PTGBase: an integrated database to study tandem duplicated genes in plants
Identifieur interne : 001A46 ( Ncbi/Curation ); précédent : 001A45; suivant : 001A47PTGBase: an integrated database to study tandem duplicated genes in plants
Auteurs : Jingyin Yu [République populaire de Chine] ; Tao Ke [République populaire de Chine] ; Sadia Tehrim [République populaire de Chine] ; Fengming Sun [République populaire de Chine] ; Boshou Liao [République populaire de Chine] ; Wei Hua [République populaire de Chine]Source :
- Database: The Journal of Biological Databases and Curation [ 1758-0463 ] ; 2015.
Abstract
Tandem duplication is a wide-spread phenomenon in plant genomes and plays significant roles in evolution and adaptation to changing environments. Tandem duplicated genes related to certain functions will lead to the expansion of gene families and bring increase of gene dosage in the form of gene cluster arrays. Many tandem duplication events have been studied in plant genomes; yet, there is a surprising shortage of efforts to systematically present the integration of large amounts of information about publicly deposited tandem duplicated gene data across the plant kingdom. To address this shortcoming, we developed the first plant tandem duplicated genes database, PTGBase. It delivers the most comprehensive resource available to date, spanning 39 plant genomes, including model species and newly sequenced species alike. Across these genomes, 54 130 tandem duplicated gene clusters (129 652 genes) are presented in the database. Each tandem array, as well as its member genes, is characterized in complete detail. Tandem duplicated genes in PTGBase can be explored through browsing or searching by identifiers or keywords of functional annotation and sequence similarity. Users can download tandem duplicated gene arrays easily to any scale, up to the complete annotation data set for an entire plant genome. PTGBase will be updated regularly with newly sequenced plant species as they become available.
Url:
DOI: 10.1093/database/bav017
PubMed: 25797062
PubMed Central: 4369376
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wicri:level="1"><nlm:aff id="bav017-AFF1">Department of Life Science and Technology, Nanyang Normal University, Wolong Road, Nanyang 473061, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Life Science and Technology, Nanyang Normal University, Wolong Road, Nanyang 473061</wicri:regionArea><wicri:noRegion>Nanyang 473061</wicri:noRegion></affiliation></author><author><name sortKey="Tehrim, Sadia" sort="Tehrim, Sadia" uniqKey="Tehrim S" first="Sadia" last="Tehrim">Sadia Tehrim</name><affiliation wicri:level="1"><nlm:aff wicri:cut=" and" id="bav017-AFF1">The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops 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type="main">PTGBase: an integrated database to study tandem duplicated genes in plants</title><author><name sortKey="Yu, Jingyin" sort="Yu, Jingyin" uniqKey="Yu J" first="Jingyin" last="Yu">Jingyin Yu</name><affiliation wicri:level="1"><nlm:aff wicri:cut=" and" id="bav017-AFF1">The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062</wicri:regionArea><wicri:noRegion>Wuhan 430062</wicri:noRegion></affiliation></author><author><name sortKey="Ke, Tao" sort="Ke, Tao" uniqKey="Ke T" first="Tao" last="Ke">Tao Ke</name><affiliation wicri:level="1"><nlm:aff id="bav017-AFF1">Department of Life Science and Technology, Nanyang Normal University, Wolong Road, Nanyang 473061, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Life Science and Technology, Nanyang Normal University, Wolong Road, Nanyang 473061</wicri:regionArea><wicri:noRegion>Nanyang 473061</wicri:noRegion></affiliation></author><author><name sortKey="Tehrim, Sadia" sort="Tehrim, Sadia" uniqKey="Tehrim S" first="Sadia" last="Tehrim">Sadia Tehrim</name><affiliation wicri:level="1"><nlm:aff wicri:cut=" and" id="bav017-AFF1">The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062</wicri:regionArea><wicri:noRegion>Wuhan 430062</wicri:noRegion></affiliation></author><author><name sortKey="Sun, Fengming" sort="Sun, Fengming" uniqKey="Sun F" first="Fengming" last="Sun">Fengming Sun</name><affiliation wicri:level="1"><nlm:aff wicri:cut=" and" id="bav017-AFF1">The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062</wicri:regionArea><wicri:noRegion>Wuhan 430062</wicri:noRegion></affiliation></author><author><name sortKey="Liao, Boshou" sort="Liao, Boshou" uniqKey="Liao B" first="Boshou" last="Liao">Boshou Liao</name><affiliation wicri:level="1"><nlm:aff wicri:cut=" and" id="bav017-AFF1">The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062</wicri:regionArea><wicri:noRegion>Wuhan 430062</wicri:noRegion></affiliation></author><author><name sortKey="Hua, Wei" sort="Hua, Wei" uniqKey="Hua W" first="Wei" last="Hua">Wei Hua</name><affiliation wicri:level="1"><nlm:aff wicri:cut=" and" id="bav017-AFF1">The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062</wicri:regionArea><wicri:noRegion>Wuhan 430062</wicri:noRegion></affiliation></author></analytic><series><title level="j">Database: The Journal of Biological Databases and Curation</title><idno type="eISSN">1758-0463</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Tandem duplication is a wide-spread phenomenon in plant genomes and plays significant roles in evolution and adaptation to changing environments. Tandem duplicated genes related to certain functions will lead to the expansion of gene families and bring increase of gene dosage in the form of gene cluster arrays. Many tandem duplication events have been studied in plant genomes; yet, there is a surprising shortage of efforts to systematically present the integration of large amounts of information about publicly deposited tandem duplicated gene data across the plant kingdom. To address this shortcoming, we developed the first plant tandem duplicated genes database, PTGBase. It delivers the most comprehensive resource available to date, spanning 39 plant genomes, including model species and newly sequenced species alike. Across these genomes, 54 130 tandem duplicated gene clusters (129 652 genes) are presented in the database. Each tandem array, as well as its member genes, is characterized in complete detail. Tandem duplicated genes in PTGBase can be explored through browsing or searching by identifiers or keywords of functional annotation and sequence similarity. Users can download tandem duplicated gene arrays easily to any scale, up to the complete annotation data set for an entire plant genome. PTGBase will be updated regularly with newly sequenced plant species as they become available.</p><p><bold>Database URL:</bold><ext-link ext-link-type="uri" xlink:href="http://ocri-genomics.org/PTGBase/">http://ocri-genomics.org/PTGBase/</ext-link>.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Davies, T J" uniqKey="Davies T">T.J. Davies</name></author><author><name sortKey="Barraclough, T G" uniqKey="Barraclough T">T.G. Barraclough</name></author><author><name sortKey="Chase, M W" uniqKey="Chase M">M.W. Chase</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Waterston, R H" uniqKey="Waterston R">R.H. 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|area= OrangerV1
|flux= Ncbi
|étape= Curation
|type= RBID
|clé= PMC:4369376
|texte= PTGBase: an integrated database to study tandem duplicated genes in plants
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Ncbi/Curation/RBID.i -Sk "pubmed:25797062" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Ncbi/Curation/biblio.hfd \
| NlmPubMed2Wicri -a OrangerV1
| This area was generated with Dilib version V0.6.25. |  |