Analysis of Alternative Splicing and Alternative Polyadenylation in Populus alba var. pyramidalis by Single-Molecular Long-Read Sequencing.
Identifieur interne : 000564 ( Main/Exploration ); précédent : 000563; suivant : 000565Analysis of Alternative Splicing and Alternative Polyadenylation in Populus alba var. pyramidalis by Single-Molecular Long-Read Sequencing.
Auteurs : Hongyin Hu [République populaire de Chine] ; Wenlu Yang [République populaire de Chine] ; Zeyu Zheng [République populaire de Chine] ; Zhimin Niu [République populaire de Chine] ; Yongzhi Yang [République populaire de Chine] ; Dongshi Wan [République populaire de Chine] ; Jianquan Liu [République populaire de Chine] ; Tao Ma [République populaire de Chine]Source :
- Frontiers in genetics [ 1664-8021 ] ; 2020.
Abstract
Poplars are worldwidely cultivated with ecologically and economically important value. Populus alba var. pyramidalis (= P. bolleana) is a main tree of the farmland shelter-belt system in the arid region of Northwest China due to its rapid growth, erect stems, and high biomass production. However, the full-length messenger RNA (mRNA) sequences and complete structure of P. alba var. pyramidalis remain unclear. In this study, using single-molecular real-time (SMRT) and next-generation high-throughput sequencing (NGS) platform, we sequenced transcripts from leaf, root, xylem, and phloem of P. alba var. pyramidalis, to obtain the full-length mRNA transcripts and annotate the complete structure. In total, 86,327 mapped full-length non-chimeric (FLNC) reads were identified, with 705 previously unannotated loci and 3,410 long noncoding RNAs (lncRNAs) and 174 fusion genes found. Alternative spicing (AS) events were detected in 7,536 genes, of which 4,652 genes had multiple AS events. A total of 10,213 alternative polyadenylation (APA) sites were identified, with two or more APA sites observed in 2,212 genes. Our transcriptome data provided the full-length sequences and gene isoforms of transcripts for P. alba var. pyramidalis, which will be helpful in improving our understanding for the genome annotation and gene structures of P. alba var. pyramidalis.
DOI: 10.3389/fgene.2020.00048
PubMed: 32117458
PubMed Central: PMC7020888
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Long-Read Sequencing.</title><author><name sortKey="Hu, Hongyin" sort="Hu, Hongyin" uniqKey="Hu H" first="Hongyin" last="Hu">Hongyin Hu</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School 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, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou</wicri:regionArea><wicri:noRegion>Lanzhou</wicri:noRegion></affiliation></author><author><name sortKey="Yang, Wenlu" sort="Yang, Wenlu" uniqKey="Yang W" first="Wenlu" last="Yang">Wenlu Yang</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu</wicri:regionArea><wicri:noRegion>Chengdu</wicri:noRegion></affiliation></author><author><name sortKey="Zheng, Zeyu" sort="Zheng, Zeyu" uniqKey="Zheng Z" first="Zeyu" last="Zheng">Zeyu Zheng</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School 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, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou</wicri:regionArea><wicri:noRegion>Lanzhou</wicri:noRegion></affiliation></author><author><name sortKey="Niu, Zhimin" sort="Niu, Zhimin" uniqKey="Niu Z" first="Zhimin" last="Niu">Zhimin Niu</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School 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, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou</wicri:regionArea><wicri:noRegion>Lanzhou</wicri:noRegion></affiliation></author><author><name sortKey="Yang, Yongzhi" sort="Yang, Yongzhi" uniqKey="Yang Y" first="Yongzhi" last="Yang">Yongzhi Yang</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School 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, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou</wicri:regionArea><wicri:noRegion>Lanzhou</wicri:noRegion></affiliation></author><author><name sortKey="Wan, Dongshi" sort="Wan, Dongshi" uniqKey="Wan D" first="Dongshi" last="Wan">Dongshi Wan</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School 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, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou</wicri:regionArea><wicri:noRegion>Lanzhou</wicri:noRegion></affiliation></author><author><name sortKey="Liu, Jianquan" sort="Liu, Jianquan" uniqKey="Liu J" first="Jianquan" last="Liu">Jianquan Liu</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School 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, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou</wicri:regionArea><wicri:noRegion>Lanzhou</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu</wicri:regionArea><wicri:noRegion>Chengdu</wicri:noRegion></affiliation></author><author><name sortKey="Ma, Tao" sort="Ma, Tao" uniqKey="Ma T" first="Tao" last="Ma">Tao Ma</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School 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, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou</wicri:regionArea><wicri:noRegion>Lanzhou</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu</wicri:regionArea><wicri:noRegion>Chengdu</wicri:noRegion></affiliation></author></analytic><series><title level="j">Frontiers in genetics</title><idno type="ISSN">1664-8021</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Poplars are worldwidely cultivated with ecologically and economically important value. <i>Populus alba</i> var. <i>pyramidalis</i> (= <i>P</i>. <i>bolleana</i>) is a main tree of the farmland shelter-belt system in the arid region of Northwest China due to its rapid growth, erect stems, and high biomass production. However, the full-length messenger RNA (mRNA) sequences and complete structure of <i>P. alba</i> var. <i>pyramidalis</i> remain unclear. In this study, using single-molecular real-time (SMRT) and next-generation high-throughput sequencing (NGS) platform, we sequenced transcripts from leaf, root, xylem, and phloem of <i>P. alba</i> var. <i>pyramidalis</i>, to obtain the full-length mRNA transcripts and annotate the complete structure. In total, 86,327 mapped full-length non-chimeric (FLNC) reads were identified, with 705 previously unannotated loci and 3,410 long noncoding RNAs (lncRNAs) and 174 fusion genes found. Alternative spicing (AS) events were detected in 7,536 genes, of which 4,652 genes had multiple AS events. A total of 10,213 alternative polyadenylation (APA) sites were identified, with two or more APA sites observed in 2,212 genes. Our transcriptome data provided the full-length sequences and gene isoforms of transcripts for <i>P. alba</i> var. <i>pyramidalis</i>, which will be helpful in improving our understanding for the genome annotation and gene structures of <i>P. alba</i> var. <i>pyramidalis</i>.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">32117458</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>28</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1664-8021</ISSN><JournalIssue CitedMedium="Print"><Volume>11</Volume><PubDate><Year>2020</Year></PubDate></JournalIssue><Title>Frontiers in genetics</Title><ISOAbbreviation>Front Genet</ISOAbbreviation></Journal><ArticleTitle>Analysis of Alternative Splicing and Alternative Polyadenylation in <i>Populus alba</i> var. <i>pyramidalis</i> by Single-Molecular Long-Read Sequencing.</ArticleTitle><Pagination><MedlinePgn>48</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3389/fgene.2020.00048</ELocationID><Abstract><AbstractText>Poplars are worldwidely cultivated with ecologically and economically important value. <i>Populus alba</i> var. <i>pyramidalis</i> (= <i>P</i>. <i>bolleana</i>) is a main tree of the farmland shelter-belt system in the arid region of Northwest China due to its rapid growth, erect stems, and high biomass production. However, the full-length messenger RNA (mRNA) sequences and complete structure of <i>P. alba</i> var. <i>pyramidalis</i> remain unclear. In this study, using single-molecular real-time (SMRT) and next-generation high-throughput sequencing (NGS) platform, we sequenced transcripts from leaf, root, xylem, and phloem of <i>P. alba</i> var. <i>pyramidalis</i>, to obtain the full-length mRNA transcripts and annotate the complete structure. In total, 86,327 mapped full-length non-chimeric (FLNC) reads were identified, with 705 previously unannotated loci and 3,410 long noncoding RNAs (lncRNAs) and 174 fusion genes found. Alternative spicing (AS) events were detected in 7,536 genes, of which 4,652 genes had multiple AS events. A total of 10,213 alternative polyadenylation (APA) sites were identified, with two or more APA sites observed in 2,212 genes. Our transcriptome data provided the full-length sequences and gene isoforms of transcripts for <i>P. alba</i> var. <i>pyramidalis</i>, which will be helpful in improving our understanding for the genome annotation and gene structures of <i>P. alba</i> var. <i>pyramidalis</i>.</AbstractText><CopyrightInformation>Copyright © 2020 Hu, Yang, Zheng, Niu, Yang, Wan, Liu and Ma.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Hu</LastName><ForeName>Hongyin</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Wenlu</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zheng</LastName><ForeName>Zeyu</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Niu</LastName><ForeName>Zhimin</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Yongzhi</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wan</LastName><ForeName>Dongshi</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Jianquan</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ma</LastName><ForeName>Tao</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>02</Month><Day>07</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Front Genet</MedlineTA><NlmUniqueID>101560621</NlmUniqueID><ISSNLinking>1664-8021</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Populus alba var. pyramidalis</Keyword><Keyword MajorTopicYN="N">alternative polyadenylation</Keyword><Keyword MajorTopicYN="N">alternative splicing</Keyword><Keyword MajorTopicYN="N">fusion genes</Keyword><Keyword MajorTopicYN="N">long non-coding ribonucleic acid</Keyword><Keyword MajorTopicYN="N">single molecule real-time technology sequencing</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>09</Month><Day>18</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>01</Month><Day>16</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>3</Month><Day>3</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>3</Month><Day>3</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>3</Month><Day>3</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32117458</ArticleId><ArticleId IdType="doi">10.3389/fgene.2020.00048</ArticleId><ArticleId 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Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Hu, Hongyin" sort="Hu, Hongyin" uniqKey="Hu H" first="Hongyin" last="Hu">Hongyin Hu</name></noRegion><name sortKey="Liu, Jianquan" sort="Liu, Jianquan" uniqKey="Liu J" first="Jianquan" last="Liu">Jianquan Liu</name><name sortKey="Liu, Jianquan" sort="Liu, Jianquan" uniqKey="Liu J" first="Jianquan" last="Liu">Jianquan Liu</name><name sortKey="Ma, Tao" sort="Ma, Tao" uniqKey="Ma T" first="Tao" last="Ma">Tao Ma</name><name sortKey="Ma, Tao" sort="Ma, Tao" uniqKey="Ma T" first="Tao" last="Ma">Tao Ma</name><name sortKey="Niu, Zhimin" sort="Niu, Zhimin" uniqKey="Niu Z" first="Zhimin" last="Niu">Zhimin Niu</name><name sortKey="Wan, Dongshi" sort="Wan, Dongshi" uniqKey="Wan D" first="Dongshi" last="Wan">Dongshi Wan</name><name sortKey="Yang, Wenlu" sort="Yang, Wenlu" uniqKey="Yang W" first="Wenlu" last="Yang">Wenlu Yang</name><name sortKey="Yang, Yongzhi" sort="Yang, Yongzhi" uniqKey="Yang Y" first="Yongzhi" last="Yang">Yongzhi Yang</name><name sortKey="Zheng, Zeyu" sort="Zheng, Zeyu" uniqKey="Zheng Z" first="Zeyu" last="Zheng">Zeyu Zheng</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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