WGDdetector: a pipeline for detecting whole genome duplication events using the genome or transcriptome annotations.
Identifieur interne : 000640 ( Main/Exploration ); précédent : 000639; suivant : 000641WGDdetector: a pipeline for detecting whole genome duplication events using the genome or transcriptome annotations.
Auteurs : Yongzhi Yang [République populaire de Chine] ; Ying Li [République populaire de Chine] ; Qiao Chen [République populaire de Chine] ; Yongshuai Sun [République populaire de Chine] ; Zhiqiang Lu [République populaire de Chine]Source :
- BMC bioinformatics [ 1471-2105 ] ; 2019.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Arabidopsis, Juglans, Populus.
- méthodes : Génomique.
- Animaux, Annotation de séquence moléculaire, Duplication de gène, Génome, Logiciel, Transcriptome, Xenopus laevis.
English descriptors
- KwdEn :
- MESH :
- genetics : Arabidopsis, Juglans, Populus.
- methods : Genomics.
- Animals, Gene Duplication, Genome, Molecular Sequence Annotation, Software, Transcriptome, Xenopus laevis.
Abstract
BACKGROUND
With the availability of well-assembled genomes of a growing number of organisms, identifying the bioinformatic basis of whole genome duplication (WGD) is a growing field of genomics. The most extant software for detecting footprints of WGDs has been restricted to a well-assembled genome. However, the massive poor quality genomes and the more accessible transcriptomes have been largely ignored, and in theoretically they are also likely to contribute to detect WGD using dS based method. Here, to resolve these problems, we have designed a universal and simple technical tool WGDdetector for detecting WGDs using either genome or transcriptome annotations in different organisms based on the widely used dS based method.
RESULTS
We have constructed WGDdetector pipeline that integrates all analyses including gene family constructing, dS estimating and phasing, and outputting the dS values of each paralogs pairs processed with only one command. We further chose four species (Arabidopsis thaliana, Juglans regia, Populus trichocarpa and Xenopus laevis) representing herb, wood and animal, to test its practicability. Our final results showed a high degree of accuracy with the previous studies using both genome and transcriptome data.
CONCLUSION
WGDdetector is not only reliable and stable for genome data, but also a new way to using the transcriptome data to obtain the correct dS distribution for detecting WGD. The source code is freely available, and is implemented in Windows and Linux operation system.
DOI: 10.1186/s12859-019-2670-3
PubMed: 30760221
PubMed Central: PMC6375192
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">WGDdetector: a pipeline for detecting whole genome duplication events using the genome or transcriptome annotations.</title><author><name sortKey="Yang, Yongzhi" sort="Yang, Yongzhi" uniqKey="Yang Y" first="Yongzhi" last="Yang">Yongzhi Yang</name><affiliation wicri:level="1"><nlm:affiliation>CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan</wicri:regionArea><wicri:noRegion>Yunnan</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Grassland Agro-Ecosystem, College of Life Sciences, Lanzhou University, Lanzhou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Grassland Agro-Ecosystem, College of Life Sciences, Lanzhou University, Lanzhou</wicri:regionArea><wicri:noRegion>Lanzhou</wicri:noRegion></affiliation></author><author><name sortKey="Li, Ying" sort="Li, Ying" uniqKey="Li Y" first="Ying" last="Li">Ying Li</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Grassland Agro-Ecosystem, College of Life Sciences, Lanzhou University, Lanzhou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Grassland Agro-Ecosystem, College of Life Sciences, Lanzhou University, Lanzhou</wicri:regionArea><wicri:noRegion>Lanzhou</wicri:noRegion></affiliation></author><author><name sortKey="Chen, Qiao" sort="Chen, Qiao" uniqKey="Chen Q" first="Qiao" last="Chen">Qiao Chen</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Grassland Agro-Ecosystem, College of Life Sciences, Lanzhou University, Lanzhou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Grassland Agro-Ecosystem, College of Life Sciences, Lanzhou University, Lanzhou</wicri:regionArea><wicri:noRegion>Lanzhou</wicri:noRegion></affiliation></author><author><name sortKey="Sun, Yongshuai" sort="Sun, Yongshuai" uniqKey="Sun Y" first="Yongshuai" last="Sun">Yongshuai Sun</name><affiliation wicri:level="1"><nlm:affiliation>CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China. sunyongshuai@xtbg.ac.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan</wicri:regionArea><wicri:noRegion>Yunnan</wicri:noRegion></affiliation></author><author><name sortKey="Lu, Zhiqiang" sort="Lu, Zhiqiang" uniqKey="Lu Z" first="Zhiqiang" last="Lu">Zhiqiang Lu</name><affiliation wicri:level="1"><nlm:affiliation>CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China. luzhiqiang@xtbg.ac.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan</wicri:regionArea><wicri:noRegion>Yunnan</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2019">2019</date><idno type="RBID">pubmed:30760221</idno><idno type="pmid">30760221</idno><idno type="doi">10.1186/s12859-019-2670-3</idno><idno type="pmc">PMC6375192</idno><idno type="wicri:Area/Main/Corpus">000A32</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000A32</idno><idno type="wicri:Area/Main/Curation">000A32</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">000A32</idno><idno type="wicri:Area/Main/Exploration">000A32</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">WGDdetector: a pipeline for detecting whole genome duplication events using the genome or transcriptome annotations.</title><author><name sortKey="Yang, Yongzhi" sort="Yang, Yongzhi" uniqKey="Yang Y" first="Yongzhi" last="Yang">Yongzhi Yang</name><affiliation wicri:level="1"><nlm:affiliation>CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan</wicri:regionArea><wicri:noRegion>Yunnan</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Grassland Agro-Ecosystem, College of Life Sciences, Lanzhou University, Lanzhou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Grassland Agro-Ecosystem, College of Life Sciences, Lanzhou University, Lanzhou</wicri:regionArea><wicri:noRegion>Lanzhou</wicri:noRegion></affiliation></author><author><name sortKey="Li, Ying" sort="Li, Ying" uniqKey="Li Y" first="Ying" last="Li">Ying Li</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Grassland Agro-Ecosystem, College of Life Sciences, Lanzhou University, Lanzhou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Grassland Agro-Ecosystem, College of Life Sciences, Lanzhou University, Lanzhou</wicri:regionArea><wicri:noRegion>Lanzhou</wicri:noRegion></affiliation></author><author><name sortKey="Chen, Qiao" sort="Chen, Qiao" uniqKey="Chen Q" first="Qiao" last="Chen">Qiao Chen</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Grassland Agro-Ecosystem, College of Life Sciences, Lanzhou University, Lanzhou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Grassland Agro-Ecosystem, College of Life Sciences, Lanzhou University, Lanzhou</wicri:regionArea><wicri:noRegion>Lanzhou</wicri:noRegion></affiliation></author><author><name sortKey="Sun, Yongshuai" sort="Sun, Yongshuai" uniqKey="Sun Y" first="Yongshuai" last="Sun">Yongshuai Sun</name><affiliation wicri:level="1"><nlm:affiliation>CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China. sunyongshuai@xtbg.ac.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan</wicri:regionArea><wicri:noRegion>Yunnan</wicri:noRegion></affiliation></author><author><name sortKey="Lu, Zhiqiang" sort="Lu, Zhiqiang" uniqKey="Lu Z" first="Zhiqiang" last="Lu">Zhiqiang Lu</name><affiliation wicri:level="1"><nlm:affiliation>CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China. luzhiqiang@xtbg.ac.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan</wicri:regionArea><wicri:noRegion>Yunnan</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals (MeSH)</term><term>Arabidopsis (genetics)</term><term>Gene Duplication (MeSH)</term><term>Genome (MeSH)</term><term>Genomics (methods)</term><term>Juglans (genetics)</term><term>Molecular Sequence Annotation (MeSH)</term><term>Populus (genetics)</term><term>Software (MeSH)</term><term>Transcriptome (MeSH)</term><term>Xenopus laevis (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Animaux (MeSH)</term><term>Annotation de séquence moléculaire (MeSH)</term><term>Arabidopsis (génétique)</term><term>Duplication de gène (MeSH)</term><term>Génome (MeSH)</term><term>Génomique (méthodes)</term><term>Juglans (génétique)</term><term>Logiciel (MeSH)</term><term>Populus (génétique)</term><term>Transcriptome (MeSH)</term><term>Xenopus laevis (MeSH)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term><term>Juglans</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Arabidopsis</term><term>Juglans</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Genomics</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Génomique</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Gene Duplication</term><term>Genome</term><term>Molecular Sequence Annotation</term><term>Software</term><term>Transcriptome</term><term>Xenopus laevis</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Animaux</term><term>Annotation de séquence moléculaire</term><term>Duplication de gène</term><term>Génome</term><term>Logiciel</term><term>Transcriptome</term><term>Xenopus laevis</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>With the availability of well-assembled genomes of a growing number of organisms, identifying the bioinformatic basis of whole genome duplication (WGD) is a growing field of genomics. The most extant software for detecting footprints of WGDs has been restricted to a well-assembled genome. However, the massive poor quality genomes and the more accessible transcriptomes have been largely ignored, and in theoretically they are also likely to contribute to detect WGD using dS based method. Here, to resolve these problems, we have designed a universal and simple technical tool WGDdetector for detecting WGDs using either genome or transcriptome annotations in different organisms based on the widely used dS based method.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>We have constructed WGDdetector pipeline that integrates all analyses including gene family constructing, dS estimating and phasing, and outputting the dS values of each paralogs pairs processed with only one command. We further chose four species (Arabidopsis thaliana, Juglans regia, Populus trichocarpa and Xenopus laevis) representing herb, wood and animal, to test its practicability. Our final results showed a high degree of accuracy with the previous studies using both genome and transcriptome data.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSION</b></p><p>WGDdetector is not only reliable and stable for genome data, but also a new way to using the transcriptome data to obtain the correct dS distribution for detecting WGD. The source code is freely available, and is implemented in Windows and Linux operation system.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">30760221</PMID><DateCompleted><Year>2019</Year><Month>03</Month><Day>06</Day></DateCompleted><DateRevised><Year>2020</Year><Month>02</Month><Day>25</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2105</ISSN><JournalIssue CitedMedium="Internet"><Volume>20</Volume><Issue>1</Issue><PubDate><Year>2019</Year><Month>Feb</Month><Day>13</Day></PubDate></JournalIssue><Title>BMC bioinformatics</Title><ISOAbbreviation>BMC Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>WGDdetector: a pipeline for detecting whole genome duplication events using the genome or transcriptome annotations.</ArticleTitle><Pagination><MedlinePgn>75</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12859-019-2670-3</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">With the availability of well-assembled genomes of a growing number of organisms, identifying the bioinformatic basis of whole genome duplication (WGD) is a growing field of genomics. The most extant software for detecting footprints of WGDs has been restricted to a well-assembled genome. However, the massive poor quality genomes and the more accessible transcriptomes have been largely ignored, and in theoretically they are also likely to contribute to detect WGD using dS based method. Here, to resolve these problems, we have designed a universal and simple technical tool WGDdetector for detecting WGDs using either genome or transcriptome annotations in different organisms based on the widely used dS based method.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We have constructed WGDdetector pipeline that integrates all analyses including gene family constructing, dS estimating and phasing, and outputting the dS values of each paralogs pairs processed with only one command. We further chose four species (Arabidopsis thaliana, Juglans regia, Populus trichocarpa and Xenopus laevis) representing herb, wood and animal, to test its practicability. Our final results showed a high degree of accuracy with the previous studies using both genome and transcriptome data.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">WGDdetector is not only reliable and stable for genome data, but also a new way to using the transcriptome data to obtain the correct dS distribution for detecting WGD. The source code is freely available, and is implemented in Windows and Linux operation system.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Yongzhi</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>State Key Laboratory of Grassland Agro-Ecosystem, College of Life Sciences, Lanzhou University, Lanzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Ying</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Grassland Agro-Ecosystem, College of Life Sciences, Lanzhou University, Lanzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Qiao</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Grassland Agro-Ecosystem, College of Life Sciences, Lanzhou University, Lanzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sun</LastName><ForeName>Yongshuai</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China. sunyongshuai@xtbg.ac.cn.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lu</LastName><ForeName>Zhiqiang</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China. luzhiqiang@xtbg.ac.cn.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>NULL</GrantID><Agency>"1000 Youth Talents Plan" of Yunnan Province</Agency><Country></Country></Grant><Grant><GrantID>NULL</GrantID><Agency>CAS "Light of West China" Program</Agency><Country></Country></Grant><Grant><GrantID>NULL</GrantID><Agency>start-up research fund of Lanzhou University to YY</Agency><Country></Country></Grant><Grant><GrantID>No. B18114BN</GrantID><Agency>start-up research fund of XTBG to ZL</Agency><Country></Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>02</Month><Day>13</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Bioinformatics</MedlineTA><NlmUniqueID>100965194</NlmUniqueID><ISSNLinking>1471-2105</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017360" MajorTopicYN="N">Arabidopsis</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020440" MajorTopicYN="Y">Gene Duplication</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016678" MajorTopicYN="Y">Genome</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="N">Genomics</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D031324" MajorTopicYN="N">Juglans</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D058977" MajorTopicYN="N">Molecular Sequence Annotation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012984" MajorTopicYN="Y">Software</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059467" MajorTopicYN="Y">Transcriptome</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014982" MajorTopicYN="N">Xenopus laevis</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Genome</Keyword><Keyword MajorTopicYN="N">Transcriptome</Keyword><Keyword MajorTopicYN="N">Whole genome duplication</Keyword><Keyword MajorTopicYN="N">dS</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>10</Month><Day>02</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>02</Month><Day>05</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>2</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>2</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>3</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">30760221</ArticleId><ArticleId IdType="doi">10.1186/s12859-019-2670-3</ArticleId><ArticleId IdType="pii">10.1186/s12859-019-2670-3</ArticleId><ArticleId IdType="pmc">PMC6375192</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Plant Mol Biol. 2000 Jan;42(1):225-49</Citation><ArticleIdList><ArticleId IdType="pubmed">10688139</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2003 Feb;13(2):137-44</Citation><ArticleIdList><ArticleId IdType="pubmed">12566392</ArticleId></ArticleIdList></Reference><Reference><Citation>J Struct Funct Genomics. 2003;3(1-4):117-29</Citation><ArticleIdList><ArticleId IdType="pubmed">12836691</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2004 Dec 12;20(18):3643-6</Citation><ArticleIdList><ArticleId IdType="pubmed">15247098</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2004 Oct 21;431(7011):946-57</Citation><ArticleIdList><ArticleId IdType="pubmed">15496914</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2005 Apr 12;102(15):5454-9</Citation><ArticleIdList><ArticleId IdType="pubmed">15800040</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2006 Jul 1;22(13):1658-9</Citation><ArticleIdList><ArticleId IdType="pubmed">16731699</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W609-12</Citation><ArticleIdList><ArticleId IdType="pubmed">16845082</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2006 Sep;16(9):1159-68</Citation><ArticleIdList><ArticleId IdType="pubmed">16951135</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Bioinformatics. 2006 Oct 12;7:447</Citation><ArticleIdList><ArticleId IdType="pubmed">17038171</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 2007 Jun 29;316(5833):1862-6</Citation><ArticleIdList><ArticleId IdType="pubmed">17600208</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biol Evol. 2008 Nov;25(11):2445-55</Citation><ArticleIdList><ArticleId IdType="pubmed">18728074</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2008 Dec;18(12):1944-54</Citation><ArticleIdList><ArticleId IdType="pubmed">18832442</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Bioinformatics. 2009 Dec 15;10:421</Citation><ArticleIdList><ArticleId IdType="pubmed">20003500</ArticleId></ArticleIdList></Reference><Reference><Citation>Curr Opin Plant Biol. 2010 Apr;13(2):153-9</Citation><ArticleIdList><ArticleId IdType="pubmed">20031477</ArticleId></ArticleIdList></Reference><Reference><Citation>Evol Bioinform Online. 2010 Oct 20;6:143-9</Citation><ArticleIdList><ArticleId IdType="pubmed">21079755</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2011 May 5;473(7345):97-100</Citation><ArticleIdList><ArticleId IdType="pubmed">21478875</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Biotechnol. 2011 May 15;29(7):644-52</Citation><ArticleIdList><ArticleId IdType="pubmed">21572440</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2012 Jan;40(2):e11</Citation><ArticleIdList><ArticleId IdType="pubmed">22102584</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2012 Apr;40(7):e49</Citation><ArticleIdList><ArticleId IdType="pubmed">22217600</ArticleId></ArticleIdList></Reference><Reference><Citation>Curr Opin Plant Biol. 2012 Apr;15(2):140-6</Citation><ArticleIdList><ArticleId IdType="pubmed">22480430</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biol Evol. 2013 Jan;30(1):177-90</Citation><ArticleIdList><ArticleId IdType="pubmed">22936721</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biol Evol. 2013 Apr;30(4):772-80</Citation><ArticleIdList><ArticleId IdType="pubmed">23329690</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2013 May 30;497(7451):579-84</Citation><ArticleIdList><ArticleId IdType="pubmed">23698360</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biol Evol. 2014 Mar;31(3):750-62</Citation><ArticleIdList><ArticleId IdType="pubmed">24361993</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2014 Aug;24(8):1334-47</Citation><ArticleIdList><ArticleId IdType="pubmed">24835588</ArticleId></ArticleIdList></Reference><Reference><Citation>Am J Bot. 2014 Jul 20;101(7):1057-1078</Citation><ArticleIdList><ArticleId IdType="pubmed">25049267</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biol Evol. 2014 Dec;31(12):3184-93</Citation><ArticleIdList><ArticleId IdType="pubmed">25158798</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biol Evol. 2015 Aug;32(8):2141-8</Citation><ArticleIdList><ArticleId IdType="pubmed">25908670</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Bioinformatics. 2015 Jul 10;16:218</Citation><ArticleIdList><ArticleId IdType="pubmed">26160651</ArticleId></ArticleIdList></Reference><Reference><Citation>J Exp Bot. 2015 Dec;66(22):6991-7003</Citation><ArticleIdList><ArticleId IdType="pubmed">26417017</ArticleId></ArticleIdList></Reference><Reference><Citation>Am J Bot. 2015 Nov;102(11):1753-6</Citation><ArticleIdList><ArticleId IdType="pubmed">26451037</ArticleId></ArticleIdList></Reference><Reference><Citation>Sci Adv. 2015 Nov 20;1(10):e1501084</Citation><ArticleIdList><ArticleId IdType="pubmed">26702445</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol Evol. 2016 Apr 11;8(4):1023-37</Citation><ArticleIdList><ArticleId IdType="pubmed">26988251</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant J. 2016 Sep;87(5):507-32</Citation><ArticleIdList><ArticleId IdType="pubmed">27145194</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Rev Genet. 2017 Jul;18(7):411-424</Citation><ArticleIdList><ArticleId IdType="pubmed">28502977</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Biotechnol. 2017 Nov;35(11):1026-1028</Citation><ArticleIdList><ArticleId IdType="pubmed">29035372</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Yang, Yongzhi" sort="Yang, Yongzhi" uniqKey="Yang Y" first="Yongzhi" last="Yang">Yongzhi Yang</name></noRegion><name sortKey="Chen, Qiao" sort="Chen, Qiao" uniqKey="Chen Q" first="Qiao" last="Chen">Qiao Chen</name><name sortKey="Li, Ying" sort="Li, Ying" uniqKey="Li Y" first="Ying" last="Li">Ying Li</name><name sortKey="Lu, Zhiqiang" sort="Lu, Zhiqiang" uniqKey="Lu Z" first="Zhiqiang" last="Lu">Zhiqiang Lu</name><name sortKey="Sun, Yongshuai" sort="Sun, Yongshuai" uniqKey="Sun Y" first="Yongshuai" last="Sun">Yongshuai Sun</name><name sortKey="Yang, Yongzhi" sort="Yang, Yongzhi" uniqKey="Yang Y" first="Yongzhi" last="Yang">Yongzhi Yang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Bois/explor/PoplarV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000640 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000640 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Bois
|area= PoplarV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:30760221
|texte= WGDdetector: a pipeline for detecting whole genome duplication events using the genome or transcriptome annotations.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:30760221" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a PoplarV1
| This area was generated with Dilib version V0.6.37. |  |