearrangements we have uncovered between the cpDNAs of C. moewusii
and C. pitschmannii (Boudreau and Turmel 1995) and between those of C. reinhardtii and C.
gelatinosa (see Tunnel et af. 1991b).
As more cpDNAs from chlorophycean green algae are investigated, we expect that a
number of the gene clusters conserved between C. moewlIsii and C. reinhardtii will be
identified in taxa residing in basal lineages relative to the Chlamydomonas lineages.
At present, the petA-petI? gene cluster is the only one that has been reported outside
Chlamydomonas. This cluster has been identified in the chlorophycean green alga Scenedesmlls
obliqulls (Kiick 1989). Like its Chlamydomonas counterparts, the Scenedesmlls petA and petD
genes are contiguous and encoded by the same DNA strand, suggesting that these genes were
present in the most recent common ancestor ofChlamydomonas and Scenedesmus. We suspect
that the gene cluster from the latter ancestor also comprised the tRNAM. (UeU) gene, which
is present immediately downstream ofpetD in both C. eugametos and Scenedesmlls. In C.
151
4. C. reinhardtii
196 kb
atpE
a'pH
rpoBl
rpoB2
rpoC2b
rpoC2.
fefS
puB
S[GCUI
atpl,rp1J.4
I;~r-;P~___J
a.......,
,,~
p.bK, CjOCAI, WICCAI
I rplid Sru:;J.1 I
ctllB TIUGUI
AIUCU]
psbE-psbF-psbL-psbJ
psbB-ycfB-psbH-petB-petD
rmS-tmt-tmA-f77lL~ rONA
rpt23-rpt2-rpsI9-rpI22-rps3-rptl6-
rpI14-rpsB-intA-rpl36-rpsll-rpaA
rpt23-rpt2-rpsl9-rpI22-rps3-rptl6-
rp/14-rpsB-infA-rpl36-rpsll-rpaA
C. moewusii
292 kb
152
'1' i
i~:': . f'Hi:;. .:,
''; .'..
l.i~
.>~
.·:fizt
. '!!l
;;r"
:;~
I
I
III(}('I·U.III, petO and Imlll ul·U) arc separaled by an exira sequcncc (II' 5.9 kh, which alSo exISis
as a linear DNA in this alga (Turmel el al. 1986).
Chlamydomonas Gild lalld plalll cpDNAs differ ill their ;,lIron content
Different sets of genes are interrupted by g';oup I and group II inIrons in land plant and
Chlamydomonas cpDNAs, indicating that most ofthese introns have a recent and independent
origin. While group I introns are more abundant than group [[ introns in Chlamydomonas
cpDNAs, the opposite situation prevails in land plant cpDNAs. A total of 24 group I intron
insertion sites located within five Chlamydomonas chloroplast genes have been described; in
contrast, a single group I intron [in the tRNALEU (UAA) gene] has been identified in land plant
cpDNAs_ Twelve of the Chlamydomonas chloroplast group I insertion sites have been found
during a recent analysis of the rrnL gene from 17 Chlamydomonas species (Turmel el al.
1991a, 1993a), while the twelve remaining sites have been identified in the rrnS (four sites),
psbA (five sites),psbC (two sites) and psaB (one site) genes of C. reinhardlii, C. eugamelos
and/or C. moewusii (see Turrnel el al. 1993b; our unpublished data). Ofthese sites, only three
(in the rmL gene) have been reported outside the polyphyletic genus Chlamydomonas (see
Turrnel e/ al. 1993a; Turrnel el al. 1995a). Five rrnL insertion sites were observed in the two
major Chlamydomonas evolutionary lineage, whereas the seven remaining ones were found
to be restricted to one or the other lineages, a result suggesting that the origin ofthe latter sites
is more recent To gain insight into the mode ofinsertion and proliferation of group I introns
in cpDNAs, we have undertaken the sequencing of the Chlamydomonas chloroplast introns
inserted at common positions as well as at distinct sites. Analysis of the intron sequences
available so far strongly suggests that, in two pairs ofrelated introns (CmpsaB'I/CepsbC'2 and
CmLSU-4/CeLSU'2), one of the members arose from transposition mediated through reversal
of the self-splicing reaction (Turrnel et al. 1993b). Some Chlamydomonas introns may have
also arrived at their present locations through transposition events imd/or lateral transfers that
were initiated by double-strand DNA breaks caused by intron-encoded endonucleases, as
CeLSU·5 (Gauthier et al. 1991), CrLSU·I (Diirrenbergerand Rochaix 1991), ChLSU·I (Cote
et al. 1993) and CPLSU·2 (Turmel et al. 1995a) have been shown to encode distinct
endonucleases that cleave specifically the exon junction sequence in the corresponding
intronless genes..
Fig. 15.2 Comparative gene organization ofthe C: moewusii and C. reinhardtii cpDNAs. DNAs are drawn to scale
and are linearized at one ofthe junctions ofthe inverted repeat (denoted by thick lines) and the single-copy
region bordering the rrnS genes. Gene loci are denoted by dark areas, with their size reflectiog the length
ofcoding regions. Note that the rrnL and psaA coding regions from both green algae as well as those of
the C. moewusii rmS, psaB and psbC are oversized in this figure, as the intraD sequences interrupting them
were not represented, All corresponding C. mo~ii and C. reinhardtii gene loci are connected by lines:
those that are part of conversed clusters (framed areas) are linked by solid lines, whereas the remaining
genes are connected by dashed lines. To,the right of five conversed clusters are indicated the land plant
chloroplast operons to which they share similarity, ForaH genes that are indicated on only one of the two
green algal cpDNAs, our heterologous hybridizations failed to identifY their counterparts in the compared
DNA- For each gene, the polarity ofthe DNA strand containing the coding region was denoted by an arrow
when this infonnation was available. Contiguous genes with the same polarity were assigned a common
arrow. This figure was modified from Boudreau et al. (1994). Note that the C. moewusii trnL (UAG) gene
was indicated at an incorrect position in the figure presented by Boudreau et ai, (1994); it was localized
by heterologous hybridization to the EcoRl fragment 10'" containing the 5' part of clpP and psaA exon 2,
but was inadvertently assigned to the adjacent fragment containing the 3' pan ofclpP, tm! (CAU) and trnjM
(CAU). The relative order of trnL (UAG) and psaA exon 2 has been recently determined by DNA
sequencing (our unpublished data)
153
5. In Chialllydolllollas, psa:l is lhe only gcne lhal is known 10 contain group II IIltrons.
Two trans-spliced psaA inlrons have been idenlified in C. reinhardlii (Klick el al. 1987;
Choquel el al. 1988). Our hybridizalions Wilh specific exon probes suggcSl lhallhe psaA
genes of six other Chiamydomonas species, including C. ellgametos and C. moewll.';il
resemble their C. reinhardtii counlerpart in consisting of three widely spaced exons
by 5'- and 3'-segments of group II introns (Turmel el al. 1995b; our unpublished data).
all lhe chloroplast psaA genes characterized so far in other algae and land plants do
feature any trans-spliced introns nor cis-spliced introns at the same locations as those
in C. reinhardtii, insertion and splitting of group II introns probably occurred
recently in a common ancestor of Chlamydomonas species.
Some Chlamydomonas chloroplast genes exhibit an unusual structure
Although the chloroplast rrnL gene is fragmented in Chlamydomonas and land plants,
corresponding gene products in these two groups oforganisms share no common
(see Turmel et al. 1993a). Four mature chloroplast large subunit rRNA fragments, called a,
f3, rand 8, have been identified in all 17 Chlamydomonas taxa examined thus far, whereas two
to three mature rRNA species have been observed in land plants. These differences reflect
variations in the location and number of short internal transcribed spacers that are excised
from the primary transcript to yield the mature rRNA species.
The Chlamydomonas chlB, clpP and rps3 are functional genes despite the presence of
long insertion sequences relative to their homologues in land plants and other organisms
(Fong and Surzycki 1992b; Li et al. 1993; Liu el al. 1993a,b; Huang et al. 1994; Turmel and IOtis 1994). Remarkably, these insertion sequences are in frame with the coding regions and
show no similarity with group I and group II introns and with known DNA sequences. They
are not excised at the RNA level; so if they are translated and not removed at the protein leve4=". ~
the corresponding proteins would be significantly larger than their land plant counterp~ :'~' ISimilar insertion sequences have been identified at the same positionS in the chlB, clpP and
rps3 genes ofspecies from the two major Chlamydomonas lineages, suggesting that they have
a common origin and that they were present in the comnion ancestor of Chlamydomonas
species. One ofthe two sites ofinsertion sequences in the C. eugametos clpP gene, howevCIj
appears to be of more recent origin, as it has not been found in all other ChlamydomonaS
species examined.
The Chlamydomonas rpoB and rpoC2 genes are very unusual in featuring more than on~
ORF. If transcription and translation occur and there is no edited RNA sites, each of these
genes would be expected to specifY separate polypeptides. Fong and Surzycki (1992a) have
reported that the C. reinhardtii rpoB consists of two ORFs (designated rpoB] and rpoB2 in
Fig. 15.2) that are closely linked to each other on the genome ofthis green alga. Their order
and polarity are those found in conventional, unfragmt;nted rpoB genes, suggesting that
insertion ofa sequence element might have led to splitting ofthe C. reinhardtii gene. In the
C. ellgametos and C. moewusii cpDNAs, the ';poB sequences corresponding to these ORFs
map also to closely linked loci (Boudreau et al. 1994). Results derived from partial
sequencing of the rpoC2 gene in both C. reinhardtii (Fong and Surzycki 1992a) and C.
eugametos (our unpublished results) and from Southern blot hybridizations (Boudreau et al.
1994) suggest that the C. reinhardtii gene displays at least two ORFs (designated rpoC2a and
rpoC2b) that are close to each other on the chloroplast genome. Disruption of one of these
ORFs has revealed that the C. reinhardtii rpoC2 gene is functional (Goldschmidt-Clermont
154
Il)l) I; ,ce Boudreau etal. I'N4). By Soulhern bioI hybridizalions. we have found lhal closely
linked loci correspond to Ihe identified C. reinhart/Iii ORFs in lhe C. C'ugolllelos and C.
1I/01!1I'lisii cpDNAs (Boudreau el al. 1994). Obviously, delerminalion of lhe complele
nucleolide scquence of the C. reinhardlii rpoC2 along wilh analyses at the RNA and protein
levels will be necessary 10 understand how this gene transcripl is translaled into a functional
protein.
In conclusion, the sequence data that have been collected from Chlamydomonas cpDNAs
indicale that a few genes have been invaded by foreign sequences, but have remained
functional. Survey of these genes for the presence of similar insertion elements among other
green algal lineages will be needed to determine when such events occurred during the
evolution of the green algal chloroplast genome.
Acknowledgment: This research was supported by grants from the National Sciences and
Engineering Research Council of Canada (GP0003293 to M.T. and GP0002830 to c.L.) and
"Le Fonds pour la Formation de Chercheurs et l'Aide ala Recherche" (93-ER-0350 to M.T.
and c.L.). M.T. and c.L. are Scholars in the Evolutionary Biology Program of the Canadian
Institute for Advanced Research
REFERENCES
Boudreau E, Tunnel M(1995): Gene rearrangements in Chlamydomonas chtoroplast DNAs are accounted for by
inversions and by the expansion/contraction of the inverted repeat. Plant Mol. BiD!.. 27: 351-364.
Boudreau E, Otis C, Tunnel M(1994): Conserved gene clusters in the highly rearranged chloroplast genomes of
Chlamydomonasmoewusii and Chlamydomonas reinhardtii. Plant Mol. Bioi. 24: 585-602.
Boynton lE, Gillham NW, Newman SM, Harris EH (1992): Organelle genetics and transformation of
Chlamydomonas. In: Hennann RG (ed) Plant Gene Research, Vol. VI. Springer-Verlag, Vienna. pp.3--{)4.
Buchheim MA, Tunnel M, Zimmer EA, Chapman RL (1990): Phylogeny of Chlamydomonas (Chlorophyta) based
on cladistic analysis ofnudear 18S rRNA sequence data. J. Phycol. 26: 689--{)99.
Chapman RL, Buchheim MA (1992): Green algae and the evolution ofland plants: inferences from nuclear-encoded
rRNA gene sequences. BioSystems 28: 127-137. ()
Choquet Y, Goldschmidt-Clennont M, Girard-Bascou 1, KUck U, Bennoun P, Rochaix lD (1988): Mutant phenotypes
support a trans-splicing mechanism for the expression of the tripartite psaA gene in the C. reinhardtii
chloroplast. Cel/52: 903-913.
Cote V, Mercier lP, Lemieux C, Tunnel M (1993) The single group-I intron in the chloroplast rrnL gene of
Chlamydomonas humicola encodes a site-specific DNA endonuclease (l-chu J). Gene 129: 69-76.
Durrenberger F. Rochaix 1D (1991): Chloroplast ribosomal intran of Cltlamydomonas reinhardtii: in vitro self-
splicing, DNA endonuclease activity and in vivo mobility. EMBOJ. 10: 3495-3501.
Ettl H(1976): Die Gattung Chlamydomonas Ehrenberg. Nova Hedwigia 49: 1-1122.
Fang SE, Surzycki S1 (1992a): Organization and structure of plastome psbF. psbL, petG and 0RF712 genes in
Chlamydomonas reinhardtii. Curro Genet. 21: 527-530.
Fong SE, Surzycki S1 (l992b): Chloroplast RNA polymerase genes of Chlamydomonas reinhardtii exhibit an
unusual structure and arrangement. Curro Genet. 21: 485-497.
Gauthier A, Tunnel M, Lemieux C (199I): A group 1intran in 'he chloroplast large subunit rRNA gene of
Chlamydomonas eugametos encodes a double-strand endonuclease that cleaves the homing site of this intran.
Curro Genet. 19: 43-47.
Goldschmidt-Clennont M(199.1): Transgenic expression of aminoglycoside adenine transferase in the chloroplast:
a selectable marker for site-specific directed transformation of Chlamydomonas. Nucleic Acids Res. 19:
4083-4089.
Hiratsuka 1, Shimada H, Whittier R, Ishibashi T, Sakamoto M, Mori M, Kondo C, Honji Y, Sun CR, Meng BY, Li
YQ, Kanno A, Nishizawa Y. Harai A, Shinozaki K, Sugiura M(1989): The complete sequence of the rice
(Or)'za sativa) chloroplast genome: Intermolecular recombination between distinct tRNA genes accounts for a
major plastid DNA inversion during the evolution of the cereals. Mol. Gen. Genet. 217: 185-194.
155
6. ,
c
;;
-~t
~
tl
.1j
i
~
j
ijj
J
I
f
J~
Huang C. Wang S. Chen L. Lemieux C. Olis C. Tunnel M. Liu XQ (1994): The CMaml'donwllas chloroplasl cJpp
gene contains translated large insertIOn sequences and is essential for cell growth. Mol. Gen. Genet.244i ~
151-159. .
Kanlz TS. Theriot EC, Zimmer EA. Chapman RL (1990): The Pleuraslrophyceae and Micromonadophyceae: a
cladistic analysis of nuclear rRNA sequence data. J. Phycol. 26: 711-721.
Klick U (1989): The intran of a plastid gene from a green alga contains an open rcading frame for a
• transcriptase·like enzyme. Mol. Gen. Genet. 218: 257-267.
Klick U, Choquet Y. Schneider M, Dron M, Bennaun P (1987): Structural and transcription analysis of twc'i
homologous genes for the P700 chlorophyll a-apoproteins in Chlamydomonas rdnhardtii: evidence for in
vivo trans-splicing. EMBO 1. 8: 2185-2195.
Lemieux B, Lemieux C (1985): Extensive sequence rearrangements in the chloroplast genomes of the green
Chlamydomonas eugametos and Chlamydomonas reinhardtii. Curro Genet. 10: 213-219.
Li J. Goldschmidt-Clennont M, Timko MP (1993): Chloroplast-encoded cMB is required for light-independent;
protochlorophyllide reductase activity in Chlamydomonas reinhardtii. Plant Cell 5: 1817-1829. :~
Liu XQ. Xu H, Huang C (1993a): Chloroplast ciliB gene is required for light-independent chlorophyll aecumulatio':'
in Chlamydomonas reinhardtii. Plant Mol. Bioi. 23, 297-308. .
Liu XQ, Huang C, Xu H (1993b): The unusual rps3-like orj712 is functionally essential and structurally conserved
in Chlamydomonas. FEBS Lell. 336: 225-230. .' .
Mattox K, Stewart K (1984): Classification ofthe green algae: a concept based on comparative cytology. In: Irvine
DEG, John DM (eds) Systematics oJthe Green Algae, Academic Press, London. pp.29-72.
Ohyama K, Fukuzawa H, Kohchi T, Shirai H, Sana T, Sana S, Umesono K, Shiki Y, Takeuchi M, Chang Z, Aota
S, Inokuchi H, Ozeki H (1986): Chloroplast gene organization deduced from complete sequence of liverwort
Marchantia polymorpha. Nature 322: 572-574..
Palmer JD (1991): Plastid chromosomes: structure and evolution. In: Bogorad L, VasiliK (eds) Cell Culture and
Somatic Cell Genetics ojPlants. Vol. 7A: The Molecular Biology ojPlastids, Academic Press, San Diego.
pp.5-53.
Saitou N, Nei N (1987): The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mal. Bioi.
Eva!. 4: 406-425.
Schlosser UG (1984): Species-specific sporangium autolysins (cell-wall-dissolving enzymes) in the genus
Chlamydomonas. In: Irvine DEG, John DM (eds) Systematics oJthe Green Algae, Academic Press, London.
pp.40~18.
Shinozaki N, Ohme M, Tanaka M, Wakasugi T, Hayashida N, Matsubayashi T, Zaita N, Chunwongse J, Obokata J,
Yamagochi-Shinozaki K, Ohto C, Torazawa K, Meng BY, Sugita M, Dena H, Komogashira T, Yamada Ki
Kusuda J, Takaiwa F, Kato A, Tohdoh N, Shimada H, Sugiura M (1986): The complete nucleotide sequence
of the tobacco chloroplast genome: its gene organization and expression. EMBO 1. 5: 2043-2049. ;
Tunnel M, Otis C (1994): The chloroplast gene cluster containing psbF, psbL, petG and rps3 is conserved in .
Chlamydomonas. Curro Genet. 27: 54--{j I . . -'
Turmel M, Bellemase G, Lee RW, Lemieux C (1986): A linear DNA molecule of 5.9 kilobase-pairs is highly
homologoos to the chloroplast DNA in the green alga Chlamydomonas moewusii. Plant Mol. Bia!. 6: 313-319:
Turmel M, Bellemare G, Lemieux C (1987): Physical mapping ofdifferences between the chloroplast DNAs ofthe
interfertile algae Chlamydomonas eugametos and Chlamydomonas moewusii. Curro Genet. II: 543-552.
Tunnel M, Boulanger J, Schnare MN, Gray MW, Lemieux C (199Ia): Six group 1 introns and three internal
transcribed spacers in the chloroplast large subunit ribosomal RNA gene of the green alga Chlamydomonas
eugametos. 1. Mo!. Bioi. 218: 293-311.
Tunnel M, Boudreau E, Boulanger J, Mercier JP, Otis C, Lemieux C (199Ib): Chloroplast DNA evolution and
phylogenetic relationships in Chlamydomonas. In: Dudley DM (ed) The Unity ojEvolutionary Biology. The
Proc. 4th Int. Congr. System. & Evo!. Bio!., Dioscorides Press, Portland, Oregon. pp.816-827. .
Tunnel M, Choquet Y, Goldschmidt-Clermont M, Rochaix JD, Otis C, Lemieux C (1995b): The trans·spliced
intron 1 in the psaA gene of the Chlamydomonas chloroplast: a comparative analysis. Curro Genet. 27:
270-279.
Tunnel M, Cote V, Otis C, Mercier JP, Gray MW, Lonergan KM, Lemieux C (I 995a): Evolutionary transfer ofORF-
containing group I introns between different subcellular compartments (chloroplast and mitochondrion). Mol.
Bioi. Evol. 12: 533-545.
Tunnel M, Gutell RR, Mercier JP, Otis C, Lemieux C (1993a): Analysis of the chloroplast large subunit ribosomal
RNA gene from 17 Chlamydomonas taxa: three internal transcribed spacers and 12 group I intran insertion sites.
1. Mal. Bioi. 232: 446-467.
Tunnel M. Mercier JP, Cote MJ (1993b): Group I introns interrupt the chloroplast psaB and psbC and the
mitochondrial rrnL gene in Chlamydomonas. Nucleic Acids Res. 21: 5242-5250.
156
_..
III•
16
Structure and Evolution of the Chloroplast Genome
in Seedless Land Plants
L.A. Raubeson' , D.B. Steint• and D.S. Conant'
Department ojBiological Science. Mount Holyoke College. South Hadley. MA 01075. USA
Department ojNatural Sciences. Lyndon State College. Lyndonville. VT 05851. USA
INTRODUCTION
Gross aspects of chloroplast DNA (cpDNA) structure are shared widely in land plants
(Palmer 199I). The circular genome typically contains a large inverted repeat (IR) that
separates the remainder ofthe molecule into regions of unique DNA - the large and small
single copy regions (LSe, SSC). Early work suggested that the structure of the genome (its
basic organization, gene content and order) was highly conserved (Palmer and Stein 1986).
Now, many instances of structural change are known, with most of the investigated land
plant cpDNAs being from flowering plants (reviewed in Palmer et al. 1988; Downie and
Palmer 199I). Still structural changes, while not quite as rare as first thought, are uncommon.
Structural mutations"that have occurred in the chloroplast genome during land plant evolution
include gene duplication, gene loss, and inversions. Where these mutations occur, the
systematic distribution of the change often provides an important phylogenetic marker.
The gene order common to the fern, Osmunda, the gymnosperm, Ginkgo, and the
·Corresponding author
157