The document summarizes comparative genomic analyses of the human pathogenic fungi Coccidioides immitis and Coccidioides posadasii. Genomes from 13 strains of the two Coccidioides species were sequenced and analyzed to reconstruct their evolutionary history and population structure. Phylogenetic analysis of the strains supported the distinction of the two species and identified potential introgression between species. Comparative genomics was also used to search for genetic differences underlying variations in virulence and distribution between strains that may provide insight into the molecular basis of Coccidioides pathogenesis.
The document describes the discovery of a new basal clade within the fungal kingdom called cryptomycota.
- Cryptomycota includes organisms like Rozella that branch with fungi genetically but appear to grow and develop without synthesizing a chitin-rich cell wall, which is a defining characteristic of fungi.
- Phylogenetic trees constructed from genetic data place cryptomycota as a sister group to Rozella and identify it as a very large, uncultured group of microbes that fundamentally challenges current understanding of fungal evolution and diversity.
This document discusses a talk given by Jason Stajich on comparative and evolutionary genomics of filamentous fungi using next generation sequencing. Stajich is from the Plant Pathology and Microbiology department at the University of California, Riverside. He discussed how next generation sequencing has allowed for comparative genomics studies of many fungal species, which has provided insights into fungal diversity, ecology, and evolution. He highlighted several examples of fungal genomes that have been sequenced and analyzed to learn about relationships between different fungal taxa.
The document is a transcript from a talk given by Jonathan A. Eisen at the Lake Arrowhead Microbial Genomes conference in 2010. It includes quotes from past conferences, suggested homework activities related to microbial genomes and Lake Arrowhead, and a discussion of increasing phylogenetic coverage of bacterial and archaeal lineages to fill gaps in genomic sampling across the domains.
A phylogeny driven genomic encyclopedia of bacteria and archaeaJonathan Eisen
This document outlines the major lineages within the phylum Actinobacteria based on 16S rRNA gene sequences. It shows that Actinobacteria contains over 25 subclasses, with some containing many families and some only having a single class. The tree demonstrates that Actinobacteria is a highly diverse phylum with significant phylogenetic diversity not yet characterized.
Connecting ultrastructure to molecules: Studying evolution of molecular comp...Jason Stajich
- Comparative genomics can help inventory genes shared or missing between fungal species and trace evolutionary transitions from aquatic to terrestrial lifestyles.
- Studying genome sequences from early diverging fungi can illuminate three major evolutionary transitions in fungi - cellular division, cell wall composition, and septa formation.
- Transitions include changing from centrioles to spindle pole bodies for cell division and gaining genes involved in making β(1,3)-glucan while potentially losing cellulose in cell walls.
Jonathan Eisen talk at ASM General Meeting 2010Jonathan Eisen
The document discusses the phylogeny of the bacterial phylum Actinobacteria. It notes that Actinobacteria contains at least 23 major lineages, but genome sequences are mostly limited to a few lineages. Expanding genomic sampling across the phylum is needed to better understand Actinobacteria diversity and evolution.
The document describes the discovery of a new basal clade within the fungal kingdom called cryptomycota.
- Cryptomycota includes organisms like Rozella that branch with fungi genetically but appear to grow and develop without synthesizing a chitin-rich cell wall, which is a defining characteristic of fungi.
- Phylogenetic trees constructed from genetic data place cryptomycota as a sister group to Rozella and identify it as a very large, uncultured group of microbes that fundamentally challenges current understanding of fungal evolution and diversity.
This document discusses a talk given by Jason Stajich on comparative and evolutionary genomics of filamentous fungi using next generation sequencing. Stajich is from the Plant Pathology and Microbiology department at the University of California, Riverside. He discussed how next generation sequencing has allowed for comparative genomics studies of many fungal species, which has provided insights into fungal diversity, ecology, and evolution. He highlighted several examples of fungal genomes that have been sequenced and analyzed to learn about relationships between different fungal taxa.
The document is a transcript from a talk given by Jonathan A. Eisen at the Lake Arrowhead Microbial Genomes conference in 2010. It includes quotes from past conferences, suggested homework activities related to microbial genomes and Lake Arrowhead, and a discussion of increasing phylogenetic coverage of bacterial and archaeal lineages to fill gaps in genomic sampling across the domains.
A phylogeny driven genomic encyclopedia of bacteria and archaeaJonathan Eisen
This document outlines the major lineages within the phylum Actinobacteria based on 16S rRNA gene sequences. It shows that Actinobacteria contains over 25 subclasses, with some containing many families and some only having a single class. The tree demonstrates that Actinobacteria is a highly diverse phylum with significant phylogenetic diversity not yet characterized.
Connecting ultrastructure to molecules: Studying evolution of molecular comp...Jason Stajich
- Comparative genomics can help inventory genes shared or missing between fungal species and trace evolutionary transitions from aquatic to terrestrial lifestyles.
- Studying genome sequences from early diverging fungi can illuminate three major evolutionary transitions in fungi - cellular division, cell wall composition, and septa formation.
- Transitions include changing from centrioles to spindle pole bodies for cell division and gaining genes involved in making β(1,3)-glucan while potentially losing cellulose in cell walls.
Jonathan Eisen talk at ASM General Meeting 2010Jonathan Eisen
The document discusses the phylogeny of the bacterial phylum Actinobacteria. It notes that Actinobacteria contains at least 23 major lineages, but genome sequences are mostly limited to a few lineages. Expanding genomic sampling across the phylum is needed to better understand Actinobacteria diversity and evolution.
This document summarizes a collaborative project involving over 140 researchers from 20 countries to improve fungal taxonomy and identification using DNA barcoding techniques. It discusses challenges with commonly used markers like Cox1 and ITS for fungal barcoding due to issues like introns and multiple copies. It evaluates the performance of different markers like SSU, RPB1, LSU, ITS individually and in combination on a dataset of 746 fungal strains from 396 species. It also discusses using secondary markers for groups where primary markers lack resolution. The document emphasizes needs like increasing sequence data for understudied groups and evaluating environmental diversity and "virtual species".
The document provides an overview of the human microbiome and its importance. It notes that the human microbiome consists of trillions of microbes, especially bacteria, that inhabit our bodies. Our microbial cells outnumber our human cells 10 to 1. The microbes play an important role in metabolism, immune function, and other processes. Ongoing research is exploring links between the microbiome and conditions like obesity, cancer, inflammatory bowel disease, and neurological disorders. The microbiome represents an exciting area of research into human health and disease.
This document summarizes Norm Pace's research on surveying microbial communities in indoor human environments using ribosomal RNA sequencing. It describes sampling aerosols from various indoor locations like subway stations, schools, hospitals, hotels, offices and universities. It finds that indoor microbiomes are dominated by a few bacterial phyla and many sequences are closely related to known species. Environments differ in their microbial makeup but human-associated microbes predominate indoors. Showerhead biofilms frequently contain potential pathogens like Mycobacterium avium. The research is providing insights into the diversity and distribution of microbes people encounter.
Global adventitious agent regulation of raw materials ibc sept 2010 final ver...chalverson
This document discusses global regulations pertaining to the control of adventitious agents in raw materials used in biopharmaceutical manufacturing. It covers regulations from agencies like the USDA, FDA, EMA, WHO, and others. It also provides information on risk assessment and minimizing risks from various adventitious agents like viruses, prions, mycoplasma, bacteria, and fungi. Specific controls are discussed like sourcing, testing, cleaning, filtration, heat treatment, pH treatment, and gamma irradiation. Challenges with certain resistant agents are also addressed.
Epidemiological marker (serotyping and bacteriocin typing)Santosh Kumar Yadav
This document discusses various epidemiological marker typing methods used to differentiate bacterial strains, including serotyping, bacteriocin typing, and colicin typing. Serotyping is based on antigenic differences expressed on bacterial cell surfaces and has good reproducibility but poor discriminatory power. Bacteriocin typing examines bacteriocin production and susceptibility patterns to distinguish strains. It has fair reproducibility and discriminatory power but some strains are non-typeable. Colicin typing specifically examines colicin production in E. coli strains using a spot culture method with indicator strains. These typing methods can help epidemiological studies and hospital infection control.
1. The study investigated antibiotic resistance and the presence of the blaCTX-M-15 gene in Enterobacter species isolated from hospitals in Tehran, Iran between 2012-2013.
2. It found high rates of resistance to common antibiotics like Augmentin and high frequencies of the blaCTX-M-15 gene (11.8% of isolates).
3. The blaCTX-M-15 gene was found to be located on conjugative plasmids in one Enterobacter isolate, demonstrating its potential for horizontal transfer between bacteria.
This document provides information on various microorganisms that can cause spoilage of meat, eggs, and poultry. It describes the key characteristics of genera including Acinetobacter, Alcaligenes, Moraxella, Psychrobacter, Aeromonas, Flavobacterium, Brochothrix, Alteromonas, Pseudomonas, Shewanella, Staphylococcus, and Micrococcus. For each genus, it discusses cell morphology, biochemical properties, habitats, and roles in food spoilage.
Infectious diseases are caused by various microorganisms like bacteria, viruses, fungi, and parasites. Microorganisms can be identified through direct microscopic examination, culture-based techniques, biochemical tests, and serological and molecular identification methods. Correct specimen collection, handling, and laboratory testing are essential for accurate microbial identification.
This document discusses clinical microbiology and methods used in the field. It provides definitions of clinical microbiology as the study of bacteria and their relation to medicine. Key methods discussed include culture-based techniques of growing bacteria in controlled conditions to isolate, identify, and determine antibiotic sensitivity. Additional non-culture methods described are use of monoclonal antibodies, enzyme immunoassays, probes, polymerase chain reaction (PCR), and ligase chain reaction.
VTU 06BT74 Unit 5 Synopsis of microorganismsdrpratimak
This document provides information on common foodborne bacteria, molds, and yeasts. It lists 29 bacterial groups with their key features such as gram staining, occurrence, and any special features. It also discusses 18 common foodborne molds including their features, occurrence, and remarks. Finally, it briefly mentions foodborne yeasts. The document serves as a useful reference for the various microorganisms commonly associated with food spoilage and foodborne illness.
Ps graminis as biocontrol agent of fire blightJorge Gonzalez
☻ Strain 49M of Pseudomonas graminis significantly protected apple blossoms and shoots against fire blight through high efficacy when applied at a concentration of 108 cfu/ml (89.0-82.8%).
☻ Survival of strain 49M bacteria on apple blossoms was high, with 10 days detecting levels of 2.0x104—6.7 x 106 cfu/blossom after introduction at 108 cfu/ml by spraying.
☻ Strain 49M produced siderophores and biofilm but not N-acyl homoserine lactones. It contained the regulatory gen gacA but not genes for selected antibiotics; and inhibited the fire blight pathogen
Identification of Unknown Bacteria Extracted from Flagstaff, AZVictoria Ziegler
This document summarizes an experiment to identify an unknown bacteria extracted from soil in Flagstaff, Arizona. A cotton swab sample was taken from a twig and various tests were performed on the isolated bacteria, including staining, biochemical tests, and analysis of growth patterns. Through purification and isolation techniques, morphological analysis using stains, and tests of enzymatic activity and metabolic processes, the student aimed to determine the specific genus and species of the unknown bacteria. The results of the staining, catalase, oxidase, carbohydrate fermentation, oxygen requirement, and nitrate reduction tests would provide information to identify the bacteria.
Wound swab collection and processing is described. Swabs tipped with rayon or dacron are optimal for bacterial recovery from wounds. Primary plating includes blood agar to detect pathogens like Staphylococcus aureus and Streptococcus pyogenes. Gram staining identifies morphology and arrangement of bacteria seen. Biochemical tests and susceptibility testing help identify and determine resistance of pathogens isolated.
The document describes identifying Salmonella typhimurium from a mixed culture using differential tests. A pure culture of the Gram-negative bacteria was obtained and tested on five types of differential media. The results identified the bacteria as S. typhimurium based on its ability to ferment glucose and perform mixed acid fermentation, utilize citrate, reduce sulfur and be motile on SIM media. Standard differential testing using affordable media can successfully identify bacterial species from mixed cultures.
This document discusses various methods for identifying bacteria in the laboratory, including:
1) Microscopic examination such as gram staining and fluorescent staining to examine cell morphology.
2) Cultural characteristics such as pigment production, hemolysis on blood agar, and lactose fermentation.
3) Biochemical reactions like catalase, coagulase, and oxidase tests.
4) Serological identification using antigen or antibody detection.
5) Molecular methods using nucleic acid probes to identify specific DNA or RNA sequences.
Bacillus anthracis causes the skin infection cutaneous anthrax. It discusses the structure of bacterial cells, which are prokaryotes without nuclei or organelles. It classifies bacteria by shape under light microscopy as cocci, bacilli, or spirilla. Examples include Staphylococcus aureus and Streptococcus pyogenes. The Gram stain procedure distinguishes Gram-positive and Gram-negative bacteria based on their cell wall structure and composition.
This document discusses microbial identification methods. It begins by outlining the objectives and topics to be covered, including identification of bacteria, fungi, algae, and viruses. For bacteria, it describes phenotypic methods like morphology, physiology/biochemistry, and genotypic techniques using genetic markers. Morphological identification of bacteria involves shape, staining, and colony appearance. Physiological/biochemical tests examine enzyme production and nutrient metabolism. Genotypic methods like nucleic acid sequencing and PCR are also discussed. The document continues by addressing identification of fungi, algae, and viruses through their distinguishing characteristics and laboratory techniques.
This document discusses various methods for identifying and characterizing prokaryotes, including phenotypic and genotypic characteristics. Identification using phenotypic characteristics involves microscopic analysis, staining techniques like Gram stain, culture characteristics on selective media, and biochemical tests of metabolic differences. Genotypic identification uses techniques like nucleic acid probes, PCR, sequencing ribosomal RNA genes. Characterizing strain differences can be done through biochemical and serological typing, genomic typing methods like PFGE and ribotyping, phage typing, and antibiograms.
The largest known organism is a honey mushroom fungus in Oregon that covers 2,200 acres. It is a single organism made of a dense network of fused mycelium. Fungi reproduce both sexually, through the fusion of hyphae and nuclei to form spores, and asexually through spore production. There are over 100,000 known fungal species divided among 5 phyla.
1. The document provides an overview of fungi, including their general characteristics, classification, morphology, reproduction, and importance.
2. Fungi are classified based on their sexual reproduction (zygomycetes, ascomycetes, basidiomycetes) or morphology (molds, yeasts, yeast-like, dimorphic). They reproduce both sexually and asexually through spores.
3. Fungi play important beneficial roles like decomposition and producing antibiotics, but can also cause diseases and spoilage. Understanding their properties, life cycles, and taxonomy is important for fields like medicine and agriculture.
This document summarizes a collaborative project involving over 140 researchers from 20 countries to improve fungal taxonomy and identification using DNA barcoding techniques. It discusses challenges with commonly used markers like Cox1 and ITS for fungal barcoding due to issues like introns and multiple copies. It evaluates the performance of different markers like SSU, RPB1, LSU, ITS individually and in combination on a dataset of 746 fungal strains from 396 species. It also discusses using secondary markers for groups where primary markers lack resolution. The document emphasizes needs like increasing sequence data for understudied groups and evaluating environmental diversity and "virtual species".
The document provides an overview of the human microbiome and its importance. It notes that the human microbiome consists of trillions of microbes, especially bacteria, that inhabit our bodies. Our microbial cells outnumber our human cells 10 to 1. The microbes play an important role in metabolism, immune function, and other processes. Ongoing research is exploring links between the microbiome and conditions like obesity, cancer, inflammatory bowel disease, and neurological disorders. The microbiome represents an exciting area of research into human health and disease.
This document summarizes Norm Pace's research on surveying microbial communities in indoor human environments using ribosomal RNA sequencing. It describes sampling aerosols from various indoor locations like subway stations, schools, hospitals, hotels, offices and universities. It finds that indoor microbiomes are dominated by a few bacterial phyla and many sequences are closely related to known species. Environments differ in their microbial makeup but human-associated microbes predominate indoors. Showerhead biofilms frequently contain potential pathogens like Mycobacterium avium. The research is providing insights into the diversity and distribution of microbes people encounter.
Global adventitious agent regulation of raw materials ibc sept 2010 final ver...chalverson
This document discusses global regulations pertaining to the control of adventitious agents in raw materials used in biopharmaceutical manufacturing. It covers regulations from agencies like the USDA, FDA, EMA, WHO, and others. It also provides information on risk assessment and minimizing risks from various adventitious agents like viruses, prions, mycoplasma, bacteria, and fungi. Specific controls are discussed like sourcing, testing, cleaning, filtration, heat treatment, pH treatment, and gamma irradiation. Challenges with certain resistant agents are also addressed.
Epidemiological marker (serotyping and bacteriocin typing)Santosh Kumar Yadav
This document discusses various epidemiological marker typing methods used to differentiate bacterial strains, including serotyping, bacteriocin typing, and colicin typing. Serotyping is based on antigenic differences expressed on bacterial cell surfaces and has good reproducibility but poor discriminatory power. Bacteriocin typing examines bacteriocin production and susceptibility patterns to distinguish strains. It has fair reproducibility and discriminatory power but some strains are non-typeable. Colicin typing specifically examines colicin production in E. coli strains using a spot culture method with indicator strains. These typing methods can help epidemiological studies and hospital infection control.
1. The study investigated antibiotic resistance and the presence of the blaCTX-M-15 gene in Enterobacter species isolated from hospitals in Tehran, Iran between 2012-2013.
2. It found high rates of resistance to common antibiotics like Augmentin and high frequencies of the blaCTX-M-15 gene (11.8% of isolates).
3. The blaCTX-M-15 gene was found to be located on conjugative plasmids in one Enterobacter isolate, demonstrating its potential for horizontal transfer between bacteria.
This document provides information on various microorganisms that can cause spoilage of meat, eggs, and poultry. It describes the key characteristics of genera including Acinetobacter, Alcaligenes, Moraxella, Psychrobacter, Aeromonas, Flavobacterium, Brochothrix, Alteromonas, Pseudomonas, Shewanella, Staphylococcus, and Micrococcus. For each genus, it discusses cell morphology, biochemical properties, habitats, and roles in food spoilage.
Infectious diseases are caused by various microorganisms like bacteria, viruses, fungi, and parasites. Microorganisms can be identified through direct microscopic examination, culture-based techniques, biochemical tests, and serological and molecular identification methods. Correct specimen collection, handling, and laboratory testing are essential for accurate microbial identification.
This document discusses clinical microbiology and methods used in the field. It provides definitions of clinical microbiology as the study of bacteria and their relation to medicine. Key methods discussed include culture-based techniques of growing bacteria in controlled conditions to isolate, identify, and determine antibiotic sensitivity. Additional non-culture methods described are use of monoclonal antibodies, enzyme immunoassays, probes, polymerase chain reaction (PCR), and ligase chain reaction.
VTU 06BT74 Unit 5 Synopsis of microorganismsdrpratimak
This document provides information on common foodborne bacteria, molds, and yeasts. It lists 29 bacterial groups with their key features such as gram staining, occurrence, and any special features. It also discusses 18 common foodborne molds including their features, occurrence, and remarks. Finally, it briefly mentions foodborne yeasts. The document serves as a useful reference for the various microorganisms commonly associated with food spoilage and foodborne illness.
Ps graminis as biocontrol agent of fire blightJorge Gonzalez
☻ Strain 49M of Pseudomonas graminis significantly protected apple blossoms and shoots against fire blight through high efficacy when applied at a concentration of 108 cfu/ml (89.0-82.8%).
☻ Survival of strain 49M bacteria on apple blossoms was high, with 10 days detecting levels of 2.0x104—6.7 x 106 cfu/blossom after introduction at 108 cfu/ml by spraying.
☻ Strain 49M produced siderophores and biofilm but not N-acyl homoserine lactones. It contained the regulatory gen gacA but not genes for selected antibiotics; and inhibited the fire blight pathogen
Identification of Unknown Bacteria Extracted from Flagstaff, AZVictoria Ziegler
This document summarizes an experiment to identify an unknown bacteria extracted from soil in Flagstaff, Arizona. A cotton swab sample was taken from a twig and various tests were performed on the isolated bacteria, including staining, biochemical tests, and analysis of growth patterns. Through purification and isolation techniques, morphological analysis using stains, and tests of enzymatic activity and metabolic processes, the student aimed to determine the specific genus and species of the unknown bacteria. The results of the staining, catalase, oxidase, carbohydrate fermentation, oxygen requirement, and nitrate reduction tests would provide information to identify the bacteria.
Wound swab collection and processing is described. Swabs tipped with rayon or dacron are optimal for bacterial recovery from wounds. Primary plating includes blood agar to detect pathogens like Staphylococcus aureus and Streptococcus pyogenes. Gram staining identifies morphology and arrangement of bacteria seen. Biochemical tests and susceptibility testing help identify and determine resistance of pathogens isolated.
The document describes identifying Salmonella typhimurium from a mixed culture using differential tests. A pure culture of the Gram-negative bacteria was obtained and tested on five types of differential media. The results identified the bacteria as S. typhimurium based on its ability to ferment glucose and perform mixed acid fermentation, utilize citrate, reduce sulfur and be motile on SIM media. Standard differential testing using affordable media can successfully identify bacterial species from mixed cultures.
This document discusses various methods for identifying bacteria in the laboratory, including:
1) Microscopic examination such as gram staining and fluorescent staining to examine cell morphology.
2) Cultural characteristics such as pigment production, hemolysis on blood agar, and lactose fermentation.
3) Biochemical reactions like catalase, coagulase, and oxidase tests.
4) Serological identification using antigen or antibody detection.
5) Molecular methods using nucleic acid probes to identify specific DNA or RNA sequences.
Bacillus anthracis causes the skin infection cutaneous anthrax. It discusses the structure of bacterial cells, which are prokaryotes without nuclei or organelles. It classifies bacteria by shape under light microscopy as cocci, bacilli, or spirilla. Examples include Staphylococcus aureus and Streptococcus pyogenes. The Gram stain procedure distinguishes Gram-positive and Gram-negative bacteria based on their cell wall structure and composition.
This document discusses microbial identification methods. It begins by outlining the objectives and topics to be covered, including identification of bacteria, fungi, algae, and viruses. For bacteria, it describes phenotypic methods like morphology, physiology/biochemistry, and genotypic techniques using genetic markers. Morphological identification of bacteria involves shape, staining, and colony appearance. Physiological/biochemical tests examine enzyme production and nutrient metabolism. Genotypic methods like nucleic acid sequencing and PCR are also discussed. The document continues by addressing identification of fungi, algae, and viruses through their distinguishing characteristics and laboratory techniques.
This document discusses various methods for identifying and characterizing prokaryotes, including phenotypic and genotypic characteristics. Identification using phenotypic characteristics involves microscopic analysis, staining techniques like Gram stain, culture characteristics on selective media, and biochemical tests of metabolic differences. Genotypic identification uses techniques like nucleic acid probes, PCR, sequencing ribosomal RNA genes. Characterizing strain differences can be done through biochemical and serological typing, genomic typing methods like PFGE and ribotyping, phage typing, and antibiograms.
The largest known organism is a honey mushroom fungus in Oregon that covers 2,200 acres. It is a single organism made of a dense network of fused mycelium. Fungi reproduce both sexually, through the fusion of hyphae and nuclei to form spores, and asexually through spore production. There are over 100,000 known fungal species divided among 5 phyla.
1. The document provides an overview of fungi, including their general characteristics, classification, morphology, reproduction, and importance.
2. Fungi are classified based on their sexual reproduction (zygomycetes, ascomycetes, basidiomycetes) or morphology (molds, yeasts, yeast-like, dimorphic). They reproduce both sexually and asexually through spores.
3. Fungi play important beneficial roles like decomposition and producing antibiotics, but can also cause diseases and spoilage. Understanding their properties, life cycles, and taxonomy is important for fields like medicine and agriculture.
Medical mycology is the study of medically important fungi. Fungi can cause superficial infections of the skin, hair, and nails (dermatophytoses) as well as subcutaneous, systemic, and opportunistic mycoses. Superficial mycoses include tinea versicolor caused by Malassezia furfur, tinea nigra caused by Hortaea werneckii, and piedra caused by fungi like Trichosporon beigelii and Piedraia hortae that form nodules on hair. Dermatophytoses or ringworm is the most common superficial mycoses, affecting the skin, hair, and nails, and is caused by fungi
Fungi are a diverse kingdom that can reproduce both sexually and asexually. They obtain nutrients through absorption or as parasites/saprophytes. Their cell walls contain chitin and they are more closely related to animals than plants. There are over 1 million known fungal species that can be classified into four phyla: Chytridiomycota, Zygomycota, Ascomycota, and Basidiomycota. These phyla contain many important and familiar fungi such as mushrooms, yeasts, molds, and lichens. The largest known organism is a honey mushroom fungus in Oregon covering over 2,200 acres.
Plasmodium are protozoan parasites that cause malaria. They have a complex life cycle that alternates between mosquito and vertebrate hosts. In vertebrates, Plasmodium parasites infect liver cells and erythrocytes, multiplying asexually before differentiating into male and female sexual forms. When ingested by a mosquito during a blood meal, the parasites fuse and multiply, forming invasive sporozoites that can infect a new vertebrate host and continue the cycle. Five Plasmodium species infect humans, with P. falciparum being the most lethal cause of malaria. Hundreds of other Plasmodium species infect other mammals, birds, and lizards.
Fungi are a diverse kingdom that can be classified into four main phyla: Chytridiomycota, Zygomycota, Ascomycota, and Basidiomycota. They are heterotrophic and can absorb nutrients, break down dead organic matter as saprophytes, or obtain nutrients from living hosts as parasites. Fungi reproduce both sexually through plasmogamy and karyogamy and asexually through spores. The largest known organism is a honey mushroom fungus in Oregon whose underground mycelial network spans over 2,200 acres.
Talk by J. Eisen at ASBMB on "Phylogeny driven genomic encyclopedia" projectJonathan Eisen
This document summarizes a talk given by Jonathan Eisen about creating a phylogeny-driven genomic encyclopedia of bacteria and archaea. It notes that while there are at least 40 phyla of bacteria, most genome sequences are from just three phyla. Additionally, some phyla are only sparsely sampled, and a similar trend exists in archaea, with sequencing concentrated in a few groups. The goal is to generate more genome sequences to better represent bacterial and archaeal diversity and evolution.
The document discusses biological classification systems. It describes Carolus Linnaeus' original two kingdom system of Plantae and Animalia. It then summarizes R.H. Whittaker's five kingdom system of Monera, Protista, Fungi, Plantae, and Animalia. Key details are provided about each kingdom, including defining characteristics, examples of organisms, and modes of reproduction. Viruses, viroids, and lichens are also briefly outlined.
Mycoplasma pneumoniae are bacteria that can cause illness by damaging the lining of the respiratory system (throat, lungs, windpipe). People can have the bacteria in their nose or throat at one time or another without being ill. People spread Mycoplasma pneumoniae bacteria to others by coughing or sneezing.
This seminar presentation summarizes anther culture and haploid plant regeneration. Anther culture involves culturing microspores or anthers to produce haploid plants. It has been successful in over 250 plant species. There are different pathways that microspores can take to develop into haploid plants, including equal or unequal division. Pretreatment of anthers and culture conditions like medium, temperature and light exposure can influence success rates. Anther culture is useful for producing haploids but requires skill and has risks of chimera or callus formation.
Bacteria are the simplest and smallest prokaryotic microorganisms. They are ubiquitous, existing everywhere from atmospheric heights of 6km to ocean depths of 5km. Bacteria exhibit a wide range of shapes and many are motile with flagella or pili. They reproduce asexually through binary fission and lack true sexual reproduction. Bacteria play important economic roles through causing diseases, food spoilage, increasing soil fertility through nitrogen fixation, and use in biotechnology and pollution control.
This document is a collection of photographs of various mushroom species from around the world, with their Latin and common names when provided. It discusses how mushrooms were originally classified as plants but are now recognized as their own kingdom of fungi due to their unusual characteristics. The photos provide close-up views of mushrooms' intricate and diverse appearances in order to showcase their beauty and encourage more understanding of their strange but interesting natural forms.
This document provides an atlas of medical parasitology. It contains 167 photographs of over 50 parasites of medical importance grouped into intestinal/urogenital parasites and blood/tissue parasites. For each parasite, there is a brief introduction and caption for each photograph. The photographs show the parasites at different life stages and in clinical samples. The goal is to provide medical students and practitioners with a visual guide to diagnosing parasitic diseases.
The document discusses fungal genomics resources including FungiDB and related projects. It provides information on:
1) FungiDB releasing genomes from 18 species including Aspergillus, Coccidioides, Fusarium, Neurospora, Candida, Saccharomyces, Cryptococcus, Puccinia and Rhizopus.
2) Future plans to include additional Cryptococcus genomes and the genomes of Tremella mesenterica and Neurospora crassa with RNA-seq data and GO annotations.
3) Strategies for querying fungal genomes and functional genomics data using FungiDB and related tools.
This document provides an overview of the FungiDB database, which contains genomic and functional genomic data for 18 fungal species. Key points include:
- FungiDB takes advantage of infrastructure developed for the Eukaryotic Pathogen Genome Database.
- 18 fungal genomes from 3 fungal phyla are included in the current release.
- The database allows browsing of gene pages, genome browsers, and querying to enable data mining across fungal species.
This document summarizes a study comparing gene family sizes across fungal genomes. It finds that changes in gene family copy numbers may be an important mechanism for adaptation. Using comparative genomics tools that model gene family evolution, the study identifies unexpectedly large expansions or contractions of specific gene families in lineages of interest, such as human pathogens. This may provide insights into the genetic basis of traits like pathogenesis. The analysis screens multiple fungal genomes, including pathogens like Coccidioides species, to find candidate gene families with lineage-specific changes in copy number that distinguish phenotypic groups.
This document summarizes the FungiDB database, which provides comparative genomics resources for fungal genomes. It includes 18 fungal genomes from Ascomycota, Basidiomycota and Zygomycota phyla. Users can perform gene and genome queries, view gene pages, analyze orthology and synteny between species. The database is powered by infrastructure from other pathogen databases and aims to facilitate research in fungal genomics, evolution and functional annotation. Feedback is sought from users to improve the resource.
This document discusses open questions in bioinformatics and computational biology from an evolutionary and molecular biology perspective. It outlines where biological data is coming from, current approaches to analyzing large datasets, and problems that remain around efficiently searching, interfacing with, and finding patterns in huge amounts of sequencing data. Future directions include more biologically focused research using these computational tools.
Comparative genomics of the fungal kingdomJason Stajich
This document discusses comparative genomics of fungi using available fungal genome sequences. It describes how comparative genomics can be used to identify shared, unique, gained and lost genes between species to study evolution. More than 65 fungal genomes are available with more in development, allowing for the study of genome organization, evolution of multicellularity, cell wall evolution and ancestral gene content. Gene prediction and annotation methods are discussed to generate consensus gene models from multiple tools.
Comparative genomics of fung: studying adaptation through gene family evolutionJason Stajich
Comparative genomics of fungi can provide insights into how fungi adapt to different environments through gene family evolution. Analysis of gene family sizes in fungi found that they often follow a power law distribution, with some gene families having many copies while others are singletons. Expansion of gene families involved in functions like secondary metabolism and pathogenesis have allowed adaptation to new niches. Case studies on Onygenales and chytrid fungi identified family expansions of genes related to virulence as well as contractions of families for plant cell wall degradation, indicating evolutionary shifts in lifestyle. Local duplications were found to be a major driver of family expansions in some species. Comparisons of gene content beyond just orthologs can provide clues about phenotypic
Evolution of gene family size change in fungiJason Stajich
The document discusses gene family size changes in fungi. It notes that gene duplications are important for new gene and function evolution. It analyzed gene family sizes across 37 fungal genomes using computational methods to identify lineage-specific expansions. The analysis used probabilistic models to evaluate gene family size changes along phylogenetic branches and identify families with unusually large size increases or decreases in specific lineages.
Comparative Genomics with GMOD and BioPerlJason Stajich
BioPerl is an open source toolkit for bioinformatics data manipulation written in Perl. It contains modules for reading and writing sequence data in common formats, manipulating sequences, parsing BLAST reports and multiple sequence alignments. BioPerl objects represent sequences, features, annotations and search results in a flexible and extensible way. The toolkit is widely used for tasks like sequence analysis, parsing bioinformatics software output, and accessing biological databases.
This slide is special for master students (MIBS & MIFB) in UUM. Also useful for readers who are interested in the topic of contemporary Islamic banking.
Introduction to AI for Nonprofits with Tapp NetworkTechSoup
Dive into the world of AI! Experts Jon Hill and Tareq Monaur will guide you through AI's role in enhancing nonprofit websites and basic marketing strategies, making it easy to understand and apply.
Exploiting Artificial Intelligence for Empowering Researchers and Faculty, In...Dr. Vinod Kumar Kanvaria
Exploiting Artificial Intelligence for Empowering Researchers and Faculty,
International FDP on Fundamentals of Research in Social Sciences
at Integral University, Lucknow, 06.06.2024
By Dr. Vinod Kumar Kanvaria
This presentation includes basic of PCOS their pathology and treatment and also Ayurveda correlation of PCOS and Ayurvedic line of treatment mentioned in classics.
Executive Directors Chat Leveraging AI for Diversity, Equity, and InclusionTechSoup
Let’s explore the intersection of technology and equity in the final session of our DEI series. Discover how AI tools, like ChatGPT, can be used to support and enhance your nonprofit's DEI initiatives. Participants will gain insights into practical AI applications and get tips for leveraging technology to advance their DEI goals.
ISO/IEC 27001, ISO/IEC 42001, and GDPR: Best Practices for Implementation and...PECB
Denis is a dynamic and results-driven Chief Information Officer (CIO) with a distinguished career spanning information systems analysis and technical project management. With a proven track record of spearheading the design and delivery of cutting-edge Information Management solutions, he has consistently elevated business operations, streamlined reporting functions, and maximized process efficiency.
Certified as an ISO/IEC 27001: Information Security Management Systems (ISMS) Lead Implementer, Data Protection Officer, and Cyber Risks Analyst, Denis brings a heightened focus on data security, privacy, and cyber resilience to every endeavor.
His expertise extends across a diverse spectrum of reporting, database, and web development applications, underpinned by an exceptional grasp of data storage and virtualization technologies. His proficiency in application testing, database administration, and data cleansing ensures seamless execution of complex projects.
What sets Denis apart is his comprehensive understanding of Business and Systems Analysis technologies, honed through involvement in all phases of the Software Development Lifecycle (SDLC). From meticulous requirements gathering to precise analysis, innovative design, rigorous development, thorough testing, and successful implementation, he has consistently delivered exceptional results.
Throughout his career, he has taken on multifaceted roles, from leading technical project management teams to owning solutions that drive operational excellence. His conscientious and proactive approach is unwavering, whether he is working independently or collaboratively within a team. His ability to connect with colleagues on a personal level underscores his commitment to fostering a harmonious and productive workplace environment.
Date: May 29, 2024
Tags: Information Security, ISO/IEC 27001, ISO/IEC 42001, Artificial Intelligence, GDPR
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A review of the growth of the Israel Genealogy Research Association Database Collection for the last 12 months. Our collection is now passed the 3 million mark and still growing. See which archives have contributed the most. See the different types of records we have, and which years have had records added. You can also see what we have for the future.
Main Java[All of the Base Concepts}.docxadhitya5119
This is part 1 of my Java Learning Journey. This Contains Custom methods, classes, constructors, packages, multithreading , try- catch block, finally block and more.
it describes the bony anatomy including the femoral head , acetabulum, labrum . also discusses the capsule , ligaments . muscle that act on the hip joint and the range of motion are outlined. factors affecting hip joint stability and weight transmission through the joint are summarized.
A workshop hosted by the South African Journal of Science aimed at postgraduate students and early career researchers with little or no experience in writing and publishing journal articles.
Evolution and exploration of the transcriptional landscape in two filamentous fungi, Coccidioides and Neurospora
1. EVOLUTION AND
EXPLORATION OF THE
TRANSCRIPTIONAL
LANDSCAPE IN TWO
FILAMENTOUS FUNGI,
COCCIDIOIDES AND
NEUROSPORA
Jason Stajich
University of California, Riverside
2. Studying Evolution with
Comparative Genomics
Reconstructing evolution from inferred changes DNA sequences.
From populations to species to kingdoms
How do mutations arise, become fixed (in a population),
influence phenotypic change, and influence formation of new
species?
Genome sequencing provides the data from extant (living) species.
Comparative genomics to identify genome changes and establish
hypotheses about importance of changes.
3. How old are the fungi?
Opisthokont
Animal/Fungi Ancestor
Taylor and Berbee,
Mycologia 2006
Opisthokont Ancestor ~1Bya
- Problems:
Few collected fossils; dates are still very debated
5. Genome samples from fungi
Dictyostelium
Monosiga Choanoflagellida
Caenorhabditis
Metazoa
Drosophila
Homo
Batrachochytrium ‘Chytrid’ Chytrid 5
Spiromyces Zygomycota
Opisthokont ‘Chytrid’
Olpidium
Rhizopus Mucormycotina Muromycotina 3
Fungi Glomus Glomeromycota Glomeromycota 1
Puccinia
Cryptococcus Basidiomycota Basidiomycota 31
Coprinopsis
Schizosaccharomyces Taphrinomycotina Taphrinomycotina 4
Yarrowia
Saccharomyces
Saccharomycotina
Saccharomycotina > 20
Ascomycota Candida
Morchella
Cochliobolus
Cladonia
Pezizomycotina Aspergillus
Coccidioides
Magnaporthe
Pezizomycotina >55
100+ Genomes Neurospora
Fusarium
Botryotinia
Tree Based on James TY et al. 2006. Nature.
http://fungalgenomes.org/wiki/Fungal_Genome_Links
6. Evolution of Fungal Diversity
Cryptococcus neoformans X. Lin Coprinopsis cinerea Ellison & Stajich Aspergillus niger. N Read Glomus sp. Univ Sydney Rozella allomycis. James et al
Puccinia graminis J. F. Hennen Batrachochytrium dendrobatidis
Laccaria bicolor Martin et al. Neurospora crassa. Hickey & Reed Phycomyces blakesleansus T. Ootaki
J. Longcore
Ustilago maydis Kai Hirdes Amanita phalloides. M Wood Xanthoria elegans. Botany POtD Rhizopus stolonifera. Rhizophydium. The Fifth Kingom
11. Building Comparative Genomics Tools
BioPerl - Perl language programming tools for bioinformatics
(Stajich et al 2002).
Parsing sequences, alignments, report output (BLAST,
HMMER, PAML, CLUSTALW, PHYLIP)
My development focuses on Sequence, Phylogenetics, and
Molecular Evolution analyses tools
Gbrowse - Genome Browser (Stein et al 2002)
12. Genome Browser data integration
Ncra_OR74A_chrIV_contig7.20
300k 310k 320k 330k
DNA_GCContent
% gc
NCBI genes (Broad called)
NCU04433 NCU04430 NCU04426
sulfate permease II CYS-14 related to aminopeptidase Y precursor; vacuolar related to cyclin-supressing protein kinase
NCU04432 NCU04429 NCU04425
hypothetical protein conserved hypothetical protein putative protein
NCU04431 NCU04428 NCU04424
related to endo-1; 3-beta-glucanase related to spindle assembly checkpoint protein related to regulator of chromatin
NCU04427
conserved hypothetical protein
PASA updated NCBI/Broad genes
NCU04433 NCU04432
[pasa:asmbl_9429,status:12],[pasa:asmbl_9430,status:12] [pasa:asmbl_9440,status:12],[pasa:asmbl_9441,status:12],[pasa:asmbl_9442,status:12]
[pasa:asmbl_9431,status:12],[pasa:asmbl_9432,status:12] [pasa:asmbl_9443,status:12],[pasa:asmbl_9444,status:12]
[pasa:asmbl_9433,status:12],[pasa:asmbl_9434,status:12],[pasa:asmbl_9435,status:12]
[pasa:asmbl_9436,status:12],[pasa:asmbl_9437,status:12],[pasa:asmbl_9438,status:12],[pasa:asmbl_9439,status:12]
[pasa:asmbl_9445,status:12],[pasa:asmbl_9446,status:12]
NCU04424
Named Genes (Radford laboratory)
cys-14 gh16-3
tRNA{phe}-9
miRNA Solexa histogram
miRNA
K4dime ChIP-Seq histogram (SOAP)
K4dime_Solexa
K9met3 ChIP-Seq histogram (SOAP) Stajich et al, unpublished
K9met3 Smith, Freitag, et al unpublished
14. Comparative Genomics and
Evolution
Population genomic inference of migration
and hybridization
Genomics approaches to finding genes
underlying adaptation
Deeper divergences: What makes a fungus?
15. Comparative Genomics and
Evolution
Population genomic inference of migration
and hybridization
Comparative genomic approaches to finding
genes underlying adaptation
Deeper divergences: What makes a fungus?
16. Human pathogen Coccidioides
Coccidioides (Valley fever)
Is a primary human pathogen - infects healthy people - most
human pathogenic fungi are opportunistic.
Endemic in US Southwest, Mexico
Requires laboratory BSL3 and is a Select Agent
Comparative analyses of Coccidoides and related species to attempt
to understand how a pathogen evolved
Comparative genomics, Population genomics, and Transcriptional
Profiling
19. Comparative & Population Genomics
of a human pathogenic fungus
Genomes from 2 species of Coccidioides diverged ~5 Mya. (dS 0.023)
Population Genomics
Genomes of 13 strains of Coccidioides
Evidence for introgression?
Differences in population size between species?
Strain variation in virulence and distribution
Molecular basis for virulence? Evolutionary signature?
20. Two species of Coccidioides
C.immitis
C.posadasii
EVOLUTION
Fisher et al, 2000
22. Phylogeny of 13 99
CP RMSCC 2133
sequenced Coccidioides CP RMSCC 3700
CP RMSCC 1037
genomes
CP RMSCC 3488
CP CPA 0001
100 C. posadasii
CP CPA 0020
95
CP1
100
CP RMSCC 1038
CPS2
99 99
CP CPA 0066
CI RMSCC 2394
100
CI RMSCC 3703 C. immitis 73 kb CDS
CIH1
ML, HKY + Γ
CI2 0.01 D. Neafsey, et al unpublished
23. Population Genomics
660 000 filtered SNPs across the 13 strain genomes (~28Mb
genome).
4 sampled from C. immitis, 9 from C. posadasii
Effective population size - but can we still estimate with different
sample numbers?
Testing for selective sweeps in region of the genome
Hybridization and Migration inferred from via FST
24. C. immitis has smaller effective
population size
C. posadasii
simulated
(N=4)
C. immitis C. posadasii actual
(N=4) (N=9)
Whiston, Stajich
27. Testing for evidence of hybridization
0.8
1 1
0.8
0.6 0.6
0.4 0.4
FST is a measure of 0.2 0.2
separation between 0 0
populations. -0.2
0.005 1.045 2.055 3.055 4.07
-0.2
0.005
Contig3 pos (Mb)
FST 1 is complete separation,
0 is no separation
1 1
Applied to whole genome
0.8 0.8
can estimate when regions 0.6 0.6
diverged and if there has 0.4 0.4
been recent hybridization 0.2 0.2
(migration of alleles). 0 0
-0.2
Neafsey, Barker, Rounsley
-0.2
28. Coccidioides population genomics
C. immitis is endemic to Central and Southern
California, mountain ranges likely block its
migration into Arizona.
Smaller effective population size consistent
with smaller geographic range or perhaps the
fission of the population due to introduced
geographic barrier.
There is evidence of inter-species
hybridization events (introgression) and
bidirectional exchange of alleles.
Some evidence for selective sweeps as well
based on populations, ongoing work to verify
and validate these observations.
29. Comparative Genomics and
Evolution
Aspergillus clavatus
Aspergillus fumigatus
Aspergillus flavus
Aspergillus oryzae
Aspergillus terreus
Population genomic inference of migration Aspergillus niger
Aspergillus nidulans
and hybridization Penicillium marneffei
Blastomyces dermatitidis
Histoplasma capsulatum 186AR
Histoplasma capsulatum 217B
Comparative genomic approaches to finding Histoplasma capsulatum WU24
Paracoccidioides brasiliensis
genes underlying adaptation Coccidioides immitis
Coccidioides posadasii
Uncinocarpus reesii
Deeper divergences: What makes a fungus? Fusarium graminearum
Sclerotinia sclerotiorum
200 100 0
31. Evolution of a pathogen
Comparing sequences from two Coccidioides species, closely
related outgroup, and many related species.
Are there genes with signatures of positive selection that may
distinguish pathogen from non-pathogen?
Are there differences in presence-absence of genes or sizes of gene
families that suggest differences in pathogen?
32. Testing of directional natural
selection
Evaluate patterns of molecular substitution in protein-coding
genes.
Ratio of replacement (dN) to silent substitutions (dS)
Ser Cys Gly
> 1 Positive
1 TCT TGT GGT replacement
= 1 Neutral
2 TCA TGC CGT silent
< 1 Purifying
Ser Cys Arg
33. Rapidly Evolving Coccidioides Proteins
Pairwise Orthologs between C. immitis and C. posadasii with Ka/Ks » 1
Coccidioides immitis
Ka/Ks p* Annotation
48 1.22 0.003 Basic salivary proline-rich protein 1 precursor -related
23 1.74 0.035 hypothetical protein
Coccidioides posadasii
74 1.79 0.049 hypothetical protein
54 1.87 0.045 hypothetical protein Uncinocarpus reesii
29 1.89 0.044 "SUA5 protein, putative"
84
91
1.90
1.93
0.006
0.049
ankyrin repeat containing protein
hypothetical protein
57 genes in Pairwise dN/dS
04 1.95 0.029 hypothetical protein
00 2.16 0.043 hypothetical protein
63
42
2.19
2.23
0.042
0.042
MT-A70 family protein
hypothetical protein
GO enrichment metabolic
92 2.24 0.018 Major Facilitator Superfamily protein
84 2.36 0.050 hypothetical protein process, phosphorylation, and
07 2.40 0.032 U1 zinc finger family protein
01
10
2.41
2.53
0.048
0.014
hypothetical protein
hypothetical protein
S-adenosylmethionine-
87 2.53 0.041 hypothetical protein
97 2.80 0.017 F-box domain containing protein dependent methyltransferase
63 2.85 0.030 Glycosyl hydrolases family 31 protein
84
11
2.88
3.20
0.016
0.048
hypothetical protein
hypothetical protein
activity
64 3.24 0.018 hypothetical protein
51 3.25 0.009 hypothetical protein
25
39
3.49
3.62
0.039
0.040
GDP dissociation inhibitor family protein
"Sterol 24-C-methyltransferase, putative"
60 genes in 3-way relative
75 3.91 0.004 hypothetical protein
13 4.01 0.008 hypothetical protein rates test
40 4.69 0.019 hypothetical protein
10 5.37 0.014 hypothetical protein
37 5.37 0.014 hypothetical protein
94 5.37 0.014 hypothetical protein GO enrichment biopolymer
69 99.00 0.026 hypothetical protein
58
10
99.00
99.00
0.032
0.040
Mitochondrial ATP synthase g subunit family protein
hypothetical protein
and RNA metabolic processes
10 99.00 0.043 TPR Domain containing protein
14 99.00 0.039 hypothetical protein Sharpton, Stajich, et al, in revision
34. Gene family changes
A mechanism for adaptation may be changes in copy number of a
gene family
Gene duplication is a source of novelty allowing for changes in
the function of one copy if the other maintains original
function
Expansions of copy number may also be an easy way to get
more protein for a particular process
Gene family losses may represent unneeded processes
Loss requires appropriate sampling to polarize changes
37. Keratinases in Onygenales
SignalP
Subtilisin_N
Onygenales are Keratinophilic
Domains: Peptidase S8, Subtilisin domains
Large expansion of putative keratinases in Onygenales
38. Keratinase expansion
I in Onygenales
14 copies in Coccidioides
1 in Histoplasma
II
III
Sharpton, Stajich, et al, in revision
39. Keratinase expansion
I in Onygenales
14 copies in Coccidioides
1 in Histoplasma
II
III
Sharpton, Stajich, et al, in revision
42. Towards genes underlying adaptation
Coccidioides is found in desert soil and associated with animals
43. Towards genes underlying adaptation
Coccidioides is found in desert soil and associated with animals
Loss of genes involved in plant product metabolism suggests
nutritional shift in Onygenales from relatives in Eurotiales
44. Towards genes underlying adaptation
Coccidioides is found in desert soil and associated with animals
Loss of genes involved in plant product metabolism suggests
nutritional shift in Onygenales from relatives in Eurotiales
Expansion of a few gene families, may be involved in metabolism -
none are Coccidioides specific though.
45. Towards genes underlying adaptation
Coccidioides is found in desert soil and associated with animals
Loss of genes involved in plant product metabolism suggests
nutritional shift in Onygenales from relatives in Eurotiales
Expansion of a few gene families, may be involved in metabolism -
none are Coccidioides specific though.
Sampling of a closer non-pathogenic outgroup can help polarize
recent changes. Expression analyses may help assign function to
some of genes with positive selection signatures
46. Comparative Genomics and
Evolution
Population genomic inference of migration
and hybridization
Comparative genomic approaches to finding
genes underlying adaptation
Comparisons of deeply diverged lineages:
What makes a fungus?
47. Making sense of differences when
comparing deep divergences
Nucleotide substitutions have been saturated (turned over enough
times we cannot reconstruct their history)
Proteins sequences evolve more slowly than DNA and homology
can be assessed across great evolutionary distances
Simple comparisons of gene content useful for gleaning high level
differences
48. Evolution of early Fungi
Physcomitrella patens
Dictyostelium discoideum
Monosiga brevicollis
Trichoplax adhaerens
Nematostella vectensis
Batrachochytrium Takifugu rubripes Animals
Homo sapiens
Drosophila melanogaster
Caenorhabditis elegans
Batrachochytrium dendrobatidis JEL423
Batrachochytrium dendrobatidis JAM81
Rhizopus oryzae
Ustilago maydis
Rhizopus Candida
Cryptococcus neoformans
Coprinopsis cinerea
Schizosaccharomyces pombe
Yarrowia lipolytica
Saccharomyces cerevisiae
Thick branches have Neurospora crassa
Bayesian (MrBayes Magnaporthe grisea
and PhyloBayes)
Aspergillus fumigatus
posterior of 1 and
Coprinopsis 100% ML (RAxML) Coccidioides immitis
Neurospora
0.1
bootstrap support. 32487 filtered concatenated amino-acid positions
49. Zoospore Young sporangia
Sporangia discharging
zoospores
Batrachochytrium dendrobatidis, ‘Chytridiomycota’
Amphibian Pathogen
2 sequenced strains, JEL423 (Sierras, USA) and JAM81 (Panama) by Joint
Genome Institute (JGI) and Broad respectively.
Rosenblum, EB Stajich JE, Maddox N,
~24 Mb genome, ~8000 genes EIsen MB, PNAS 2008
Stajich, et al, in prep
50. Batrachochytrium dendrobatidis
growing in a frog
Speare, Berger, Hyatt et al. 1999!
Daszak et al. 1999. EID !
James Cook University, Townsville, Australia! http://www.jcu.edu.au/school/phtm/PHTM/frogs/chpr1/fc13.htm!
51. Exploring deep divergences with
phylogenetic profiling
Classification of gene content
For each gene in a genome.
Identify which other species have a homlog.
Consolidate this per Clade (i.e. Animals, Plants, Ascomycetes,
etc)
For Chytrid comparison: Compare 7 Clades across 40 genomes
Pairwise similarities (BLAST) refined with shuffled Smith-
Waterman alignment for empirical pairwise E-value
Interact with results via Web Browser
64. B. dendrobatidis cell wall
biosynthesis missing genes
No 1,3-beta Glucan synthetase genes (2 genes)
No1,3-beta-glucanase genes (4 genes)
No KTR family genes (mannosyltranserase) (8 genes)
Need enzyme assay to assess cell wall composition ...
65. B. dendrobatidis cell wall
biochemical analysis
β (1,3)- β(1,6)- α(1,3)-
Cellulose Chitin
glucan glucan glucan
X X X ✓ ✓
Currently No cellulose synthase gene found in genome
based on genes defined in bacteria, oomyctes, or plants.
Stajich et al, in prep. with JP Latgé
66. Nuclear Division differs across
the fungal kingdom
Chytrids and Animals have centrioles and basal bodies for
microtuble attachment
Ascomycetes and Basidiomycetes have Spindle Pole Bodies for
microtuble attachment
Not homologous to centrioles
67. Paired Centrioles in
Animal and Chytrid centrosome homology
the Centrosome!
Metaphase in Newt cells! Centric division in a Chytrid with highlighted centrioles!
Centrosome!
McNitt 1973 Taken from Introductory Mycology!
Rieder and Khodjakov 2003. Science!
68. Chytrid and Animal centrioles
are homologous
Zoospore of a chytrid showing
two kinetocores (basal bodies).
Longcore 1995. Mycologia
69. Missing chromosome segregation and
mitosis related genes in chytrid
genome (S.cerevisiae names)
MSP3, KAR1, KAR2 for nuclear membrane fusion during
karyogamy and Spindle-body duplication
SPC42 - central plaque component of spindle pole bodies
CEP3 - essential kinetochore protein
CIN2 - Tubulin folding protein
REC8 for sister chromatid cohesion
DASH Complex for kinetochores coupling during mitosis (10
genes)
70. Ancient Photoreceptors?
Rhodopsin molecule implicated in zoospore
phototaxis in A!omyces
Sequence similarity identifies a candidate 7-
transmembrane protein found in both Bd and
A!omyces (draft).
Some critical residues and changes in helix 6 are
are different
insertion?
71. Transitions inferred from genomes
AFTER CHYTRID SPLIT Monosiga brevicollis
Loss of:
• Flagella, centrioles Homo sapiens
• 1,4 Beta-glucan Batrachochytrium dendrobatidis
synthesis
Gain of: Rhizopus oryzae
• STE50 adaptor
• Some glucan synthase Cryptococcus neoformans
and transferases
• Rhodopsin-like Coprinopsis cinerea
7TM
Dikarya Laccaria bicolor
IN DIKARYA, Gain of: Schizosaccharomyces pombe
• Spindle-pole bodies
• 1,3 Beta glucan synthase Saccharomyces cerevisiae
• Thiamine biosynthesis
• STE3 pheremone receptor
Neurospora crassa
• DASH complex Aspergillus nidulans
• KTR mannosylphosphate family
Loss of: Coccidioides immitis
• Chitosanase
72. Comparative genomics to build
evolutionary hypotheses
Population genomics approaches to studying differences between
species and populations identified evidence of recent
hybridization between species
Working to identify loci under directional selection.
Comparative genomics of recently diverged species suggests
differences in nutritional shift in the human pathogen Coccidioides
Comparisons between distantly related species can identify large
pathway or morphological differences to test
Reconstructing the ancestral fungus through inference of order
of evolutionary events
73. Acknowledgements
John Taylor, UC Berkeley Genome sequencing at
Broad Institute, JCVI,
Thomas Sharpton, Emily Genoscope, and DOE Joint
Whiston [Coccidiodies] Genome Institute
Erica Rosenblum (U Idaho),
JP Latgé (Pasteur Inst)
Christina Cuomo (Broad Inst)
[Batrachochytrium]
Dan Neafsey, (Broad Inst)
Steve Rounsley, Bridget
Barker, Marc Orbach (U
Arizona) [Coccidioides]
74. Acknowledgements
John Taylor, UC Berkeley Genome sequencing at
Broad Institute, JCVI,
Thomas Sharpton, Emily Genoscope, and DOE Joint
Whiston [Coccidiodies] Genome Institute
Erica Rosenblum (U Idaho), News about fungi and their genomes,
JP Latgé (Pasteur Inst) genome browsers, and community wiki
Christina Cuomo (Broad Inst) http://fungalgenomes.org
[Batrachochytrium]
Dan Neafsey, (Broad Inst)
Steve Rounsley, Bridget
Barker, Marc Orbach (U
Arizona) [Coccidioides]
75. Fungal Genomics @UCR
My lab will be starting at
University of California, Riverside
July 2009
Interested in research in fungal genomics?
Evolution of fungal development
Post-transcriptional gene regulation and
small RNAs
Fungal cell evolution in early branching
fungi
Bioinformatics and genome informatics
76. Fungal Genomics @UCR
My lab will be starting at
University of California, Riverside
July 2009
Interested in research in fungal genomics?
Evolution of fungal development
Post-transcriptional gene regulation and
small RNAs
Fungal cell evolution in early branching
fungi
Bioinformatics and genome informatics