PoplarV1, Main, Exploration, bibRecord, 003609

Genome-wide identification of lineage-specific genes in Arabidopsis, Oryza and Populus.

Identifieur interne : 003609 ( Main/Exploration ); précédent : 003608; suivant : 003610

Genome-wide identification of lineage-specific genes in Arabidopsis, Oryza and Populus.

Auteurs : Xiaohan Yang [États-Unis] ; Sara Jawdy ; Timothy J. Tschaplinski ; Gerald A. Tuskan

Source :

Genomics [ 1089-8646 ] ; 2009.

RBID : pubmed:19442640

Descripteurs français

KwdFr :
- Arabidopsis (anatomie et histologie), Arabidopsis (génétique), Génome végétal (MeSH), Oryza (anatomie et histologie), Oryza (génétique), Populus (anatomie et histologie), Populus (génétique), Régulation de l'expression des gènes végétaux (MeSH), Spécificité d'espèce (MeSH), Étude d'association pangénomique (MeSH).
MESH :
- anatomie et histologie : Arabidopsis, Oryza, Populus.
- génétique : Arabidopsis, Oryza, Populus.
- Génome végétal, Régulation de l'expression des gènes végétaux, Spécificité d'espèce, Étude d'association pangénomique.

English descriptors

KwdEn :
- Arabidopsis (anatomy & histology), Arabidopsis (genetics), Gene Expression Regulation, Plant (MeSH), Genome, Plant (MeSH), Genome-Wide Association Study (MeSH), Oryza (anatomy & histology), Oryza (genetics), Populus (anatomy & histology), Populus (genetics), Species Specificity (MeSH).
MESH :
- anatomy & histology : Arabidopsis, Oryza, Populus.
- genetics : Arabidopsis, Oryza, Populus.
- Gene Expression Regulation, Plant, Genome, Plant, Genome-Wide Association Study, Species Specificity.

Abstract

Protein sequences were compared among Arabidopsis, Oryza and Populus to identify differential gene (DG) sets that are in one but not the other two genomes. The DG sets were screened against a plant transcript database, the NR protein database and six newly-sequenced genomes (Carica, Glycine, Medicago, Sorghum, Vitis and Zea) to identify a set of species-specific genes (SS). Gene expression, protein motif and intron number were examined. 165, 638 and 109 SS genes were identified in Arabidopsis, Oryza and Populus, respectively. Some SS genes were preferentially expressed in flowers, roots, xylem and cambium or up-regulated by stress. Six conserved motifs in Arabidopsis and OryzaSS proteins were found in other distant lineages. The SS gene sets were enriched with intronless genes. The results reflect functional and/or anatomical differences between monocots and eudicots or between herbaceous and woody plants. The Populus-specific genes are candidates for carbon sequestration and biofuel research.

DOI: 10.1016/j.ygeno.2009.01.002
PubMed: 19442640

Affiliations:

Links toward previous steps (curation, corpus...)

to stream Main, to step Corpus: 003567
to stream Main, to step Curation: 003567

Le document en format XML

<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Genome-wide identification of lineage-specific genes in Arabidopsis, Oryza and Populus.</title>
<author><name sortKey="Yang, Xiaohan" sort="Yang, Xiaohan" uniqKey="Yang X" first="Xiaohan" last="Yang">Xiaohan Yang</name>
<affiliation wicri:level="2"><nlm:affiliation>Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422</wicri:regionArea>
<placeName><region type="state">Tennessee</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Jawdy, Sara" sort="Jawdy, Sara" uniqKey="Jawdy S" first="Sara" last="Jawdy">Sara Jawdy</name>
</author>
<author><name sortKey="Tschaplinski, Timothy J" sort="Tschaplinski, Timothy J" uniqKey="Tschaplinski T" first="Timothy J" last="Tschaplinski">Timothy J. Tschaplinski</name>
</author>
<author><name sortKey="Tuskan, Gerald A" sort="Tuskan, Gerald A" uniqKey="Tuskan G" first="Gerald A" last="Tuskan">Gerald A. Tuskan</name>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2009">2009</date>
<idno type="RBID">pubmed:19442640</idno>
<idno type="pmid">19442640</idno>
<idno type="doi">10.1016/j.ygeno.2009.01.002</idno>
<idno type="wicri:Area/Main/Corpus">003567</idno>
<idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">003567</idno>
<idno type="wicri:Area/Main/Curation">003567</idno>
<idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">003567</idno>
<idno type="wicri:Area/Main/Exploration">003567</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">Genome-wide identification of lineage-specific genes in Arabidopsis, Oryza and Populus.</title>
<author><name sortKey="Yang, Xiaohan" sort="Yang, Xiaohan" uniqKey="Yang X" first="Xiaohan" last="Yang">Xiaohan Yang</name>
<affiliation wicri:level="2"><nlm:affiliation>Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422</wicri:regionArea>
<placeName><region type="state">Tennessee</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Jawdy, Sara" sort="Jawdy, Sara" uniqKey="Jawdy S" first="Sara" last="Jawdy">Sara Jawdy</name>
</author>
<author><name sortKey="Tschaplinski, Timothy J" sort="Tschaplinski, Timothy J" uniqKey="Tschaplinski T" first="Timothy J" last="Tschaplinski">Timothy J. Tschaplinski</name>
</author>
<author><name sortKey="Tuskan, Gerald A" sort="Tuskan, Gerald A" uniqKey="Tuskan G" first="Gerald A" last="Tuskan">Gerald A. Tuskan</name>
</author>
</analytic>
<series><title level="j">Genomics</title>
<idno type="eISSN">1089-8646</idno>
<imprint><date when="2009" type="published">2009</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Arabidopsis (anatomy & histology)</term>
<term>Arabidopsis (genetics)</term>
<term>Gene Expression Regulation, Plant (MeSH)</term>
<term>Genome, Plant (MeSH)</term>
<term>Genome-Wide Association Study (MeSH)</term>
<term>Oryza (anatomy & histology)</term>
<term>Oryza (genetics)</term>
<term>Populus (anatomy & histology)</term>
<term>Populus (genetics)</term>
<term>Species Specificity (MeSH)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Arabidopsis (anatomie et histologie)</term>
<term>Arabidopsis (génétique)</term>
<term>Génome végétal (MeSH)</term>
<term>Oryza (anatomie et histologie)</term>
<term>Oryza (génétique)</term>
<term>Populus (anatomie et histologie)</term>
<term>Populus (génétique)</term>
<term>Régulation de l'expression des gènes végétaux (MeSH)</term>
<term>Spécificité d'espèce (MeSH)</term>
<term>Étude d'association pangénomique (MeSH)</term>
</keywords>
<keywords scheme="MESH" qualifier="anatomie et histologie" xml:lang="fr"><term>Arabidopsis</term>
<term>Oryza</term>
<term>Populus</term>
</keywords>
<keywords scheme="MESH" qualifier="anatomy & histology" xml:lang="en"><term>Arabidopsis</term>
<term>Oryza</term>
<term>Populus</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term>
<term>Oryza</term>
<term>Populus</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Arabidopsis</term>
<term>Oryza</term>
<term>Populus</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Gene Expression Regulation, Plant</term>
<term>Genome, Plant</term>
<term>Genome-Wide Association Study</term>
<term>Species Specificity</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Génome végétal</term>
<term>Régulation de l'expression des gènes végétaux</term>
<term>Spécificité d'espèce</term>
<term>Étude d'association pangénomique</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">Protein sequences were compared among Arabidopsis, Oryza and Populus to identify differential gene (DG) sets that are in one but not the other two genomes. The DG sets were screened against a plant transcript database, the NR protein database and six newly-sequenced genomes (Carica, Glycine, Medicago, Sorghum, Vitis and Zea) to identify a set of species-specific genes (SS). Gene expression, protein motif and intron number were examined. 165, 638 and 109 SS genes were identified in Arabidopsis, Oryza and Populus, respectively. Some SS genes were preferentially expressed in flowers, roots, xylem and cambium or up-regulated by stress. Six conserved motifs in Arabidopsis and OryzaSS proteins were found in other distant lineages. The SS gene sets were enriched with intronless genes. The results reflect functional and/or anatomical differences between monocots and eudicots or between herbaceous and woody plants. The Populus-specific genes are candidates for carbon sequestration and biofuel research.</div>
</front>
</TEI>
<pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">19442640</PMID>
<DateCompleted><Year>2009</Year>
<Month>08</Month>
<Day>03</Day>
</DateCompleted>
<DateRevised><Year>2015</Year>
<Month>11</Month>
<Day>19</Day>
</DateRevised>
<Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1089-8646</ISSN>
<JournalIssue CitedMedium="Internet"><Volume>93</Volume>
<Issue>5</Issue>
<PubDate><Year>2009</Year>
<Month>May</Month>
</PubDate>
</JournalIssue>
<Title>Genomics</Title>
<ISOAbbreviation>Genomics</ISOAbbreviation>
</Journal>
<ArticleTitle>Genome-wide identification of lineage-specific genes in Arabidopsis, Oryza and Populus.</ArticleTitle>
<Pagination><MedlinePgn>473-80</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1016/j.ygeno.2009.01.002</ELocationID>
<Abstract><AbstractText>Protein sequences were compared among Arabidopsis, Oryza and Populus to identify differential gene (DG) sets that are in one but not the other two genomes. The DG sets were screened against a plant transcript database, the NR protein database and six newly-sequenced genomes (Carica, Glycine, Medicago, Sorghum, Vitis and Zea) to identify a set of species-specific genes (SS). Gene expression, protein motif and intron number were examined. 165, 638 and 109 SS genes were identified in Arabidopsis, Oryza and Populus, respectively. Some SS genes were preferentially expressed in flowers, roots, xylem and cambium or up-regulated by stress. Six conserved motifs in Arabidopsis and OryzaSS proteins were found in other distant lineages. The SS gene sets were enriched with intronless genes. The results reflect functional and/or anatomical differences between monocots and eudicots or between herbaceous and woody plants. The Populus-specific genes are candidates for carbon sequestration and biofuel research.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Yang</LastName>
<ForeName>Xiaohan</ForeName>
<Initials>X</Initials>
<AffiliationInfo><Affiliation>Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Jawdy</LastName>
<ForeName>Sara</ForeName>
<Initials>S</Initials>
</Author>
<Author ValidYN="Y"><LastName>Tschaplinski</LastName>
<ForeName>Timothy J</ForeName>
<Initials>TJ</Initials>
</Author>
<Author ValidYN="Y"><LastName>Tuskan</LastName>
<ForeName>Gerald A</ForeName>
<Initials>GA</Initials>
</Author>
</AuthorList>
<Language>eng</Language>
<PublicationTypeList><PublicationType UI="D003160">Comparative Study</PublicationType>
<PublicationType UI="D016428">Journal Article</PublicationType>
<PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic"><Year>2009</Year>
<Month>01</Month>
<Day>29</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo><Country>United States</Country>
<MedlineTA>Genomics</MedlineTA>
<NlmUniqueID>8800135</NlmUniqueID>
<ISSNLinking>0888-7543</ISSNLinking>
</MedlineJournalInfo>
<CitationSubset>IM</CitationSubset>
<MeshHeadingList><MeshHeading><DescriptorName UI="D017360" MajorTopicYN="N">Arabidopsis</DescriptorName>
<QualifierName UI="Q000033" MajorTopicYN="N">anatomy & histology</QualifierName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D018506" MajorTopicYN="Y">Gene Expression Regulation, Plant</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D055106" MajorTopicYN="N">Genome-Wide Association Study</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D012275" MajorTopicYN="N">Oryza</DescriptorName>
<QualifierName UI="Q000033" MajorTopicYN="N">anatomy & histology</QualifierName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName>
<QualifierName UI="Q000033" MajorTopicYN="N">anatomy & histology</QualifierName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D013045" MajorTopicYN="N">Species Specificity</DescriptorName>
</MeshHeading>
</MeshHeadingList>
</MedlineCitation>
<PubmedData><History><PubMedPubDate PubStatus="received"><Year>2008</Year>
<Month>10</Month>
<Day>08</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="revised"><Year>2008</Year>
<Month>12</Month>
<Day>11</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="accepted"><Year>2009</Year>
<Month>01</Month>
<Day>15</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="entrez"><Year>2009</Year>
<Month>5</Month>
<Day>16</Day>
<Hour>9</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="pubmed"><Year>2009</Year>
<Month>5</Month>
<Day>16</Day>
<Hour>9</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline"><Year>2009</Year>
<Month>8</Month>
<Day>4</Day>
<Hour>9</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>ppublish</PublicationStatus>
<ArticleIdList><ArticleId IdType="pubmed">19442640</ArticleId>
<ArticleId IdType="pii">S0888-7543(09)00008-1</ArticleId>
<ArticleId IdType="doi">10.1016/j.ygeno.2009.01.002</ArticleId>
</ArticleIdList>
</PubmedData>
</pubmed>
<affiliations><list><country><li>États-Unis</li>
</country>
<region><li>Tennessee</li>
</region>
</list>
<tree><noCountry><name sortKey="Jawdy, Sara" sort="Jawdy, Sara" uniqKey="Jawdy S" first="Sara" last="Jawdy">Sara Jawdy</name>
<name sortKey="Tschaplinski, Timothy J" sort="Tschaplinski, Timothy J" uniqKey="Tschaplinski T" first="Timothy J" last="Tschaplinski">Timothy J. Tschaplinski</name>
<name sortKey="Tuskan, Gerald A" sort="Tuskan, Gerald A" uniqKey="Tuskan G" first="Gerald A" last="Tuskan">Gerald A. Tuskan</name>
</noCountry>
<country name="États-Unis"><region name="Tennessee"><name sortKey="Yang, Xiaohan" sort="Yang, Xiaohan" uniqKey="Yang X" first="Xiaohan" last="Yang">Xiaohan Yang</name>
</region>
</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 003609 | SxmlIndent | more

HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 003609 | 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:19442640
   |texte=   Genome-wide identification of lineage-specific genes in Arabidopsis, Oryza and Populus.
}}

Pour générer des pages wiki

HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i   -Sk "pubmed:19442640" \
       | HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd   \
       | NlmPubMed2Wicri -a PoplarV1

This area was generated with Dilib version V0.6.37.
Data generation: Wed Nov 18 12:07:19 2020. Site generation: Wed Nov 18 12:16:31 2020

	Serveur d'exploration sur le peuplier
	Attention, ce site est en cours de développement ! Attention, site généré par des moyens informatiques à partir de corpus bruts. Les informations ne sont donc pas validées.

Serveur d'exploration sur le peuplier

Genome-wide identification of lineage-specific genes in Arabidopsis, Oryza and Populus.

Genome-wide identification of lineage-specific genes in Arabidopsis, Oryza and Populus.

Source :

Descripteurs français

English descriptors

Abstract

Links toward previous steps (curation, corpus...)

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki