Stable predictive markers for Phytophthora sojae avirulence genes that impair infection of soybean uncovered by whole genome sequencing of 31 isolates.
Identifieur interne : 000661 ( Main/Exploration ); précédent : 000660; suivant : 000662Stable predictive markers for Phytophthora sojae avirulence genes that impair infection of soybean uncovered by whole genome sequencing of 31 isolates.
Auteurs : Geneviève Arsenault-Labrecque [Canada] ; Humira Sonah [Canada] ; Amandine Lebreton [Canada] ; Caroline Labbé [Canada] ; Geneviève Marchand [Canada] ; Allen Xue [Canada] ; François Belzile [Canada] ; Brian J. Knaus [États-Unis] ; Niklaus J. Grünwald [États-Unis] ; Richard R. Bélanger [Canada]Source :
- BMC biology [ 1741-7007 ] ; 2018.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Phytophthora, Soja.
- microbiologie : Maladies des plantes, Soja.
- pathogénicité : Phytophthora.
- classification : Haplotypes, Phytophthora, Séquençage du génome entier, Variations de nombre de copies de segment d'ADN, Virulence.
English descriptors
- KwdEn :
- MESH :
- classification : Phytophthora.
- genetics : Phytophthora, Soybeans.
- microbiology : Plant Diseases, Soybeans.
- pathogenicity : Phytophthora.
- DNA Copy Number Variations, Haplotypes, Virulence, Whole Genome Sequencing.
Abstract
BACKGROUND
The interaction between oomycete plant pathogen Phytophthora sojae and soybean is characterized by the presence of avirulence (Avr) genes in P. sojae, which encode for effectors that trigger immune responses and resistance in soybean via corresponding resistance genes (Rps). A recent survey highlighted a rapid diversification of P. sojae Avr genes in soybean fields and the need to deploy new Rps genes. However, the full genetic diversity of P. sojae isolates remains complex and dynamic and is mostly characterized on the basis of phenotypic associations with differential soybean lines.
RESULTS
We sequenced the genomes of 31 isolates of P. sojae, representing a large spectrum of the pathotypes found in soybean fields, and compared all the genetic variations associated with seven Avr genes (1a, 1b, 1c, 1d, 1k, 3a, 6) and how the derived haplotypes matched reported phenotypes in 217 interactions. We discovered new variants, copy number variations and some discrepancies with the virulence of previously described isolates with Avr genes, notably with Avr1b and Avr1c. In addition, genomic signatures revealed 11.5% potentially erroneous phenotypes. When these interactions were re-phenotyped, and the Avr genes re-sequenced over time and analyzed for expression, our results showed that genomic signatures alone accurately predicted 99.5% of the interactions.
CONCLUSIONS
This comprehensive genomic analysis of seven Avr genes of P. sojae in a population of 31 isolates highlights that genomic signatures can be used as accurate predictors of phenotypes for compatibility with Rps genes in soybean. Our findings also show that spontaneous mutations, often speculated as a source of aberrant phenotypes, did not occur within the confines of our experiments and further suggest that epigenesis or gene silencing do not account alone for previous discordance between genotypes and phenotypes. Furthermore, on the basis of newly identified virulence patterns within Avr1c, our results offer an explanation why Rps1c has failed more rapidly in the field than the reported information on virulence pathotypes.
DOI: 10.1186/s12915-018-0549-9
PubMed: 30049268
PubMed Central: PMC6060493
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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wicri:step="Curation">000708</idno><idno type="wicri:Area/Main/Exploration">000708</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Stable predictive markers for Phytophthora sojae avirulence genes that impair infection of soybean uncovered by whole genome sequencing of 31 isolates.</title><author><name sortKey="Arsenault Labrecque, Genevieve" sort="Arsenault Labrecque, Genevieve" uniqKey="Arsenault Labrecque G" first="Geneviève" last="Arsenault-Labrecque">Geneviève Arsenault-Labrecque</name><affiliation wicri:level="4"><nlm:affiliation>Département de Phytologie, Université Laval, Québec, QC, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Département de Phytologie, Université Laval, Québec, QC</wicri:regionArea><orgName type="university">Université Laval</orgName><placeName><settlement type="city">Québec (ville)</settlement><region type="state">Québec</region></placeName></affiliation></author><author><name sortKey="Sonah, Humira" sort="Sonah, Humira" uniqKey="Sonah H" first="Humira" last="Sonah">Humira Sonah</name><affiliation wicri:level="4"><nlm:affiliation>Département de Phytologie, Université Laval, Québec, QC, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Département de Phytologie, Université Laval, Québec, QC</wicri:regionArea><orgName type="university">Université Laval</orgName><placeName><settlement type="city">Québec (ville)</settlement><region type="state">Québec</region></placeName></affiliation></author><author><name sortKey="Lebreton, Amandine" sort="Lebreton, Amandine" uniqKey="Lebreton A" first="Amandine" last="Lebreton">Amandine Lebreton</name><affiliation wicri:level="4"><nlm:affiliation>Département de Phytologie, Université Laval, Québec, QC, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Département de Phytologie, Université Laval, Québec, QC</wicri:regionArea><orgName type="university">Université 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Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Agriculture and Agri-Food Canada, Harrow, ON</wicri:regionArea><wicri:noRegion>ON</wicri:noRegion></affiliation></author><author><name sortKey="Xue, Allen" sort="Xue, Allen" uniqKey="Xue A" first="Allen" last="Xue">Allen Xue</name><affiliation wicri:level="1"><nlm:affiliation>Agriculture and Agri-Food Canada, Ontario, ON, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Agriculture and Agri-Food Canada, Ontario, ON</wicri:regionArea><wicri:noRegion>ON</wicri:noRegion></affiliation></author><author><name sortKey="Belzile, Francois" sort="Belzile, Francois" uniqKey="Belzile F" first="François" last="Belzile">François Belzile</name><affiliation wicri:level="4"><nlm:affiliation>Département de Phytologie, Université Laval, Québec, QC, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Département de Phytologie, Université Laval, Québec, QC</wicri:regionArea><orgName type="university">Université Laval</orgName><placeName><settlement type="city">Québec (ville)</settlement><region type="state">Québec</region></placeName></affiliation></author><author><name sortKey="Knaus, Brian J" sort="Knaus, Brian J" uniqKey="Knaus B" first="Brian J" last="Knaus">Brian J. Knaus</name><affiliation wicri:level="2"><nlm:affiliation>Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, OR, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, OR</wicri:regionArea><placeName><region type="state">Oregon</region></placeName></affiliation></author><author><name sortKey="Grunwald, Niklaus J" sort="Grunwald, Niklaus J" uniqKey="Grunwald N" first="Niklaus J" last="Grünwald">Niklaus J. Grünwald</name><affiliation wicri:level="2"><nlm:affiliation>Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, OR, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, OR</wicri:regionArea><placeName><region type="state">Oregon</region></placeName></affiliation></author><author><name sortKey="Belanger, Richard R" sort="Belanger, Richard R" uniqKey="Belanger R" first="Richard R" last="Bélanger">Richard R. Bélanger</name><affiliation wicri:level="4"><nlm:affiliation>Département de Phytologie, Université Laval, Québec, QC, Canada. richard.belanger@fsaa.ulaval.ca.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Département de Phytologie, Université Laval, Québec, QC</wicri:regionArea><orgName type="university">Université Laval</orgName><placeName><settlement type="city">Québec (ville)</settlement><region type="state">Québec</region></placeName></affiliation></author></analytic><series><title level="j">BMC biology</title><idno type="eISSN">1741-7007</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>DNA Copy Number Variations (MeSH)</term><term>Haplotypes (MeSH)</term><term>Phytophthora (classification)</term><term>Phytophthora (genetics)</term><term>Phytophthora (pathogenicity)</term><term>Plant Diseases (microbiology)</term><term>Soybeans (genetics)</term><term>Soybeans (microbiology)</term><term>Virulence (MeSH)</term><term>Whole Genome Sequencing (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Haplotypes (MeSH)</term><term>Maladies des plantes (microbiologie)</term><term>Phytophthora (classification)</term><term>Phytophthora (génétique)</term><term>Phytophthora (pathogénicité)</term><term>Soja (génétique)</term><term>Soja (microbiologie)</term><term>Séquençage du génome entier (MeSH)</term><term>Variations de nombre de copies de segment d'ADN (MeSH)</term><term>Virulence (MeSH)</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Phytophthora</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Phytophthora</term><term>Soybeans</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Phytophthora</term><term>Soja</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Maladies des plantes</term><term>Soja</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Plant Diseases</term><term>Soybeans</term></keywords><keywords scheme="MESH" qualifier="pathogenicity" xml:lang="en"><term>Phytophthora</term></keywords><keywords scheme="MESH" qualifier="pathogénicité" xml:lang="fr"><term>Phytophthora</term></keywords><keywords scheme="MESH" xml:lang="en"><term>DNA Copy Number Variations</term><term>Haplotypes</term><term>Virulence</term><term>Whole Genome Sequencing</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="fr"><term>Haplotypes</term><term>Phytophthora</term><term>Séquençage du génome entier</term><term>Variations de nombre de copies de segment d'ADN</term><term>Virulence</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>The interaction between oomycete plant pathogen Phytophthora sojae and soybean is characterized by the presence of avirulence (Avr) genes in P. sojae, which encode for effectors that trigger immune responses and resistance in soybean via corresponding resistance genes (Rps). A recent survey highlighted a rapid diversification of P. sojae Avr genes in soybean fields and the need to deploy new Rps genes. However, the full genetic diversity of P. sojae isolates remains complex and dynamic and is mostly characterized on the basis of phenotypic associations with differential soybean lines.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>We sequenced the genomes of 31 isolates of P. sojae, representing a large spectrum of the pathotypes found in soybean fields, and compared all the genetic variations associated with seven Avr genes (1a, 1b, 1c, 1d, 1k, 3a, 6) and how the derived haplotypes matched reported phenotypes in 217 interactions. We discovered new variants, copy number variations and some discrepancies with the virulence of previously described isolates with Avr genes, notably with Avr1b and Avr1c. In addition, genomic signatures revealed 11.5% potentially erroneous phenotypes. When these interactions were re-phenotyped, and the Avr genes re-sequenced over time and analyzed for expression, our results showed that genomic signatures alone accurately predicted 99.5% of the interactions.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>This comprehensive genomic analysis of seven Avr genes of P. sojae in a population of 31 isolates highlights that genomic signatures can be used as accurate predictors of phenotypes for compatibility with Rps genes in soybean. Our findings also show that spontaneous mutations, often speculated as a source of aberrant phenotypes, did not occur within the confines of our experiments and further suggest that epigenesis or gene silencing do not account alone for previous discordance between genotypes and phenotypes. Furthermore, on the basis of newly identified virulence patterns within Avr1c, our results offer an explanation why Rps1c has failed more rapidly in the field than the reported information on virulence pathotypes.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">30049268</PMID><DateCompleted><Year>2019</Year><Month>05</Month><Day>13</Day></DateCompleted><DateRevised><Year>2019</Year><Month>05</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1741-7007</ISSN><JournalIssue CitedMedium="Internet"><Volume>16</Volume><Issue>1</Issue><PubDate><Year>2018</Year><Month>07</Month><Day>26</Day></PubDate></JournalIssue><Title>BMC biology</Title><ISOAbbreviation>BMC Biol</ISOAbbreviation></Journal><ArticleTitle>Stable predictive markers for Phytophthora sojae avirulence genes that impair infection of soybean uncovered by whole genome sequencing of 31 isolates.</ArticleTitle><Pagination><MedlinePgn>80</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12915-018-0549-9</ELocationID><Abstract><AbstractText Label="BACKGROUND">The interaction between oomycete plant pathogen Phytophthora sojae and soybean is characterized by the presence of avirulence (Avr) genes in P. sojae, which encode for effectors that trigger immune responses and resistance in soybean via corresponding resistance genes (Rps). A recent survey highlighted a rapid diversification of P. sojae Avr genes in soybean fields and the need to deploy new Rps genes. However, the full genetic diversity of P. sojae isolates remains complex and dynamic and is mostly characterized on the basis of phenotypic associations with differential soybean lines.</AbstractText><AbstractText Label="RESULTS">We sequenced the genomes of 31 isolates of P. sojae, representing a large spectrum of the pathotypes found in soybean fields, and compared all the genetic variations associated with seven Avr genes (1a, 1b, 1c, 1d, 1k, 3a, 6) and how the derived haplotypes matched reported phenotypes in 217 interactions. We discovered new variants, copy number variations and some discrepancies with the virulence of previously described isolates with Avr genes, notably with Avr1b and Avr1c. In addition, genomic signatures revealed 11.5% potentially erroneous phenotypes. When these interactions were re-phenotyped, and the Avr genes re-sequenced over time and analyzed for expression, our results showed that genomic signatures alone accurately predicted 99.5% of the interactions.</AbstractText><AbstractText Label="CONCLUSIONS">This comprehensive genomic analysis of seven Avr genes of P. sojae in a population of 31 isolates highlights that genomic signatures can be used as accurate predictors of phenotypes for compatibility with Rps genes in soybean. Our findings also show that spontaneous mutations, often speculated as a source of aberrant phenotypes, did not occur within the confines of our experiments and further suggest that epigenesis or gene silencing do not account alone for previous discordance between genotypes and phenotypes. Furthermore, on the basis of newly identified virulence patterns within Avr1c, our results offer an explanation why Rps1c has failed more rapidly in the field than the reported information on virulence pathotypes.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Arsenault-Labrecque</LastName><ForeName>Geneviève</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Département de Phytologie, Université Laval, Québec, QC, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sonah</LastName><ForeName>Humira</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Département de Phytologie, Université Laval, Québec, QC, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lebreton</LastName><ForeName>Amandine</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Département de Phytologie, Université Laval, Québec, QC, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Labbé</LastName><ForeName>Caroline</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Département de Phytologie, Université Laval, Québec, QC, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Marchand</LastName><ForeName>Geneviève</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Agriculture and Agri-Food Canada, Harrow, ON, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xue</LastName><ForeName>Allen</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Agriculture and Agri-Food Canada, Ontario, ON, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Belzile</LastName><ForeName>François</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Département de Phytologie, Université Laval, Québec, QC, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Knaus</LastName><ForeName>Brian J</ForeName><Initials>BJ</Initials><AffiliationInfo><Affiliation>Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, OR, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Grünwald</LastName><ForeName>Niklaus J</ForeName><Initials>NJ</Initials><AffiliationInfo><Affiliation>Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, OR, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bélanger</LastName><ForeName>Richard R</ForeName><Initials>RR</Initials><Identifier Source="ORCID">0000-0001-8549-975X</Identifier><AffiliationInfo><Affiliation>Département de Phytologie, Université Laval, Québec, QC, Canada. richard.belanger@fsaa.ulaval.ca.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2018</Year><Month>07</Month><Day>26</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Biol</MedlineTA><NlmUniqueID>101190720</NlmUniqueID><ISSNLinking>1741-7007</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D056915" MajorTopicYN="N">DNA Copy Number Variations</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006239" MajorTopicYN="N">Haplotypes</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010838" MajorTopicYN="N">Phytophthora</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="Y">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000472" MajorTopicYN="Y">pathogenicity</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010935" MajorTopicYN="N">Plant Diseases</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013025" MajorTopicYN="N">Soybeans</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014774" MajorTopicYN="N">Virulence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000073336" MajorTopicYN="N">Whole Genome Sequencing</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Avr genes</Keyword><Keyword MajorTopicYN="Y">Effectors</Keyword><Keyword MajorTopicYN="Y">Genomics</Keyword><Keyword MajorTopicYN="Y">Haplotype analysis</Keyword><Keyword MajorTopicYN="Y">Oomycete</Keyword><Keyword MajorTopicYN="Y">Phytophthora sojae</Keyword><Keyword MajorTopicYN="Y">Plant pathogen</Keyword><Keyword MajorTopicYN="Y">R genes</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>04</Month><Day>11</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2018</Year><Month>07</Month><Day>19</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2018</Year><Month>7</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2018</Year><Month>7</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>5</Month><Day>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">30049268</ArticleId><ArticleId IdType="doi">10.1186/s12915-018-0549-9</ArticleId><ArticleId IdType="pii">10.1186/s12915-018-0549-9</ArticleId><ArticleId IdType="pmc">PMC6060493</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>PLoS One. 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sort="Belanger, Richard R" uniqKey="Belanger R" first="Richard R" last="Bélanger">Richard R. Bélanger</name><name sortKey="Belzile, Francois" sort="Belzile, Francois" uniqKey="Belzile F" first="François" last="Belzile">François Belzile</name><name sortKey="Labbe, Caroline" sort="Labbe, Caroline" uniqKey="Labbe C" first="Caroline" last="Labbé">Caroline Labbé</name><name sortKey="Lebreton, Amandine" sort="Lebreton, Amandine" uniqKey="Lebreton A" first="Amandine" last="Lebreton">Amandine Lebreton</name><name sortKey="Marchand, Genevieve" sort="Marchand, Genevieve" uniqKey="Marchand G" first="Geneviève" last="Marchand">Geneviève Marchand</name><name sortKey="Sonah, Humira" sort="Sonah, Humira" uniqKey="Sonah H" first="Humira" last="Sonah">Humira Sonah</name><name sortKey="Xue, Allen" sort="Xue, Allen" uniqKey="Xue A" first="Allen" last="Xue">Allen Xue</name></country><country name="États-Unis"><region name="Oregon"><name sortKey="Knaus, Brian J" sort="Knaus, Brian J" uniqKey="Knaus B" first="Brian J" last="Knaus">Brian J. Knaus</name></region><name sortKey="Grunwald, Niklaus J" sort="Grunwald, Niklaus J" uniqKey="Grunwald N" first="Niklaus J" last="Grünwald">Niklaus J. Grünwald</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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