This document summarizes the current state of phylogenetic research on the genus Phytophthora. It discusses how genomics and high-throughput sequencing have provided new insights into the early evolution and relationships within the genus. Several key findings are highlighted, including that genomics studies have identified genes in Phytophththora species similar to those in red algae and cyanobacteria, suggesting a complex evolutionary history. Finer-scale phylogenetic analyses using multiple genes are providing a more robust phylogeny with some clades showing distinct geographic distributions.
AHPND, also known as Early Mortality Syndrome, is a new bacterial disease affecting shrimp farms. It is caused by a strain of Vibrio parahaemolyticus bacteria. The disease causes the shrimp's hepatopancreas to deteriorate and become infected, leading to mortality within 10-30 days. It has spread to several Asian countries since 2010. While the bacteria can survive for weeks in refrigerated or aquatic environments, freezing or high heat kills it. Farms can prevent transmission by disinfecting and avoiding use of live feeds from infected areas.
Lee Miller Current PhD research - extension presentationncsufairyring
Presentation to golf course superintendents outlining work on identification of fairy ring pathogens and a preventive fungicide control program for fairy ring control on golf putting greens.
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.
This document summarizes the complete genomic sequence of a novel betanucleorhabdovirus identified from a Cnidium officinale plant and tentatively named Cnidium virus 1 (CnV1). The genome of CnV1 was sequenced and found to be 13,994 nucleotides in length. BLAST searches showed CnV1 is most closely related to betanucleorhabdoviruses. Several viruses have previously been reported to infect C. officinale including two secoviruses and an alphaflexivirus. This represents the first report of a betanucleorhabdovirus infecting C. officinale.
Bartonella Henselae In Ixodes Ricinus Ticks (Acari Ixodida) Removed From Hum...guest19344fe
1. Bartonella henselae DNA was detected in 4 out of 271 Ixodes ricinus ticks removed from humans in Italy using PCR and sequencing of the 60 kDa heat shock protein, pap31, and ftsZ genes.
2. The DNA was identified as the Houston-1 genotype of B. henselae, which can cause cat-scratch disease in humans.
3. This is the first report of a human-pathogenic Bartonella species being detected in the common European tick I. ricinus, suggesting ticks may play a role in transmission of bartonellosis. Further study is needed to investigate the potential for tick-borne transmission.
This document describes a study that aimed to identify chicken species in processed food products using PCR-RFLP analysis of the mitochondrial cytochrome b gene. The study collected 7 food samples, extracted DNA from them, amplified the cyt b gene using PCR, and digested the amplified products with restriction enzymes. The digestion products were analyzed via agarose gel electrophoresis and Agilent bioanalyzer to determine if patterns matched chicken DNA. The results showed PCR-RFLP analysis of the cyt b gene can authenticate chicken species in processed foods. Improved DNA extraction and testing from the start was recommended to obtain more accurate results.
AHPND, also known as Early Mortality Syndrome, is a new bacterial disease affecting shrimp farms. It is caused by a strain of Vibrio parahaemolyticus bacteria. The disease causes the shrimp's hepatopancreas to deteriorate and become infected, leading to mortality within 10-30 days. It has spread to several Asian countries since 2010. While the bacteria can survive for weeks in refrigerated or aquatic environments, freezing or high heat kills it. Farms can prevent transmission by disinfecting and avoiding use of live feeds from infected areas.
Lee Miller Current PhD research - extension presentationncsufairyring
Presentation to golf course superintendents outlining work on identification of fairy ring pathogens and a preventive fungicide control program for fairy ring control on golf putting greens.
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.
This document summarizes the complete genomic sequence of a novel betanucleorhabdovirus identified from a Cnidium officinale plant and tentatively named Cnidium virus 1 (CnV1). The genome of CnV1 was sequenced and found to be 13,994 nucleotides in length. BLAST searches showed CnV1 is most closely related to betanucleorhabdoviruses. Several viruses have previously been reported to infect C. officinale including two secoviruses and an alphaflexivirus. This represents the first report of a betanucleorhabdovirus infecting C. officinale.
Bartonella Henselae In Ixodes Ricinus Ticks (Acari Ixodida) Removed From Hum...guest19344fe
1. Bartonella henselae DNA was detected in 4 out of 271 Ixodes ricinus ticks removed from humans in Italy using PCR and sequencing of the 60 kDa heat shock protein, pap31, and ftsZ genes.
2. The DNA was identified as the Houston-1 genotype of B. henselae, which can cause cat-scratch disease in humans.
3. This is the first report of a human-pathogenic Bartonella species being detected in the common European tick I. ricinus, suggesting ticks may play a role in transmission of bartonellosis. Further study is needed to investigate the potential for tick-borne transmission.
This document describes a study that aimed to identify chicken species in processed food products using PCR-RFLP analysis of the mitochondrial cytochrome b gene. The study collected 7 food samples, extracted DNA from them, amplified the cyt b gene using PCR, and digested the amplified products with restriction enzymes. The digestion products were analyzed via agarose gel electrophoresis and Agilent bioanalyzer to determine if patterns matched chicken DNA. The results showed PCR-RFLP analysis of the cyt b gene can authenticate chicken species in processed foods. Improved DNA extraction and testing from the start was recommended to obtain more accurate results.
This document summarizes the results of a molecular re-evaluation of Phytophthora species isolated during 30 years of vegetation health surveys in Western Australia. Several key findings are reported: 1) At least seven new Phytophthora species were identified that are genetically distinct from currently described species; 2) The molecular identification of many isolates did not match the original morphological identification; and 3) Several Phytophthora species newly recorded in Western Australia were identified, including P. inundata, P. gonapodyides, and P. sp. asparagi. The significance of identifying new Phytophthora species is discussed.
This document summarizes research on Phytophthora taxon Agathis (PTA), a pathogen threatening New Zealand's iconic kauri trees. PTA was first identified in 1972 infecting trees on Great Barrier Island. The pathogen causes foliage yellowing, crown thinning, bleeding trunk lesions, and tree death. Molecular analysis identified PTA as a unique, unnamed species closely related to P. katsurae. Pathogenicity tests showed PTA was lethal to kauri seedlings while having little effect on other tree species. Field surveys found a kauri forest with abundant PTA infections, suggesting the pathogen may shift the forest composition by preferentially killing kauri. PTA poses a serious threat to kauri forests and
This document summarizes a survey of Phytophthora and Pythium species associated with export crops in Guatemala. Samples were collected from various crops across several regions and departments of Guatemala. Six Phytophthora species (P. capsici, P. cinnamomi, P. citrophthora, P. palmivora, P. nicotianae, and P. tropicalis) and several Pythium species (Py. cucurbitacearum, Py. splendens, Py. sylvaticum, Py. ultimum, and Pythium sp.) were identified based on morphological characteristics and molecular analysis. The study provides information on the distribution and identification of
The document describes a phylogenetic analysis of Pythium taxa using nuclear and mitochondrial DNA markers. It proposes a new genus, Phytopythium gen. nov., based on the analysis which separated some Pythium taxa into a distinct clade. The analysis included 80 Pythium species and relatives and involved sequencing nuclear 28S rDNA and mitochondrial cytochrome c oxidase I (COI) gene regions.
The document discusses the history and future of the World Oomycetes Genetic Resource Collection (WOGRC), formerly known as the World Phytophthora Collection (WPC). It describes how the WPC was originally founded in the 1960s with 600 accessions and has since grown significantly to over 9,500 Phytophthora accessions representing over 95 species. The collection also includes over 900 Pythium accessions representing 97 species. Cultures are preserved through cryopreservation at liquid nitrogen temperatures. The collection serves as an important genetic resource for research on Phytophthora and Pythium species.
The rapid expansion of global trade and travel has increased the spread of pathogens. Climate change also influences pathogen communities directly and indirectly. Sudden Oak Death is provided as an example. There are challenges in accurately identifying pathogen species, understanding pathogen diversity in nature, and facilitating global cooperation on knowledge sharing. The Phytophthora Database was created as cyberinfrastructure to support identification and monitoring of Phytophthora species through genetic fingerprinting and phenotypic data on known isolates.
The document describes an ongoing study analyzing the molecular phylogeny of marine Halophytophthora species using DNA sequence data from the internal transcribed spacer (ITS), large subunit (LSU), and cytochrome c oxidase subunit 1 (COX1) regions. Phylogenetic trees were constructed from the sequence alignments to examine relationships between Halophytophthora species and other oomycete genera. BLAST searches were also performed with some ITS sequences to identify close matches in GenBank.
This document summarizes work done to clarify the taxonomic status of Phytophthora cryptogea and P. drechsleri using molecular data. Sequences from the internal transcribed spacer region, large subunit of ribosomal RNA, and cytochrome oxidase I gene from over 200 accessions validated separating P. cryptogea and P. drechsleri into two distinct phylogenetic species. Preliminary results also indicate there are 6-10 additional phylogenetic species within what was originally described as P. cryptogea or P. drechsleri. The work was supported by grants from the USDA National Research Initiative Plant Biosecurity program.
This document describes the development of a nanobiotechnology-based diagnostic system for detecting Phytophthora species. The system uses a microchip containing a PCR chip for DNA amplification and a DNA chip for species-specific detection of Phytophthora DNA fragments via hybridization. Initial results showed the PCR chip could successfully amplify DNA from P. ramorum, and the DNA chip could specifically detect P. ramorum DNA using species-specific probes. The goal is to create a sensitive, robust, easy-to-use diagnostic tool that can identify Phytophthora species directly in the field within a short period of time.
This document summarizes the origins of the World Phytophthora Genetic Resource Collection (WPC). The WPC was founded in 1966 in Denver by Professors D.C. Erwin and G.A. Zentmyer of the University of California, Riverside, who collected isolates of Phytophthora from alfalfa and cacao respectively, forming the basis of the collection. The WPC is an important collection of Phytophthora isolates that has its origins in the research work of Erwin and Zentmyer in the 1960s.
The document discusses the number of known and unknown Phytophthora species over time. It notes that in 1876 there was 1 known species, increasing to around 60 known species pre-2000, but estimates there could be 200-600 total species, meaning 140-540 were still unknown around 2000. It also estimates that around 10-20% of pre-2000 known species damaged forests or natural ecosystems, suggesting 34 +/- 20 species with that potential remained unknown in 2000. Since 2000 over 50 new species have been described. The document introduces the concept of "virtual taxa" or phylotypes identified through DNA sequencing of environmental samples.
The document describes two simple methods for inoculating plants with Phytophthora: the rice grain method and agar disk method. The rice grain method involves autoclaving rice grains with Phytophthora culture, loosening the matted rice, and placing individual grains near plants. The agar disk method uses small disks cut from two-week-old Phytophthora cultures grown on agar that are placed near plants. Both methods provide a simple way to introduce Phytophthora and study its effects on plants.
Irrigation water recycling in the greenhouseSteven Newman
Presented at the 2013 Utah Green Conference sponsored by the Utah Nursery and Landscape Association, 28 January 2013.
The entire slide set was recorded with audio and you can view it at: http://youtu.be/GCd6P85dBmg
This document discusses the plant pathogen Phytophthora. It is an oomycete, not a true fungus, that causes many diseases in plants. Phytophthora reproduces both sexually, requiring two mating types, and asexually through sporangia and zoospores. It infects a wide range of hosts and causes symptoms like leaf spots, stem cankers, root rot, and top dieback. Phytophthora spreads through splashing water or movement of infected plants and soil. It is active in wet and warm conditions. Detection methods include ELISA tests, culturing on selective media, and PCR tests for specific species.
This document summarizes research on Phytophthora and Pythium diversity found in UK gardens. Over 25 Phytophthora species and 17 Pythium species have been identified. The most common host plants are Taxus, Rhododendron, Rubus, and Viburnum for Phytophthora, and Taxus, Prunus, Rubus, and Cornus for Pythium. Detection methods like apple baiting, nested PCR, and immunoassay were used and compared over multiple years.
This document summarizes research on the genera Phytophthora and Pythium in Argentina. It provides an inventory of species reported in Argentina, including 17 Pythium species found on 235 hosts and 18 Phytophthora species found on 180 hosts. Maps show the geographical distribution of species within Argentina. Data on affected crops, symptoms, and references are presented in tables. P. ultimum and P. debaryanum are identified as the most aggressive Pythium species, affecting a wide variety of horticultural, ornamental, forest and fruit crops. P. cinnamomi is noted for its wide host range. The results provide an updated understanding of these fungal genera in Argentina.
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".
Automated phylogenetic taxonomy in Fungi. DS. HibbettRoderic Page
The document discusses automated phylogenetic taxonomy in fungi using comprehensive phylogenetic trees. It outlines several uses of comprehensive phylogenetic trees, including identification, curation of sequence databases, identification of environmental samples, discovery of new species, biogeography, epidemiology, conservation, and character evolution analyses. It also discusses uses of taxonomic classifications in communication, research, teaching, and legislation. The document then provides details on progress in phylogenetic reconstruction and classification in fungi and agaricomycetes specifically. It outlines the large number of described and estimated total fungal species, as well as the amount of fungal sequence data currently available. It also provides information on research labs, data, publications, and informatics resources involved in fungal phylogenetic taxonomy work.
This document summarizes a research study on the biodegradation of polystyrene foam by microorganisms found in a landfill in Thailand. Samples of microbes were taken from polystyrene foam and contaminated soil in the landfill. The microbes were cultured with polystyrene as the sole carbon source to identify those capable of degrading it. Analysis of the cultures over time found shifts in the dominant microbial species. Selected species were identified through molecular techniques as known aromatic compound degraders, including Herbaspirillum seropedicae and Ochrobactrum sp. Scanning electron microscopy was used to observe physical changes to polystyrene exposed to the cultures, indicating biodegradation
This document discusses advances in molecular techniques for identifying Phytophthora, Pythium, and related genera. It describes the challenges of morphological identification and outlines desired characteristics for molecular markers. Several nuclear and mitochondrial molecular loci used for species identification are discussed, including rDNA, Î2-tubulin, elicitin genes, and mitochondrial genes like cox1 and cox2. Techniques for molecular identification of isolates and subpopulations are summarized, such as DNA sequencing, PCR-RFLP, and development of species-specific PCR for pathogen detection.
1. Three new species of Pythiogeton, a genus of plant pathogenic oomycetes, were isolated from diseased ornamental plant roots in North Carolina.
2. The Pythiogeton species were characterized based on their morphology and ITS rDNA sequences.
3. A phylogenetic tree showed that the new Pythiogeton species grouped together and were more closely related to Pythium grandisporangium than the genus Phytophthora.
This document summarizes the results of a molecular re-evaluation of Phytophthora species isolated during 30 years of vegetation health surveys in Western Australia. Several key findings are reported: 1) At least seven new Phytophthora species were identified that are genetically distinct from currently described species; 2) The molecular identification of many isolates did not match the original morphological identification; and 3) Several Phytophthora species newly recorded in Western Australia were identified, including P. inundata, P. gonapodyides, and P. sp. asparagi. The significance of identifying new Phytophthora species is discussed.
This document summarizes research on Phytophthora taxon Agathis (PTA), a pathogen threatening New Zealand's iconic kauri trees. PTA was first identified in 1972 infecting trees on Great Barrier Island. The pathogen causes foliage yellowing, crown thinning, bleeding trunk lesions, and tree death. Molecular analysis identified PTA as a unique, unnamed species closely related to P. katsurae. Pathogenicity tests showed PTA was lethal to kauri seedlings while having little effect on other tree species. Field surveys found a kauri forest with abundant PTA infections, suggesting the pathogen may shift the forest composition by preferentially killing kauri. PTA poses a serious threat to kauri forests and
This document summarizes a survey of Phytophthora and Pythium species associated with export crops in Guatemala. Samples were collected from various crops across several regions and departments of Guatemala. Six Phytophthora species (P. capsici, P. cinnamomi, P. citrophthora, P. palmivora, P. nicotianae, and P. tropicalis) and several Pythium species (Py. cucurbitacearum, Py. splendens, Py. sylvaticum, Py. ultimum, and Pythium sp.) were identified based on morphological characteristics and molecular analysis. The study provides information on the distribution and identification of
The document describes a phylogenetic analysis of Pythium taxa using nuclear and mitochondrial DNA markers. It proposes a new genus, Phytopythium gen. nov., based on the analysis which separated some Pythium taxa into a distinct clade. The analysis included 80 Pythium species and relatives and involved sequencing nuclear 28S rDNA and mitochondrial cytochrome c oxidase I (COI) gene regions.
The document discusses the history and future of the World Oomycetes Genetic Resource Collection (WOGRC), formerly known as the World Phytophthora Collection (WPC). It describes how the WPC was originally founded in the 1960s with 600 accessions and has since grown significantly to over 9,500 Phytophthora accessions representing over 95 species. The collection also includes over 900 Pythium accessions representing 97 species. Cultures are preserved through cryopreservation at liquid nitrogen temperatures. The collection serves as an important genetic resource for research on Phytophthora and Pythium species.
The rapid expansion of global trade and travel has increased the spread of pathogens. Climate change also influences pathogen communities directly and indirectly. Sudden Oak Death is provided as an example. There are challenges in accurately identifying pathogen species, understanding pathogen diversity in nature, and facilitating global cooperation on knowledge sharing. The Phytophthora Database was created as cyberinfrastructure to support identification and monitoring of Phytophthora species through genetic fingerprinting and phenotypic data on known isolates.
The document describes an ongoing study analyzing the molecular phylogeny of marine Halophytophthora species using DNA sequence data from the internal transcribed spacer (ITS), large subunit (LSU), and cytochrome c oxidase subunit 1 (COX1) regions. Phylogenetic trees were constructed from the sequence alignments to examine relationships between Halophytophthora species and other oomycete genera. BLAST searches were also performed with some ITS sequences to identify close matches in GenBank.
This document summarizes work done to clarify the taxonomic status of Phytophthora cryptogea and P. drechsleri using molecular data. Sequences from the internal transcribed spacer region, large subunit of ribosomal RNA, and cytochrome oxidase I gene from over 200 accessions validated separating P. cryptogea and P. drechsleri into two distinct phylogenetic species. Preliminary results also indicate there are 6-10 additional phylogenetic species within what was originally described as P. cryptogea or P. drechsleri. The work was supported by grants from the USDA National Research Initiative Plant Biosecurity program.
This document describes the development of a nanobiotechnology-based diagnostic system for detecting Phytophthora species. The system uses a microchip containing a PCR chip for DNA amplification and a DNA chip for species-specific detection of Phytophthora DNA fragments via hybridization. Initial results showed the PCR chip could successfully amplify DNA from P. ramorum, and the DNA chip could specifically detect P. ramorum DNA using species-specific probes. The goal is to create a sensitive, robust, easy-to-use diagnostic tool that can identify Phytophthora species directly in the field within a short period of time.
This document summarizes the origins of the World Phytophthora Genetic Resource Collection (WPC). The WPC was founded in 1966 in Denver by Professors D.C. Erwin and G.A. Zentmyer of the University of California, Riverside, who collected isolates of Phytophthora from alfalfa and cacao respectively, forming the basis of the collection. The WPC is an important collection of Phytophthora isolates that has its origins in the research work of Erwin and Zentmyer in the 1960s.
The document discusses the number of known and unknown Phytophthora species over time. It notes that in 1876 there was 1 known species, increasing to around 60 known species pre-2000, but estimates there could be 200-600 total species, meaning 140-540 were still unknown around 2000. It also estimates that around 10-20% of pre-2000 known species damaged forests or natural ecosystems, suggesting 34 +/- 20 species with that potential remained unknown in 2000. Since 2000 over 50 new species have been described. The document introduces the concept of "virtual taxa" or phylotypes identified through DNA sequencing of environmental samples.
The document describes two simple methods for inoculating plants with Phytophthora: the rice grain method and agar disk method. The rice grain method involves autoclaving rice grains with Phytophthora culture, loosening the matted rice, and placing individual grains near plants. The agar disk method uses small disks cut from two-week-old Phytophthora cultures grown on agar that are placed near plants. Both methods provide a simple way to introduce Phytophthora and study its effects on plants.
Irrigation water recycling in the greenhouseSteven Newman
Presented at the 2013 Utah Green Conference sponsored by the Utah Nursery and Landscape Association, 28 January 2013.
The entire slide set was recorded with audio and you can view it at: http://youtu.be/GCd6P85dBmg
This document discusses the plant pathogen Phytophthora. It is an oomycete, not a true fungus, that causes many diseases in plants. Phytophthora reproduces both sexually, requiring two mating types, and asexually through sporangia and zoospores. It infects a wide range of hosts and causes symptoms like leaf spots, stem cankers, root rot, and top dieback. Phytophthora spreads through splashing water or movement of infected plants and soil. It is active in wet and warm conditions. Detection methods include ELISA tests, culturing on selective media, and PCR tests for specific species.
This document summarizes research on Phytophthora and Pythium diversity found in UK gardens. Over 25 Phytophthora species and 17 Pythium species have been identified. The most common host plants are Taxus, Rhododendron, Rubus, and Viburnum for Phytophthora, and Taxus, Prunus, Rubus, and Cornus for Pythium. Detection methods like apple baiting, nested PCR, and immunoassay were used and compared over multiple years.
This document summarizes research on the genera Phytophthora and Pythium in Argentina. It provides an inventory of species reported in Argentina, including 17 Pythium species found on 235 hosts and 18 Phytophthora species found on 180 hosts. Maps show the geographical distribution of species within Argentina. Data on affected crops, symptoms, and references are presented in tables. P. ultimum and P. debaryanum are identified as the most aggressive Pythium species, affecting a wide variety of horticultural, ornamental, forest and fruit crops. P. cinnamomi is noted for its wide host range. The results provide an updated understanding of these fungal genera in Argentina.
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".
Automated phylogenetic taxonomy in Fungi. DS. HibbettRoderic Page
The document discusses automated phylogenetic taxonomy in fungi using comprehensive phylogenetic trees. It outlines several uses of comprehensive phylogenetic trees, including identification, curation of sequence databases, identification of environmental samples, discovery of new species, biogeography, epidemiology, conservation, and character evolution analyses. It also discusses uses of taxonomic classifications in communication, research, teaching, and legislation. The document then provides details on progress in phylogenetic reconstruction and classification in fungi and agaricomycetes specifically. It outlines the large number of described and estimated total fungal species, as well as the amount of fungal sequence data currently available. It also provides information on research labs, data, publications, and informatics resources involved in fungal phylogenetic taxonomy work.
This document summarizes a research study on the biodegradation of polystyrene foam by microorganisms found in a landfill in Thailand. Samples of microbes were taken from polystyrene foam and contaminated soil in the landfill. The microbes were cultured with polystyrene as the sole carbon source to identify those capable of degrading it. Analysis of the cultures over time found shifts in the dominant microbial species. Selected species were identified through molecular techniques as known aromatic compound degraders, including Herbaspirillum seropedicae and Ochrobactrum sp. Scanning electron microscopy was used to observe physical changes to polystyrene exposed to the cultures, indicating biodegradation
This document discusses advances in molecular techniques for identifying Phytophthora, Pythium, and related genera. It describes the challenges of morphological identification and outlines desired characteristics for molecular markers. Several nuclear and mitochondrial molecular loci used for species identification are discussed, including rDNA, Î2-tubulin, elicitin genes, and mitochondrial genes like cox1 and cox2. Techniques for molecular identification of isolates and subpopulations are summarized, such as DNA sequencing, PCR-RFLP, and development of species-specific PCR for pathogen detection.
1. Three new species of Pythiogeton, a genus of plant pathogenic oomycetes, were isolated from diseased ornamental plant roots in North Carolina.
2. The Pythiogeton species were characterized based on their morphology and ITS rDNA sequences.
3. A phylogenetic tree showed that the new Pythiogeton species grouped together and were more closely related to Pythium grandisporangium than the genus Phytophthora.
Medical Conferences, Pharma Conferences, Engineering Conferences, Science Conferences, Manufacturing Conferences, Social Science Conferences, Business Conferences, Scientific Conferences Malaysia, Thailand, Singapore, Hong Kong, Dubai, Turkey 2014 2015 2016
Global Research & Development Services (GRDS) is a leading academic event organizer, publishing Open Access Journals and conducting several professionally organized international conferences all over the globe annually. GRDS aims to disseminate knowledge and innovation with the help of its International Conferences and open access publications. GRDS International conferences are world-class events which provide a meaningful platform for researchers, students, academicians, institutions, entrepreneurs, industries and practitioners to create, share and disseminate knowledge and innovation and to develop long-lasting network and collaboration.
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1. The researchers collected frog egg masses from bodies of water in Illinois to isolate water mold pathogens.
2. They obtained DNA sequences from the ITS region of fourteen water mold isolates and classified the isolates using phylogenetic analysis.
3. The researchers designed a locked nucleic acid primer/probe set for quantitative PCR (qPCR) to identify a specific Saprolegnia strain. They are currently testing the probe's ability to only amplify the desired strain.
The document summarizes a presentation about using multi-locus phylogenetic analysis to study the relationships within the genus Phytophthora. It discusses the importance of Phytophthora species as plant pathogens, provides background on their taxonomy and relevant disease examples. It then describes the development of phylogenetic markers from genome sequences of several Phytophthora species and the analysis of sequence data from multiple loci to infer evolutionary relationships among 82 Phytophthora species.
This document describes a quantitative multiplex detection method for plant pathogens using padlock probe (PLP) technology and the OpenArray platform. PLPs allow for high specificity detection of multiple targets simultaneously through ligation-dependent amplification and quantification. Testing showed specific detection of various pathogens individually and in mixtures. The method provides advantages over existing technologies through its quantitative, high-throughput and multiplex capabilities. It has applications in disease management, microbial community analysis and gene expression studies.
Endosymbiont hunting in the metagenome of Asian citrus psyllid (Diaphorina ci...Surya Saha
The Asian citrus psyllid (D. citri Kuwayama or ACP) is host to 7+ bacterial endosymbionts and is the insect vector of Ca. liberibacter asiaticus (Las), causal agent of citrus greening. To gain a better understanding of endosymbiont and pathogen ecology and develop improved detection strategies for Las, DNA from D. citri was sequenced to 108X coverage. Initial analyses have focused on Wolbachia, an alpha-proteobacterial primary endosymbiont typically found in the reproductive tissues of ACP and other arthropods. The metagenomic sequences were mined for wACP reads using BLAST and 4 sequenced Wolbachia genomes as bait. Putative wACP reads were then assembled using Velvet and MIRA3 assemblers over a range of parameter settings. The resulting wACP contigs were annotated using the RAST pipeline and compared to Wolbachia endosymbiont of Culex quinquefasciatus (wPip). MIRA3 was able to reconstruct a majority of the wPip CDS regions and was selected for scaffolding with Minimus2, SSPACE and SOPRA using large insert mate-pair libraries. The wACP scaffolds were compared to wPip using Abacas and Mauve contig mover to orient and order the contigs. The functional annotation of scaffolds was evaluated by comparing it to wPip genome using RAST. The draft assembly was verified using an OrthoMCL based comparison to the 4 sequenced Wolbachia genomes. We expanded the scope of endosymbiont characterization beyond wACP using 16S rDNA and partial 23S rDNA analysis as a guide. Results will be presented regarding endosymbionts, their potential interactions and their impact on the disease of citrus greening.
1. The document summarizes Yamuna R's PhD viva voce examination on her thesis titled "Studies on bioactive compounds in Camponotus compresses (Fab.,) (Hymenoptera: Formicidae) for cutaneous wound healing in the Rat model".
2. It includes details of the external examiner, research supervisor, date and time of examination, various chapters that will be discussed and their contents like ethnentomology, biochemical analysis, antimicrobial activity etc.
3. It provides information on the diagnostic characters, measurements and microscopic view of Camponotus compressus which was selected for the study based on its availability, collection techniques and distribution.
The document discusses the development of Phytophthora and Pythium databases to support the identification and monitoring of these major plant pathogen groups. It describes the objectives of building a cyberinfrastructure to archive genotype, phenotype and distribution data on Phytophthora species/isolates. The Phytophthora Database provides tools for sequence analysis, phylogenetic analysis and molecular identification. Future directions include expanding to other plant pathogen databases and integrating genomic and geospatial data.
Biodegradation of Polystyrene foam by the Microorganism from LandfillPat Pataranutaporn
This document summarizes a research project on biodegrading polystyrene foam. The project aimed to identify microbes from a landfill that can use polystyrene as a sole carbon source. Microbes were sampled from styrofoam and soil in the landfill. Community analysis identified several bacterial species growing on polystyrene, including Caulobacter segnis, Massilia aerilata, and Herbaspirillum seropedicae. Scanning electron microscopy showed signs of polystyrene degradation by microbes from styrofoam and soil. The research suggests certain landfill microbes are capable of biodegrading polystyrene.
Evolution and exploration of the transcriptional landscape in two filamentous...Jason Stajich
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 discusses past, present, and future work on oomycete genomics. In the past, genome comparisons found conserved gene order and effector genes associated with repeats. The P. sojae genome is being finished using new sequencing methods. In the future, sequencing capacity is rapidly improving which will enable more oomycete genomes to be sequenced cheaply.
The document discusses the challenge of identifying effector genes in the wheat stripe rust fungus Puccinia striiformis f.sp. tritici. Effector genes are small secreted proteins that help the fungus infect wheat plants. Next-generation sequencing allows genomic and transcriptomic analysis but has limitations in assembling repetitive sequences like effectors. The author has analyzed transcriptomes of the fungus grown in planta to predict 100 small secreted protein candidates as potential effector genes for further laboratory tests. Identifying the fungus's effector genes could help develop resistant wheat varieties to reduce annual losses from stripe rust in Australian wheat production.
This document describes the development of a PCR-RFLP assay to identify Plasmodium species and variants of P. vivax infecting Anopheles mosquitoes. Specific primers were designed that target regions of the circumsporozoite gene to distinguish P. falciparum, P. malariae, and P. vivax variants VK210, VK247, and P. vivax-like. The assay was tested on artificially infected mosquitoes and showed good agreement with nested PCR. The PCR-RFLP method provides a sensitive way to detect Plasmodium species and variants, which can help understand malaria transmission dynamics.
Alt. GDG Cloud Southlake #33: Boule & Rebala: Effective AppSec in SDLC using ...James Anderson
Effective Application Security in Software Delivery lifecycle using Deployment Firewall and DBOM
The modern software delivery process (or the CI/CD process) includes many tools, distributed teams, open-source code, and cloud platforms. Constant focus on speed to release software to market, along with the traditional slow and manual security checks has caused gaps in continuous security as an important piece in the software supply chain. Today organizations feel more susceptible to external and internal cyber threats due to the vast attack surface in their applications supply chain and the lack of end-to-end governance and risk management.
The software team must secure its software delivery process to avoid vulnerability and security breaches. This needs to be achieved with existing tool chains and without extensive rework of the delivery processes. This talk will present strategies and techniques for providing visibility into the true risk of the existing vulnerabilities, preventing the introduction of security issues in the software, resolving vulnerabilities in production environments quickly, and capturing the deployment bill of materials (DBOM).
Speakers:
Bob Boule
Robert Boule is a technology enthusiast with PASSION for technology and making things work along with a knack for helping others understand how things work. He comes with around 20 years of solution engineering experience in application security, software continuous delivery, and SaaS platforms. He is known for his dynamic presentations in CI/CD and application security integrated in software delivery lifecycle.
Gopinath Rebala
Gopinath Rebala is the CTO of OpsMx, where he has overall responsibility for the machine learning and data processing architectures for Secure Software Delivery. Gopi also has a strong connection with our customers, leading design and architecture for strategic implementations. Gopi is a frequent speaker and well-known leader in continuous delivery and integrating security into software delivery.
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.
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
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.
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.
In the rapidly evolving landscape of technologies, XML continues to play a vital role in structuring, storing, and transporting data across diverse systems. The recent advancements in artificial intelligence (AI) present new methodologies for enhancing XML development workflows, introducing efficiency, automation, and intelligent capabilities. This presentation will outline the scope and perspective of utilizing AI in XML development. The potential benefits and the possible pitfalls will be highlighted, providing a balanced view of the subject.
We will explore the capabilities of AI in understanding XML markup languages and autonomously creating structured XML content. Additionally, we will examine the capacity of AI to enrich plain text with appropriate XML markup. Practical examples and methodological guidelines will be provided to elucidate how AI can be effectively prompted to interpret and generate accurate XML markup.
Further emphasis will be placed on the role of AI in developing XSLT, or schemas such as XSD and Schematron. We will address the techniques and strategies adopted to create prompts for generating code, explaining code, or refactoring the code, and the results achieved.
The discussion will extend to how AI can be used to transform XML content. In particular, the focus will be on the use of AI XPath extension functions in XSLT, Schematron, Schematron Quick Fixes, or for XML content refactoring.
The presentation aims to deliver a comprehensive overview of AI usage in XML development, providing attendees with the necessary knowledge to make informed decisions. Whether you’re at the early stages of adopting AI or considering integrating it in advanced XML development, this presentation will cover all levels of expertise.
By highlighting the potential advantages and challenges of integrating AI with XML development tools and languages, the presentation seeks to inspire thoughtful conversation around the future of XML development. We’ll not only delve into the technical aspects of AI-powered XML development but also discuss practical implications and possible future directions.
GraphSummit Singapore | The Art of the Possible with Graph - Q2 2024Neo4j
Neha Bajwa, Vice President of Product Marketing, Neo4j
Join us as we explore breakthrough innovations enabled by interconnected data and AI. Discover firsthand how organizations use relationships in data to uncover contextual insights and solve our most pressing challenges – from optimizing supply chains, detecting fraud, and improving customer experiences to accelerating drug discoveries.
Enchancing adoption of Open Source Libraries. A case study on Albumentations.AIVladimir Iglovikov, Ph.D.
Presented by Vladimir Iglovikov:
- https://www.linkedin.com/in/iglovikov/
- https://x.com/viglovikov
- https://www.instagram.com/ternaus/
This presentation delves into the journey of Albumentations.ai, a highly successful open-source library for data augmentation.
Created out of a necessity for superior performance in Kaggle competitions, Albumentations has grown to become a widely used tool among data scientists and machine learning practitioners.
This case study covers various aspects, including:
People: The contributors and community that have supported Albumentations.
Metrics: The success indicators such as downloads, daily active users, GitHub stars, and financial contributions.
Challenges: The hurdles in monetizing open-source projects and measuring user engagement.
Development Practices: Best practices for creating, maintaining, and scaling open-source libraries, including code hygiene, CI/CD, and fast iteration.
Community Building: Strategies for making adoption easy, iterating quickly, and fostering a vibrant, engaged community.
Marketing: Both online and offline marketing tactics, focusing on real, impactful interactions and collaborations.
Mental Health: Maintaining balance and not feeling pressured by user demands.
Key insights include the importance of automation, making the adoption process seamless, and leveraging offline interactions for marketing. The presentation also emphasizes the need for continuous small improvements and building a friendly, inclusive community that contributes to the project's growth.
Vladimir Iglovikov brings his extensive experience as a Kaggle Grandmaster, ex-Staff ML Engineer at Lyft, sharing valuable lessons and practical advice for anyone looking to enhance the adoption of their open-source projects.
Explore more about Albumentations and join the community at:
GitHub: https://github.com/albumentations-team/albumentations
Website: https://albumentations.ai/
LinkedIn: https://www.linkedin.com/company/100504475
Twitter: https://x.com/albumentations
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.
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!
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.
TrustArc Webinar - 2024 Global Privacy SurveyTrustArc
How does your privacy program stack up against your peers? What challenges are privacy teams tackling and prioritizing in 2024?
In the fifth annual Global Privacy Benchmarks Survey, we asked over 1,800 global privacy professionals and business executives to share their perspectives on the current state of privacy inside and outside of their organizations. This year’s report focused on emerging areas of importance for privacy and compliance professionals, including considerations and implications of Artificial Intelligence (AI) technologies, building brand trust, and different approaches for achieving higher privacy competence scores.
See how organizational priorities and strategic approaches to data security and privacy are evolving around the globe.
This webinar will review:
- The top 10 privacy insights from the fifth annual Global Privacy Benchmarks Survey
- The top challenges for privacy leaders, practitioners, and organizations in 2024
- Key themes to consider in developing and maintaining your privacy program
For the full video of this presentation, please visit: https://www.edge-ai-vision.com/2024/06/building-and-scaling-ai-applications-with-the-nx-ai-manager-a-presentation-from-network-optix/
Robin van Emden, Senior Director of Data Science at Network Optix, presents the “Building and Scaling AI Applications with the Nx AI Manager,” tutorial at the May 2024 Embedded Vision Summit.
In this presentation, van Emden covers the basics of scaling edge AI solutions using the Nx tool kit. He emphasizes the process of developing AI models and deploying them globally. He also showcases the conversion of AI models and the creation of effective edge AI pipelines, with a focus on pre-processing, model conversion, selecting the appropriate inference engine for the target hardware and post-processing.
van Emden shows how Nx can simplify the developer’s life and facilitate a rapid transition from concept to production-ready applications.He provides valuable insights into developing scalable and efficient edge AI solutions, with a strong focus on practical implementation.
Cosa hanno in comune un mattoncino Lego e la backdoor XZ?Speck&Tech
ABSTRACT: A prima vista, un mattoncino Lego e la backdoor XZ potrebbero avere in comune il fatto di essere entrambi blocchi di costruzione, o dipendenze di progetti creativi e software. La realtà è che un mattoncino Lego e il caso della backdoor XZ hanno molto di più di tutto ciò in comune.
Partecipate alla presentazione per immergervi in una storia di interoperabilità, standard e formati aperti, per poi discutere del ruolo importante che i contributori hanno in una comunità open source sostenibile.
BIO: Sostenitrice del software libero e dei formati standard e aperti. È stata un membro attivo dei progetti Fedora e openSUSE e ha co-fondato l'Associazione LibreItalia dove è stata coinvolta in diversi eventi, migrazioni e formazione relativi a LibreOffice. In precedenza ha lavorato a migrazioni e corsi di formazione su LibreOffice per diverse amministrazioni pubbliche e privati. Da gennaio 2020 lavora in SUSE come Software Release Engineer per Uyuni e SUSE Manager e quando non segue la sua passione per i computer e per Geeko coltiva la sua curiosità per l'astronomia (da cui deriva il suo nickname deneb_alpha).
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.
Large Language Model (LLM) and it’s Geospatial Applications
O4 Cooke
1. A clearing picture of
Phytophthora evolution: from
the wide-angle to the zoom lens
for optimal phylogenetic focus
David Cooke, SCRI
2. • Introduction – aims of paper
• Early evolution of oomycetes
• Lessons learned from genomics
• Current status of Phytophthora phylogeny
• Tools and drivers: fine-scale population shifts
• Conclusions
• Acknowledgements
3. Genomics in the oomycetes
P. infestans
P. ramorum
P. sojae
H. parasitica
P. capsici
P. andina
P. mirabilis
P. phaseoli
Albugo
Pythium?
Saprolegnia?
Aphanomyces
High throughput sequencing technologies
providing many new opportunities
5. Contributions of genomics
Tyler et al., 2006 Science
P. ramorum and P. sojae genomes
Found 855 Phytophthora
genes with similarity to red
algae or cyanobacteria
Whisson et al 2007 Nature
Shared mechanisms of
effector transport into host
cells – oomycete and
Apicomplexans
Lane & Archibald, TREE 2008
RxLR class of effectors considered key to pathogenicity: a reduced
repertoire noted in Hy. parasitica genome (Warwick HRI).
Also an absence of genes involved in zoospore formation…
6. Long history of parasitism in oomycetes
Gordon Beakes – Chapter in “Oomycete
Genetics and Genomics: Diversity, Plant
and Animal Interactions, and Toolbox”
(in press, 2008)
Long history of parasitism in oomycetes
– diverse and elegant range of infection
devices & abundance of marine species.
Tree of Life upgrade planned
7. Basal oomycetes
rDNA 18S tree
The Development,
Ultrastructural Cytology, and
Molecular Phylogeny of the
Basal Oomycete
Eurychasma dicksonii …
Satoshi Sekimoto, Gordon W.
Beakes, Claire M.M. Gachon,
Dieter G. Müller, Frithjof C.
Küpper, Daiske Honda Protist,
2008
Parasites of plants across
oomycete lineages
8. Cooke et al 2000
c.f. Blair et al 2007
• Multigene
approach
more robust
• Clades shared
• Basal branch
structure
similar
9. Pquininea
Pmacrochl
Prichard
EU301150Psp.TIB20079
Pfallax
Pcaptiosa
EU644726Psp.BFA
EU196368Psp.167008
EU196369Psp.167011
Pgallica
Pboehmeriae
DQ066921Psp.Drimys winteri
DQ002008Psp.cc2124
Pkernoviae 9 & 10
ITS Tree 2008
Ppolonica
Pinsol cooke
EF590254Pcuyabensis
EF680320Pnapoensis
EU419612Psp.6216900
EU419615Psp.8021391
EU334634Pirrigata23J7
EU644721Psp.BF3
EU644715Psp.BF4
EU644714Psp.BFK
EF680321Pthermophilum
EU644725Psp.BF1
EU583798Phydropathica
SCRP237
Rf6
EU164426.1Pzentmyerii
EF590256Plagoariana
EU644720Psp.BFR
EU644722Psp.BF36
Rf17
• Scan of GenBank Taxonomy
Pbrassicae
Pfoliorum
Pramorum
Pprimulae
Pporri
Phibernalis
browser for ITS seq.
Plateralis
Pmedicaginis
Ptrifolii
Psansomea
Psyringae
P. austrocedrae
Pdrechsleri 8 • 146 seq but some redundancy
Pkelmania
Pcryptogea
Perythroseptica
P. fragaefolia
Psojae
Pniederhauserii
Ppistaciae
Pmelonis • Clade 8 position of P.
7
Pcajani
Pvignae
Pcinnamomi
Pfvr
Pcinnparvi
Puliginosa
Peuropaea
cryptogea & drechsleri
Palnimult
Pcambivora
Pquercina
Pilicis
Ppsychrophila
Ppseudosyringae
Pnemorosa
Pheveae
3 • Clade 7 P. fragaefolia on deep
Pkatsurae
EF067922Psp.NZICMP 5
P. novaeguinee
Ppseudotsugae
Pcact
Pidaei
root
Phedraiandra
Pnicotianae
Ptentaculata
Pclandestina
Piranica
Pinfestans & andina
Pipomoeae
Pmirabilis
1 • Clade 5 P. novaeguinee and a
Pphaseoli
P. frigida
EU644723Psp.BLW71
Pmultivesiculata
EU301125Psp.TIB20072 strain
Pbisheria
NZ isolate
Pcolocasiae
Pbotryosa
EU419614Psp.204B
Pcitrophthora
EU419613Psp.1211
EF523387Psiskiyouensis
Ptropicalis
Pcapsici
Pglovera
DQ821185Psp.BR514
2 • Clade 2 P. frigida in basal
EU301132Psp.TIB20074
Pcitricola
Pinflata
EU877749Psp.59
position
EU877753.1Psp.63
EU877755Psp.65
EU877754Psp.64
Pmegakarya
Pelitch vogl
EU419617Psp.1931
• Clade 4 ‘tropical and
P. alticola
P. quercetorum
EU301118Psp.TIB20071 strain
Psp banksia
Ppalmivora
Parecae
4 australasian flavour?’
Paspara
EF590257Psulawesiensis
EU593265Psp.IMI329669
EU301170Psp.TIB20076
Pinundata
Phumicola
EU000108Psp.77231
EU594601Psp.1FFL2008
EF153672Psp.P12745
• Clade 6 dramatic expansion &
Pmegasperma
EU301174Psp.TIB20077
DQ396412Psp.AG34UASWS0200
EU000143Psp.AG43 appearance of aerial habit
6
EU106591Psp.92209C
EU594600Psp.2FFL2008
EU106590Psp.92207
EU301176Psp.TIB20078
EU869199PaustralisVHS
EU301158.1Psp.TIB20073 strai
EF152514Psp.GD2f
EF522140Psylvatica
EU725809Ppinifolia
EU594598Phungarica
EU594599Psp.4FFL2008
Pgonapodyides
EU419616Psp.B6
EU000124Psp.91112
AY787023Psp.AG52
0.1
10. Expansion of clade 9 & 10
P. quininea
P. macrochlamydospora
P. richardiae
EU301150Psp.TIB20079 • Discrete lineage from
P. fallax
P. captiosa
9 majority of genus
EU644726Psp.BFA
EU196368Psp.167008
EU196369Psp.167011
• No obvious common
P. gallica
10 morphological/behaviour
P. boehmeriae
al traits
P. kernoviae
P. polonica • Distinct geographical
P. insolita
P. cuyabensis origin but blurred by
P. napoensis
EU419612Psp.6216900 migration?
EU419615Psp.8021391
P. irrigata
EU644721Psp.BF3
EU644715Psp.BF4
EU644714Psp.BFK
P. thermophilum
EU644725Psp.BF1
P. hydropathica 9
P. parsiana
P. zentmyerii
P. lagoariana
EU644720Psp.BFR
EU644722Psp.BF36
Rf17
11. Status of Phytophthora phylogenetics?
• Move from single gene to multigene phylogenies
• ITS remains good starting point
• Number of species increasing but main structure unchanged
• Expansion of clades 9 & 10 most marked
• Ever expanding range of taxa in clade 6
• Monitoring methods by Silvia Scibetta – powerful tool
• Still issues with GenBank – reference collection better in
independent source (Phytophthora database)
12. Oomycete pathogen population analysis
• Mutation
• Neutral markers • Recombination
• Natural selection
AFLPs • Gene flow
SSRs • Random genetic drift
P. infestans, P. ramorum, Pl. viticola • Migration
Accelerated discovery examined by Schena and
Cooke (BMC Genomics submitted)
Sequencing
Coalescent analysis
• Functional markers
Carbone web page
Host range
Virulence
Aggressiveness & Fitness
Fungicide resistance
Sequencing genes under strong selection
effector genes e.g. RxLRs P. infestans, Hy. parasitica
13. Simple Sequence Repeats – P. infestans
Marker G11
Isolate 1
Isolate 2
ABI 3730 capillary sequencer
Isolate 3
Isolate 4
Multiplex PCR – protocols
on www.eucablight.org
14. Changes in British P. infestans population
• Eucablight
Scotland database - powerful
• Increase in A2
mating type seen in
GB
• What about
genotypes?
England
15. Derived data plotted on web
• Differences in
allele frequency
between
countries
• Expansion to
South and
Central America
complete
• Further
expansion
under
discussion
16. Great Britain SSR genotypes 1982-2007
GB genotypes
100%
90%
3
80%
10
70% 13
71%
60%
Fre que nc y
US1
old A2
50% 7,8
40%
misc.
6
30%
2
20%
A1
10% 4 5 10%
12
0%
1982 1995 1996 1997/8 2003 2004 2005 2006 2007
Isolate no. 34 85 188 264 290 581 73 899 1452
• Major change in 2006 and 2007
• Some genotypes very durable, others not. Why?
17. GB genotype frequency within 2006 season
100%
90%
80%
70%
60%
50%
40%
30%
20%
Number of 10%
outbreaks
0%
May(1-31) June(1-15) June(16-30) July(1-15) July(16-31) Aug(1-15) Aug(16-31) Sep(1-30)
5 44 27 20 13 10 18 18
31 249 152 116 82 60 112 87
Number
of isolates
18. GB genotype frequency within 2007 season
100%
90%
80%
70%
60% What drives this change?
50%
40%
30%
20%
10%
Number of
outbreaks 0%
May(1-15) May(16-31) June(1-15) June(16-30) July(1-15) July(16-31) Aug(1-15)
4 4 22 80 139 45 14
29 23 144 387 574 220 52
Number
of isolates
19. Lesion area
•
•
6_
A1
_4
0
2
4
6
8
10
12
14
16
10
0A
N
13 L0
_A 62
2_ 69
6_ 388
A1 4
_3 B
92
0A
N
13 L0
_A 42
2_ 46
13 39
_A 64
2_ A
17 39
_A 2
2_ 8A
43
7_ 88
A1 D
_4
7_ 16
A1 8C
10 _41
_A 6
2_ 8B
13 44
_A 40
C
10 2_4
_A 13
2_ 2
39 B
36
C
S 2
E0
30
S 58
E
2_ 030
A1 8
_3 7
3b 88
_A 8A
2_
42
2_ 44
A1 E
_4
06
LD 8B
15
1
P
8a M
_A P6
1_ 22
42
3_ 56
A2 B
_4
01
2F
M
P
On average, genotype 13 isolates result in
61
8_ 8
larger lesions than other genotypes at 13oC
2a
Genotype 6 largest lesions of A1 genotypes
_A
1_ C4
42
32
E
C
Lesion area (mean of all varieties)
2
13 oC
20. Days
13
_A
0
1
2
3
4
5
6
7
8
2_
•
•
38
84
N B
L0
4 24
N 6
L0
13oC
6_ 6 26
A1 9
_ 41
13 00
_A A
2_
13 39
_A 64
2_ A
17 41
_A 32
2_ B
13 43
_A 88 D
2_
39
6_ 28
A1 A
_3
3b 92
_A 0A
2_
10 42
_A 44
2_ E
44
2_ 4
A1 0C
10 _4
_A 06
2_ 8B
39
2_ 36
A1 C2
_3
7_ 88
A1 8A
_4
16
8
LD C
3 _ 15 1
A2 P
_4
7_ 01
A1 2F
_4
16
8
SE B
sooner than other genotypes at 13oC
03
05
8
M
P6
22
Genotype 6 shortest LP of A1 genotypes
8_ SE
2a 03
_A 08
1_ 7
On average, genotype 13 isolates sporulate
8a 42
Latent period
_A 32E
1_
42
56
B
M
P6
18
21. Field trial results
100.00%
Percentage of each genotype
90.00%
80.00%
70.00% x
60.00% 7
50.00% 2
40.00% 8
6
30.00%
13
20.00%
10.00%
0.00%
D1 D2 D3 D4 D5 D6
No. lesions 67 67 99 100 17 20
• All isolates were pathogenic in lab test at D0
• Domination of genotype 13 clear
• Four other genotypes (1 alien) rare
22. Virulence of genotype 8- A1
R1 R2 R3 R4 R5 R6 R7 R8 R10 R11
BPC_06_4256B = 8_A1 1,4,7,10,11
Less complex and less aggressive (note 7,10&11)
23. Virulence of genotype 13 - A2
R1 R2 R3 R4 R5 R6 R7 R8 R10 R11
BPC_06_3928A = 13_A2 1,2,3,4,5,6,7,9,10,11
Complex virulence and aggressive
Resistant to metalaxyl
24. Structured screening of RxLR diversity
• Study of evolutionary forces on key pathogen traits
3 D Panel of 30 GB isolates
3_A2
2 B • Avr 3a
10_A2
• 3 SNPs (3 replacement changes)
• 23 EM homozygous (virulent)
• 6 EM/KI heterozygous (avirulent)
13_A2 • 1 KI homozygous (avirulent)
4 A
• avirulent strains confined to a specific lineage which explains
decline of this avirulence
• R3a not deployed widely (3.5% area) – low selection pressure
implies no ‘cost’ to virulence for avr3a
• PEX 161
2 C
1_A1 • 9 SNPs (1 outside ORF, 2 silent, 6 replacement)
2 A • 5 haplotypes
6_A1 • 7 TTGAATCGC A
3 D • 2 YTGMWWYRY B
2_A1
• 2 YWRMWWYRY C
6 D • 14 YWRAAWYRY D
7&8_A1
• 1 CAAAAATAT E
• Haplotypes correspond to SSR lineages
7/1A/B/D/E
rare
25. Conclusions
• Genomics
High throughput, affordable (£5K per 100 Mb) DNA sequencing offering insights into mechanisms of
pathogenicity, host range and ultimately host resistance responses. Post-genomics is going to be
a ‘long haul’.
• Phylogenetics
Exciting prospects for environmental monitoring of Phytophthora diversity in support of conventional
approaches. Evaluating risks. Exploring what happens in ‘balanced’ natural ecosystems as an aid
to understanding invasive species. Phylogeography to improve our understanding of origins of
species. Phylogenomics to understand mechanisms conserved across genus.
• Population analysis
Tracking populations – co-ordinated responses needed – tracking using standardised tools – sharing
‘intelligence’ on local problems. Predicting risk? How does population structure influence
management? Examining selection pressures on key genes.
26. Acknowledgments
• Eucablight team Jens Hansen, Poul Lassen & Alison Lees
• SCRI Team: Alison Lees, Naomi Williams and Louise
Sullivan,
• Italian team: Silvia Scibetta, Leonardo Schena, Santina
Cacciola and others
• BPC team: David Shaw, Ruairidh Bain, Nick Bradshaw,
Moray Taylor
• Many, many people who have contributed inspiration,
friendship & cultures
• Potato Council & RERAD for funding