Author
Etienne Danchin
Other affiliations: University of Toulouse, Pierre-and-Marie-Curie University, University of Provence ...read more
Bio: Etienne Danchin is an academic researcher from Centre national de la recherche scientifique. The author has contributed to research in topics: Genome & Population. The author has an hindex of 64, co-authored 243 publications receiving 21651 citations. Previous affiliations of Etienne Danchin include University of Toulouse & Pierre-and-Marie-Curie University.
Topics: Genome, Population, Reproductive success, Gene, Meloidogyne incognita
Papers published on a yearly basis
Papers
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Broad Institute1, University of Amsterdam2, University of California, Riverside3, University of Arizona4, Université Paris-Saclay5, University of Córdoba (Spain)6, Oregon State University7, Aix-Marseille University8, Pennsylvania State University9, Texas A&M University10, Purdue University11, University of California, Irvine12, Rothamsted Research13, Pacific Northwest National Laboratory14, University of Minnesota15, United States Department of Agriculture16, Centre national de la recherche scientifique17, University of Texas Southwestern Medical Center18, University of California, Los Angeles19, Commonwealth Scientific and Industrial Research Organisation20, Seoul National University21, University of Texas at Dallas22, University of Cambridge23, University of Wisconsin-Madison24, Cornell University25
TL;DR: Comparison of genomes of three phenotypically diverse Fusarium species revealed lineage-specific genomic regions in F. oxysporum that include four entire chromosomes and account for more than one-quarter of the genome, putting the evolution of fungal pathogenicity into a new perspective.
Abstract: Fusarium species are among the most important phytopathogenic and toxigenic fungi. To understand the molecular underpinnings of pathogenicity in the genus Fusarium, we compared the genomes of three phenotypically diverse species: Fusarium graminearum, Fusarium verticillioides and Fusarium oxysporum f. sp. lycopersici. Our analysis revealed lineage-specific (LS) genomic regions in F. oxysporum that include four entire chromosomes and account for more than one-quarter of the genome. LS regions are rich in transposons and genes with distinct evolutionary profiles but related to pathogenicity, indicative of horizontal acquisition. Experimentally, we demonstrate the transfer of two LS chromosomes between strains of F. oxysporum, converting a non-pathogenic strain into a pathogen. Transfer of LS chromosomes between otherwise genetically isolated strains explains the polyphyletic origin of host specificity and the emergence of new pathogenic lineages in F. oxysporum. These findings put the evolution of fungal pathogenicity into a new perspective.
1,386 citations
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TL;DR: A large body of evidence suggests that human decision-making is strongly influenced by the behavior of others, which may then affect biological evolution.
Abstract: Psychologists, economists, and advertising moguls have long known that human decision-making is strongly influenced by the behavior of others A rapidly accumulating body of evidence suggests that the same is true in animals Individuals can use information arising from cues inadvertently produced by the behavior of other individuals with similar requirements Many of these cues provide public information about the quality of alternatives The use of public information is taxonomically widespread and can enhance fitness Public information can lead to cultural evolution, which we suggest may then affect biological evolution
1,335 citations
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TL;DR: The aim of this review was to undertake a survey of researchers working with plant-parasitic nematodes in order to determine a 'top 10' list of these pathogens based on scientific and economic importance.
Abstract: The aim of this review was to undertake a survey of researchers working with plant-parasitic nematodes in order to determine a ‘top 10’ list of these pathogens based on scientific and economic importance. Any such list will not be definitive as economic importance will vary depending on the region of the world in which a researcher is based. However, care was taken to include researchers from as many parts of the world as possible when carrying out the survey. The top 10 list emerging from the survey is composed of: (1) root-knot nematodes (Meloidogyne spp.); (2) cyst nematodes (Heterodera and Globodera spp.); (3) root lesion nematodes (Pratylenchus spp.); (4) the burrowing nematode Radopholus similis; (5) Ditylenchus dipsaci; (6) the pine wilt nematode Bursaphelenchus xylophilus; (7) the reniform nematode Rotylenchulus reniformis; (8) Xiphinema index (the only virus vector nematode to make the list); (9) Nacobbus aberrans; and (10) Aphelenchoides besseyi. The biology of each nematode (or nematode group) is reviewed briefly.
1,215 citations
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DSM1, Delft University of Technology2, University of Nottingham3, Technical University of Denmark4, Wageningen University and Research Centre5, University of Sheffield6, Utrecht University7, Biomax Informatics AG8, CLC bio9, University of Liverpool10, Ghent University11, University of Manchester12, University of Provence13, University of Groningen14, Pasteur Institute15, University of Amsterdam16, University of Angers17, Leiden University18, Radboud University Nijmegen19, University of Szeged20
TL;DR: The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for the production of enzymes and organic acids, particularly citric acid, and the sequenced genome revealed a large number of major facilitator superfamily transporters and fungal zinc binuclear cluster transcription factors.
Abstract: The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for the production of enzymes and organic acids, particularly citric acid. We sequenced the 33.9-megabase genome of A. niger CBS 513.88, the ancestor of currently used enzyme production strains. A high level of synteny was observed with other aspergilli sequenced. Strong function predictions were made for 6,506 of the 14,165 open reading frames identified. A detailed description of the components of the protein secretion pathway was made and striking differences in the hydrolytic enzyme spectra of aspergilli were observed. A reconstructed metabolic network comprising 1,069 unique reactions illustrates the versatile metabolism of A. niger. Noteworthy is the large number of major facilitator superfamily transporters and fungal zinc binuclear cluster transcription factors, and the presence of putative gene clusters for fumonisin and ochratoxin A synthesis.
1,161 citations
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Los Alamos National Laboratory1, University of New Mexico2, Novozymes3, University of Provence4, VTT Technical Research Centre of Finland5, Pacific Northwest National Laboratory6, Joint Genome Institute7, United States Department of Agriculture8, Vienna University of Technology9, Pontifical Catholic University of Chile10, Oregon State University11, Genencor12
TL;DR: This work assembled 89 scaffolds to generate 34 Mbp of nearly contiguous T. reesei genome sequence comprising 9,129 predicted gene models, providing a roadmap for constructing enhanced T.Reesei strains for industrial applications such as biofuel production.
Abstract: Trichoderma reesei is the main industrial source of cellulases and hemicellulases used to depolymerize biomass to simple sugars that are converted to chemical intermediates and biofuels, such as ethanol. We assembled 89 scaffolds (sets of ordered and oriented contigs) to generate 34 Mbp of nearly contiguous T. reesei genome sequence comprising 9,129 predicted gene models. Unexpectedly, considering the industrial utility and effectiveness of the carbohydrate-active enzymes of T. reesei, its genome encodes fewer cellulases and hemicellulases than any other sequenced fungus able to hydrolyze plant cell wall polysaccharides. Many T. reesei genes encoding carbohydrate-active enzymes are distributed nonrandomly in clusters that lie between regions of synteny with other Sordariomycetes. Numerous genes encoding biosynthetic pathways for secondary metabolites may promote survival of T. reesei in its competitive soil habitat, but genome analysis provided little mechanistic insight into its extraordinary capacity for protein secretion. Our analysis, coupled with the genome sequence data, provides a roadmap for constructing enhanced T. reesei strains for industrial applications such as biofuel production.
1,085 citations
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TL;DR: Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols used xiii 1.
Abstract: Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201
14,171 citations
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TL;DR: It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.
11,521 citations
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: For the next few weeks the course is going to be exploring a field that’s actually older than classical population genetics, although the approach it’ll be taking to it involves the use of population genetic machinery.
Abstract: So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to
9,847 citations