[Molecular evolution of Orf1 gene in plant LTR-retrotransposons].
Identifieur interne : 002415 ( Main/Exploration ); précédent : 002414; suivant : 002416[Molecular evolution of Orf1 gene in plant LTR-retrotransposons].
Auteurs : Jing Liu [République populaire de Chine] ; Jian-Chang Du [République populaire de Chine]Source :
- Yi chuan = Hereditas [ 0253-9772 ] ; 2013.
Descripteurs français
- KwdFr :
- Alignement de séquences (MeSH), Données de séquences moléculaires (MeSH), Génome végétal (MeSH), Phylogenèse (MeSH), Plantes (classification), Plantes (composition chimique), Plantes (génétique), Protéines végétales (composition chimique), Protéines végétales (génétique), Rétroéléments (MeSH), Séquence d'acides aminés (MeSH).
- MESH :
- composition chimique : Plantes, Protéines végétales.
- génétique : Plantes, Protéines végétales.
- Alignement de séquences, Données de séquences moléculaires, Génome végétal, Phylogenèse, Rétroéléments, Séquence d'acides aminés.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Plant Proteins.
- chemical , genetics : Plant Proteins.
- chemistry : Plants.
- classification : Plants.
- genetics : Plants.
- Amino Acid Sequence, Genome, Plant, Molecular Sequence Data, Phylogeny, Retroelements, Sequence Alignment.
Abstract
LTR-Retrotransposons are the major DNA components in plant genomes. They usually contain gag and pol, two genes necessary for transpositinal process. Our previous study on soybean genome annotation identified a SARE LTR-Retrotransposon family, which carries the third gene, Orf1. Using a bioinformatics approach, we here reported that 7 out of 33 sequenced genomes have some LTR-Retrotransposons with an extra Orf1 gene/gene fragment (approximately 1-2 kb) in the region between 5' LTR and gag gene, including Eucalyptus grandis, Populus trichocarpa, Gossypium raimondii, Glycine max, Lotus japonica, Linum usitatissimum, and Medicago truncatula. The majority of these elements were inserted into the genomes they reside within the last 3 million years, but their structures, frequencies, intensity, and activity in different host genomes are quite different. Phylogenetic analysis indicated that these unusual elements were clustered in a eudicot branch, suggesting that they may be generated in the evolution of some eudicot species. The relative conservation, transcriptional activity, and the presence of multiple potential conserved motifs suggest that Orf1 gene may still be functional.
DOI: 10.3724/sp.j.1005.2013.01117
PubMed: 24400486
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">[Molecular evolution of Orf1 gene in plant LTR-retrotransposons].</title><author><name sortKey="Liu, Jing" sort="Liu, Jing" uniqKey="Liu J" first="Jing" last="Liu">Jing Liu</name><affiliation wicri:level="1"><nlm:affiliation>Bioinformatics Group, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Nanjing 210014, China. liujing200809@163.com</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Bioinformatics Group, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Nanjing 210014</wicri:regionArea><wicri:noRegion>Nanjing 210014</wicri:noRegion></affiliation></author><author><name sortKey="Du, Jian Chang" sort="Du, Jian Chang" uniqKey="Du J" first="Jian-Chang" last="Du">Jian-Chang Du</name><affiliation wicri:level="1"><nlm:affiliation>Bioinformatics Group, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Nanjing 210014, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Bioinformatics Group, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Nanjing 210014</wicri:regionArea><wicri:noRegion>Nanjing 210014</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2013">2013</date><idno type="RBID">pubmed:24400486</idno><idno type="pmid">24400486</idno><idno type="doi">10.3724/sp.j.1005.2013.01117</idno><idno type="wicri:Area/Main/Corpus">002337</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">002337</idno><idno type="wicri:Area/Main/Curation">002337</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">002337</idno><idno type="wicri:Area/Main/Exploration">002337</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">[Molecular evolution of Orf1 gene in plant LTR-retrotransposons].</title><author><name sortKey="Liu, Jing" sort="Liu, Jing" uniqKey="Liu J" first="Jing" last="Liu">Jing Liu</name><affiliation wicri:level="1"><nlm:affiliation>Bioinformatics Group, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Nanjing 210014, China. liujing200809@163.com</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Bioinformatics Group, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Nanjing 210014</wicri:regionArea><wicri:noRegion>Nanjing 210014</wicri:noRegion></affiliation></author><author><name sortKey="Du, Jian Chang" sort="Du, Jian Chang" uniqKey="Du J" first="Jian-Chang" last="Du">Jian-Chang Du</name><affiliation wicri:level="1"><nlm:affiliation>Bioinformatics Group, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Nanjing 210014, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Bioinformatics Group, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Nanjing 210014</wicri:regionArea><wicri:noRegion>Nanjing 210014</wicri:noRegion></affiliation></author></analytic><series><title level="j">Yi chuan = Hereditas</title><idno type="ISSN">0253-9772</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Molecular Sequence Data (MeSH)</term><term>Phylogeny (MeSH)</term><term>Plant Proteins (chemistry)</term><term>Plant Proteins (genetics)</term><term>Plants (chemistry)</term><term>Plants (classification)</term><term>Plants (genetics)</term><term>Retroelements (MeSH)</term><term>Sequence Alignment (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Alignement de séquences (MeSH)</term><term>Données de séquences moléculaires (MeSH)</term><term>Génome végétal (MeSH)</term><term>Phylogenèse (MeSH)</term><term>Plantes (classification)</term><term>Plantes (composition chimique)</term><term>Plantes (génétique)</term><term>Protéines végétales (composition chimique)</term><term>Protéines végétales (génétique)</term><term>Rétroéléments (MeSH)</term><term>Séquence d'acides aminés (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Plant Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Plant Proteins</term></keywords><keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>Plants</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Plants</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Plantes</term><term>Protéines végétales</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Plants</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Plantes</term><term>Protéines végétales</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Genome, Plant</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Retroelements</term><term>Sequence Alignment</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Alignement de séquences</term><term>Données de séquences moléculaires</term><term>Génome végétal</term><term>Phylogenèse</term><term>Rétroéléments</term><term>Séquence d'acides aminés</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">LTR-Retrotransposons are the major DNA components in plant genomes. They usually contain gag and pol, two genes necessary for transpositinal process. Our previous study on soybean genome annotation identified a SARE LTR-Retrotransposon family, which carries the third gene, Orf1. Using a bioinformatics approach, we here reported that 7 out of 33 sequenced genomes have some LTR-Retrotransposons with an extra Orf1 gene/gene fragment (approximately 1-2 kb) in the region between 5' LTR and gag gene, including Eucalyptus grandis, Populus trichocarpa, Gossypium raimondii, Glycine max, Lotus japonica, Linum usitatissimum, and Medicago truncatula. The majority of these elements were inserted into the genomes they reside within the last 3 million years, but their structures, frequencies, intensity, and activity in different host genomes are quite different. Phylogenetic analysis indicated that these unusual elements were clustered in a eudicot branch, suggesting that they may be generated in the evolution of some eudicot species. The relative conservation, transcriptional activity, and the presence of multiple potential conserved motifs suggest that Orf1 gene may still be functional.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24400486</PMID><DateCompleted><Year>2014</Year><Month>02</Month><Day>11</Day></DateCompleted><DateRevised><Year>2019</Year><Month>09</Month><Day>23</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0253-9772</ISSN><JournalIssue CitedMedium="Print"><Volume>35</Volume><Issue>9</Issue><PubDate><Year>2013</Year><Month>Sep</Month></PubDate></JournalIssue><Title>Yi chuan = Hereditas</Title><ISOAbbreviation>Yi Chuan</ISOAbbreviation></Journal><ArticleTitle>[Molecular evolution of Orf1 gene in plant LTR-retrotransposons].</ArticleTitle><Pagination><MedlinePgn>1117-24</MedlinePgn></Pagination><Abstract><AbstractText>LTR-Retrotransposons are the major DNA components in plant genomes. They usually contain gag and pol, two genes necessary for transpositinal process. Our previous study on soybean genome annotation identified a SARE LTR-Retrotransposon family, which carries the third gene, Orf1. Using a bioinformatics approach, we here reported that 7 out of 33 sequenced genomes have some LTR-Retrotransposons with an extra Orf1 gene/gene fragment (approximately 1-2 kb) in the region between 5' LTR and gag gene, including Eucalyptus grandis, Populus trichocarpa, Gossypium raimondii, Glycine max, Lotus japonica, Linum usitatissimum, and Medicago truncatula. The majority of these elements were inserted into the genomes they reside within the last 3 million years, but their structures, frequencies, intensity, and activity in different host genomes are quite different. Phylogenetic analysis indicated that these unusual elements were clustered in a eudicot branch, suggesting that they may be generated in the evolution of some eudicot species. The relative conservation, transcriptional activity, and the presence of multiple potential conserved motifs suggest that Orf1 gene may still be functional.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Jing</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Bioinformatics Group, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Nanjing 210014, China. liujing200809@163.com</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Du</LastName><ForeName>Jian-Chang</ForeName><Initials>JC</Initials><AffiliationInfo><Affiliation>Bioinformatics Group, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Nanjing 210014, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>chi</Language><PublicationTypeList><PublicationType UI="D004740">English Abstract</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>China</Country><MedlineTA>Yi Chuan</MedlineTA><NlmUniqueID>9436478</NlmUniqueID><ISSNLinking>0253-9772</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018626">Retroelements</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="Y">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010944" MajorTopicYN="N">Plants</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018626" MajorTopicYN="Y">Retroelements</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016415" MajorTopicYN="N">Sequence Alignment</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2014</Year><Month>1</Month><Day>10</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2014</Year><Month>1</Month><Day>10</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2014</Year><Month>2</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">24400486</ArticleId><ArticleId IdType="doi">10.3724/sp.j.1005.2013.01117</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Liu, Jing" sort="Liu, Jing" uniqKey="Liu J" first="Jing" last="Liu">Jing Liu</name></noRegion><name sortKey="Du, Jian Chang" sort="Du, Jian Chang" uniqKey="Du J" first="Jian-Chang" last="Du">Jian-Chang Du</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 002415 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 002415 | 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:24400486
|texte= [Molecular evolution of Orf1 gene in plant LTR-retrotransposons].
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:24400486" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a PoplarV1
| This area was generated with Dilib version V0.6.37. |  |