Author
Sylvain Raffaele
Other affiliations: Sainsbury Laboratory, Norwich Research Park, John Innes Centre ...read more
Bio: Sylvain Raffaele is an academic researcher from University of Toulouse. The author has contributed to research in topics: Sclerotinia sclerotiorum & Gene. The author has an hindex of 32, co-authored 66 publications receiving 7417 citations. Previous affiliations of Sylvain Raffaele include Sainsbury Laboratory & Norwich Research Park.
Topics: Sclerotinia sclerotiorum, Gene, Genome, Effector, Phytophthora infestans
Papers published on a yearly basis
Papers
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Broad Institute1, Ohio Agricultural Research and Development Center2, Sainsbury Laboratory3, Uppsala University4, Wageningen University and Research Centre5, Virginia Bioinformatics Institute6, University of California, Riverside7, University of Aberdeen8, Scottish Crop Research Institute9, University of Warwick10, Agricultural Research Service11, Royal Institute of Technology12, Cornell University13, Oregon State University14, Lafayette College15, University of Glasgow16, Harvard University17, Delaware Biotechnology Institute18, North Carolina State University19, University of Delaware20, University of Tennessee21, University of Maryland, Baltimore22, Vanderbilt University23, College of Wooster24, Bowling Green State University25, Edinburgh Cancer Research Centre26, J. Craig Venter Institute27, Tel Aviv University28, University of Wisconsin-Madison29, University of Hohenheim30, University of Dundee31
TL;DR: The sequence of the P. infestans genome is reported, which at ∼240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates and probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.
Abstract: Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brown algae and diatoms. As the agent of the Irish potato famine in the mid-nineteenth century, P. infestans has had a tremendous effect on human history, resulting in famine and population displacement(1). To this day, it affects world agriculture by causing the most destructive disease of potato, the fourth largest food crop and a critical alternative to the major cereal crops for feeding the world's population(1). Current annual worldwide potato crop losses due to late blight are conservatively estimated at $6.7 billion(2). Management of this devastating pathogen is challenged by its remarkable speed of adaptation to control strategies such as genetically resistant cultivars(3,4). Here we report the sequence of the P. infestans genome, which at similar to 240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates. Its expansion results from a proliferation of repetitive DNA accounting for similar to 74% of the genome. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes that are induced during infection or are predicted to have activities that alter host physiology. These fast-evolving effector genes are localized to highly dynamic and expanded regions of the P. infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.
1,341 citations
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TL;DR: Cases in which genome plasticity has contributed to the emergence of new virulence traits are illustrated and how genome expansions may have had an impact on the co-evolutionary conflict between these filamentous plant pathogens and their hosts are discussed.
Abstract: Many species of fungi and oomycetes are plant pathogens of great economic importance. Over the past 7 years, the genomes of more than 30 of these filamentous plant pathogens have been sequenced, revealing remarkable diversity in genome size and architecture. Whereas the genomes of many parasites and bacterial symbionts have been reduced over time, the genomes of several lineages of filamentous plant pathogens have been shaped by repeat-driven expansions. In these lineages, the genes encoding proteins involved in host interactions are frequently polymorphic and reside within repeat-rich regions of the genome. Here, we review the properties of these adaptable genome regions and the mechanisms underlying their plasticity, and we illustrate cases in which genome plasticity has contributed to the emergence of new virulence traits. We also discuss how genome expansions may have had an impact on the co-evolutionary conflict between these filamentous plant pathogens and their hosts.
622 citations
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TL;DR: A group of papers analyzes pathogen genomes to find the roots of virulence, opportunism, and life-style determinants, demonstrating that dynamic repeat-rich genome compartments underpin accelerated gene evolution following host jumps in this pathogen lineage.
Abstract: Many plant pathogens, including those in the lineage of the Irish potato famine organism Phytophthora infestans, evolve by host jumps followed by specialization. However, how host jumps affect genome evolution remains largely unknown. To determine the patterns of sequence variation in the P. infestans lineage, we resequenced six genomes of four sister species. This revealed uneven evolutionary rates across genomes with genes in repeat-rich regions showing higher rates of structural polymorphisms and positive selection. These loci are enriched in genes induced in planta, implicating host adaptation in genome evolution. Unexpectedly, genes involved in epigenetic processes formed another class of rapidly evolving residents of the gene-sparse regions. These results demonstrate that dynamic repeat-rich genome compartments underpin accelerated gene evolution following host jumps in this pathogen lineage.
409 citations
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TL;DR: How plant pathogens are great model systems to study evolutionary adaptations at multiple time scales is discussed and the 'two-speed genome' model in which filamentous pathogen genomes have a bipartite architecture with gene sparse, repeat rich compartments serving as a cradle for adaptive evolution is reviewed.
398 citations
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TL;DR: Genome-wide catalogs of P. infestans effectors are available, enabling effectoromics approaches that accelerate R gene cloning and specificity profiling and monitoring effector allelic diversity in pathogen populations can assist in R gene deployment in agriculture.
Abstract: Potato (Solanum tuberosum) is the world's third-largest food crop. It severely suffers from late blight, a devastating disease caused by Phytophthora infestans. This oomycete pathogen secretes host-translocated RXLR effectors that include avirulence (AVR) proteins, which are targeted by resistance (R) proteins from wild Solanum species. Most Solanum R genes appear to have coevolved with P. infestans at its center of origin in central Mexico. Various R and Avr genes were recently cloned, and here we catalog characterized R-AVR pairs. We describe the mechanisms that P. infestans employs for evading R protein recognition and discuss partial resistance and partial virulence phenotypes in the context of our knowledge of effector diversity and activity. Genome-wide catalogs of P. infestans effectors are available, enabling effectoromics approaches that accelerate R gene cloning and specificity profiling. Engineering R genes with expanded pathogen recognition has also become possible. Importantly, monitoring eff...
393 citations
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01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.
10,124 citations
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TL;DR: The recent convergence of molecular studies of plant immunity and pathogen infection strategies is revealing an integrated picture of the plant–pathogen interaction from the perspective of both organisms, suggesting novel biotechnological approaches to crop protection.
Abstract: Plants are engaged in a continuous co-evolutionary struggle for dominance with their pathogens. The outcomes of these interactions are of particular importance to human activities, as they can have dramatic effects on agricultural systems. The recent convergence of molecular studies of plant immunity and pathogen infection strategies is revealing an integrated picture of the plant-pathogen interaction from the perspective of both organisms. Plants have an amazing capacity to recognize pathogens through strategies involving both conserved and variable pathogen elicitors, and pathogens manipulate the defence response through secretion of virulence effector molecules. These insights suggest novel biotechnological approaches to crop protection.
2,666 citations
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TL;DR: Genetic studies reveal an increasingly complex network of proteins required for SA-mediated defense signaling, and this process is amplified by several regulatory feedback loops.
Abstract: For more than 200 years, the plant hormone salicylic acid (SA) has been studied for its medicinal use in humans. However, its extensive signaling role in plants, particularly in defense against pathogens, has only become evident during the past 20 years. This review surveys how SA in plants regulates both local disease resistance mechanisms, including host cell death and defense gene expression, and systemic acquired resistance (SAR). Genetic studies reveal an increasingly complex network of proteins required for SA-mediated defense signaling, and this process is amplified by several regulatory feedback loops. The interaction between the SA signaling pathway and those regulated by other plant hormones and/or defense signals is also discussed.
2,030 citations
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TL;DR: The R package poppr is developed providing unique tools for analysis of data from admixed, clonal, mixed, and/or sexual populations, and functions for genotypic diversity and clone censoring are specific for clonal populations.
Abstract: Many microbial, fungal, or oomcyete populations violate assumptions for population genetic analysis because these populations are clonal, admixed, partially clonal, and/or sexual. Furthermore, few tools exist that are specifically designed for analyzing data from clonal populations, making analysis difficult and haphazard. We developed the R package poppr providing unique tools for analysis of data from admixed, clonal, mixed, and/or sexual populations. Currently, poppr can be used for dominant/codominant and haploid/diploid genetic data. Data can be imported from several formats including GenAlEx formatted text files and can be analyzed on a user-defined hierarchy that includes unlimited levels of subpopulation structure and clone censoring. New functions include calculation of Bruvo’s distance for microsatellites, batch-analysis of the index of association with several indices of genotypic diversity, and graphing including dendrograms with bootstrap support and minimum spanning networks. While functions for genotypic diversity and clone censoring are specific for clonal populations, several functions found in poppr are also valuable to analysis of any populations. A manual with documentation and examples is provided. Poppr is open source and major releases are available on CRAN: http://cran.r-project.org/package=poppr. More supporting documentation and tutorials can be found under ‘resources’ at: http://grunwaldlab.cgrb.oregonstate.edu/.
1,942 citations
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Beijing Institute of Genomics1, Cayetano Heredia University2, Indian Council of Agricultural Research3, Russian Academy of Sciences4, University of Dundee5, Huazhong Agricultural University6, Hunan Agricultural University7, Imperial College London8, Polish Academy of Sciences9, International Potato Center10, J. Craig Venter Institute11, National University of La Plata12, Michigan State University13, James Hutton Institute14, Teagasc15, Plant & Food Research16, Aalborg University17, University of Wisconsin-Madison18, Virginia Tech19, Wageningen University and Research Centre20
TL;DR: The potato genome sequence provides a platform for genetic improvement of this vital crop and predicts 39,031 protein-coding genes and presents evidence for at least two genome duplication events indicative of a palaeopolyploid origin.
Abstract: Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop.
1,813 citations