Transcriptomic analysis of ‘Suli’ pear (Pyrus pyrifolia white pear group) buds during the dormancy by RNA-Seq
Identifieur interne : 001160 ( Main/Exploration ); précédent : 001159; suivant : 001161Transcriptomic analysis of ‘Suli’ pear (Pyrus pyrifolia white pear group) buds during the dormancy by RNA-Seq
Auteurs : Guoqin Liu [République populaire de Chine] ; Wanshun Li [République populaire de Chine] ; Penghua Zheng [République populaire de Chine] ; Tong Xu [République populaire de Chine] ; Lijuan Chen [République populaire de Chine] ; Dongfeng Liu [République populaire de Chine] ; Sayed Hussain [République populaire de Chine] ; Yuanwen Teng [République populaire de Chine]Source :
- BMC Genomics [ 1471-2164 ] ; 2012.
Abstract
Bud dormancy is a critical developmental process that allows perennial plants to survive unfavorable environmental conditions. Pear is one of the most important deciduous fruit trees in the world, but the mechanisms regulating bud dormancy in this species are unknown. Because genomic information for pear is currently unavailable, transcriptome and digital gene expression data for this species would be valuable resources to better understand the molecular and biological mechanisms regulating its bud dormancy.
We performed
The new transcriptomes offer comprehensive sequence and DGE profiling data for a dynamic view of transcriptomic variation during bud dormancy in pear. These data provided a basis for future studies of metabolism during bud dormancy in non-model but economically-important perennial species.
Url:
DOI: 10.1186/1471-2164-13-700
PubMed: 23234335
PubMed Central: 3562153
Affiliations:
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Horticultural Plant Growth, Development & Quality Improvement, Zhejiang University, Hangzhou, 310058,, Zhejiang Province</wicri:regionArea><orgName type="university">Université de Zhejiang</orgName><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">23234335</idno><idno type="pmc">3562153</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3562153</idno><idno type="RBID">PMC:3562153</idno><idno type="doi">10.1186/1471-2164-13-700</idno><date when="2012">2012</date><idno type="wicri:Area/Pmc/Corpus">000B17</idno><idno type="wicri:Area/Pmc/Curation">000B16</idno><idno type="wicri:Area/Pmc/Checkpoint">000B94</idno><idno type="wicri:Area/Ncbi/Merge">001173</idno><idno type="wicri:Area/Ncbi/Curation">001173</idno><idno type="wicri:Area/Ncbi/Checkpoint">001173</idno><idno 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Hangzhou, 310058,, Zhejiang Province</wicri:regionArea><orgName type="university">Université de Zhejiang</orgName><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="I2">College of Agriculture, Guizhou University, Guiyang, 550025,, Guizhou Province, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Agriculture, Guizhou University, Guiyang, 550025,, Guizhou Province</wicri:regionArea><wicri:noRegion>Guizhou Province</wicri:noRegion></affiliation></author><author><name sortKey="Li, Wanshun" sort="Li, Wanshun" uniqKey="Li W" first="Wanshun" last="Li">Wanshun Li</name><affiliation wicri:level="1"><nlm:aff id="I3">BGI-tech, Shenzhen, 518083,, Guangdong Province, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>BGI-tech, Shenzhen, 518083,, Guangdong Province</wicri:regionArea><wicri:noRegion>Guangdong Province</wicri:noRegion></affiliation></author><author><name sortKey="Zheng, Penghua" sort="Zheng, Penghua" uniqKey="Zheng P" first="Penghua" last="Zheng">Penghua Zheng</name><affiliation wicri:level="4"><nlm:aff id="I1">Department of Horticulture, The State Agricultural Ministry’s Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Zhejiang University, Hangzhou, 310058,, Zhejiang Province, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Horticulture, The State Agricultural Ministry’s Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Zhejiang University, Hangzhou, 310058,, Zhejiang Province</wicri:regionArea><orgName type="university">Université de Zhejiang</orgName><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName></affiliation></author><author><name sortKey="Xu, Tong" sort="Xu, Tong" uniqKey="Xu T" first="Tong" last="Xu">Tong Xu</name><affiliation wicri:level="1"><nlm:aff id="I3">BGI-tech, Shenzhen, 518083,, Guangdong Province, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>BGI-tech, Shenzhen, 518083,, Guangdong Province</wicri:regionArea><wicri:noRegion>Guangdong Province</wicri:noRegion></affiliation></author><author><name sortKey="Chen, Lijuan" sort="Chen, Lijuan" uniqKey="Chen L" first="Lijuan" last="Chen">Lijuan Chen</name><affiliation wicri:level="1"><nlm:aff id="I3">BGI-tech, Shenzhen, 518083,, Guangdong Province, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>BGI-tech, Shenzhen, 518083,, Guangdong Province</wicri:regionArea><wicri:noRegion>Guangdong Province</wicri:noRegion></affiliation></author><author><name sortKey="Liu, Dongfeng" sort="Liu, Dongfeng" uniqKey="Liu D" first="Dongfeng" last="Liu">Dongfeng Liu</name><affiliation wicri:level="4"><nlm:aff id="I1">Department of Horticulture, The State Agricultural Ministry’s Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Zhejiang University, Hangzhou, 310058,, Zhejiang Province, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Horticulture, The State Agricultural Ministry’s Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Zhejiang University, Hangzhou, 310058,, Zhejiang Province</wicri:regionArea><orgName type="university">Université de Zhejiang</orgName><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName></affiliation></author><author><name sortKey="Hussain, Sayed" sort="Hussain, Sayed" uniqKey="Hussain S" first="Sayed" last="Hussain">Sayed Hussain</name><affiliation wicri:level="4"><nlm:aff id="I1">Department of Horticulture, The State Agricultural Ministry’s Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Zhejiang University, Hangzhou, 310058,, Zhejiang Province, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Horticulture, The State Agricultural Ministry’s Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Zhejiang University, Hangzhou, 310058,, Zhejiang Province</wicri:regionArea><orgName type="university">Université de Zhejiang</orgName><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName></affiliation></author><author><name sortKey="Teng, Yuanwen" sort="Teng, Yuanwen" uniqKey="Teng Y" first="Yuanwen" last="Teng">Yuanwen Teng</name><affiliation wicri:level="4"><nlm:aff id="I1">Department of Horticulture, The State Agricultural Ministry’s Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Zhejiang University, Hangzhou, 310058,, Zhejiang Province, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Horticulture, The State Agricultural Ministry’s Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Zhejiang University, Hangzhou, 310058,, Zhejiang Province</wicri:regionArea><orgName type="university">Université de Zhejiang</orgName><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Bud dormancy is a critical developmental process that allows perennial plants to survive unfavorable environmental conditions. Pear is one of the most important deciduous fruit trees in the world, but the mechanisms regulating bud dormancy in this species are unknown. Because genomic information for pear is currently unavailable, transcriptome and digital gene expression data for this species would be valuable resources to better understand the molecular and biological mechanisms regulating its bud dormancy.</p></sec><sec><title>Results</title><p>We performed <italic>de novo</italic> transcriptome assembly and digital gene expression (DGE) profiling analyses of ‘Suli’ pear (<italic>Pyrus pyrifolia</italic> white pear group) using the Illumina RNA-seq system. RNA-Seq generated approximately 100 M high-quality reads that were assembled into 69,393 unigenes (mean length = 853 bp), including 14,531 clusters and 34,194 singletons. A total of 51,448 (74.1%) unigenes were annotated using public protein databases with a cut-off E-value above 10<sup>-5</sup>. We mainly compared gene expression levels at four time-points during bud dormancy. Between Nov. 15 and Dec. 15, Dec. 15 and Jan. 15, and Jan. 15 and Feb. 15, 1,978, 1,024, and 3,468 genes were differentially expressed, respectively. Hierarchical clustering analysis arranged 190 significantly differentially-expressed genes into seven groups. Seven genes were randomly selected to confirm their expression levels using quantitative real-time PCR.</p></sec><sec><title>Conclusions</title><p>The new transcriptomes offer comprehensive sequence and DGE profiling data for a dynamic view of transcriptomic variation during bud dormancy in pear. These data provided a basis for future studies of metabolism during bud dormancy in non-model but economically-important perennial species.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Lang, G" uniqKey="Lang G">G Lang</name></author><author><name sortKey="Early, J" uniqKey="Early J">J Early</name></author><author><name sortKey="Martin, G" uniqKey="Martin G">G Martin</name></author><author><name sortKey="Darnell, R" uniqKey="Darnell R">R Darnell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Heide, O" uniqKey="Heide O">O Heide</name></author><author><name sortKey="Prestrud, A" uniqKey="Prestrud A">A Prestrud</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chao, Ws" uniqKey="Chao W">WS Chao</name></author><author><name sortKey="Serpe, Md" uniqKey="Serpe M">MD Serpe</name></author><author><name sortKey="Anderson, Jv" uniqKey="Anderson J">JV 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J" uniqKey="Dudley J">J Dudley</name></author><author><name sortKey="Nei, M" uniqKey="Nei M">M Nei</name></author><author><name sortKey="Kumar, S" uniqKey="Kumar S">S Kumar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhang, D" uniqKey="Zhang D">D Zhang</name></author><author><name sortKey="Yu, B" uniqKey="Yu B">B Yu</name></author><author><name sortKey="Bai, J" uniqKey="Bai J">J Bai</name></author><author><name sortKey="Qian, M" uniqKey="Qian M">M Qian</name></author><author><name sortKey="Shu, Q" uniqKey="Shu Q">Q Shu</name></author><author><name sortKey="Su, J" uniqKey="Su J">J Su</name></author><author><name sortKey="Teng, Y" uniqKey="Teng Y">Y Teng</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>République populaire de Chine</li></country><region><li>Zhejiang</li></region><settlement><li>Hangzhou</li></settlement><orgName><li>Université de Zhejiang</li></orgName></list><tree><country name="République populaire de Chine"><region name="Zhejiang"><name sortKey="Liu, Guoqin" sort="Liu, Guoqin" uniqKey="Liu G" first="Guoqin" last="Liu">Guoqin Liu</name></region><name sortKey="Chen, Lijuan" sort="Chen, Lijuan" uniqKey="Chen L" first="Lijuan" last="Chen">Lijuan Chen</name><name sortKey="Hussain, Sayed" sort="Hussain, Sayed" uniqKey="Hussain S" first="Sayed" last="Hussain">Sayed Hussain</name><name sortKey="Li, Wanshun" sort="Li, Wanshun" uniqKey="Li W" first="Wanshun" last="Li">Wanshun Li</name><name sortKey="Liu, Dongfeng" sort="Liu, Dongfeng" uniqKey="Liu D" first="Dongfeng" last="Liu">Dongfeng Liu</name><name sortKey="Liu, Guoqin" sort="Liu, Guoqin" uniqKey="Liu G" first="Guoqin" last="Liu">Guoqin Liu</name><name sortKey="Teng, Yuanwen" sort="Teng, Yuanwen" uniqKey="Teng Y" first="Yuanwen" last="Teng">Yuanwen Teng</name><name sortKey="Xu, Tong" sort="Xu, Tong" uniqKey="Xu T" first="Tong" last="Xu">Tong Xu</name><name sortKey="Zheng, Penghua" sort="Zheng, Penghua" uniqKey="Zheng P" first="Penghua" last="Zheng">Penghua Zheng</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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