A Global View of Transcriptome Dynamics During Male Floral Bud Development in Populus tomentosa.
Identifieur interne : 001090 ( Main/Exploration ); précédent : 001089; suivant : 001091A Global View of Transcriptome Dynamics During Male Floral Bud Development in Populus tomentosa.
Auteurs : Zhong Chen [République populaire de Chine] ; Pian Rao [République populaire de Chine] ; Xiaoyu Yang [République populaire de Chine] ; Xiaoxing Su [République populaire de Chine] ; Tianyun Zhao [République populaire de Chine] ; Kai Gao [République populaire de Chine] ; Xiong Yang [République populaire de Chine] ; Xinmin An [République populaire de Chine, États-Unis]Source :
- Scientific reports [ 2045-2322 ] ; 2018.
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English descriptors
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Abstract
To obtain a comprehensive overview of the dynamic transcriptome during male floral bud development in Populus tomentosa, high-throughput RNA-seq was conducted during eight flowering-related stages. Among the 109,212 de novo assembled unigenes, 6,959 were differentially expressed during the eight stages. The overrepresented classed of genes identified by Gene Ontology (GO) enrichment included 'response to environmental stimuli' and 'plant-type spore development'. One-third of the differentially expressed genes were transcription factors (TFs). Several genes and gene families were analyzed in depth, including MADS-box TFs, Squamosa promoter binding protein-like family, receptor-like kinases, FLOWERING LOCUS T/TERMINAL-FLOWER-LIKE 1 family, key genes involved in anther and tapetum development, as well as LEAFY, WUSCHEL and CONSTANS. The results provided new insights into the roles of these and other well known gene families during the annual flowering cycle. To explore the mechanisms regulating poplar flowering, a weighted gene co-expression network was constructed using 98 floral-related genes involved in flower meristem identity and flower development. Many modules of co-expressed genes and hub genes were identified, such as APETALA1 and HUA1. This work provides many new insights on the annual flowering cycle in a perennial plant, and a major new resource for plant biology and biotechnology.
DOI: 10.1038/s41598-017-18084-5
PubMed: 29335419
PubMed Central: PMC5768756
Affiliations:
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100083</wicri:regionArea><wicri:noRegion>100083</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China. zhongchen@bjfu.edu.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083</wicri:regionArea><wicri:noRegion>100083</wicri:noRegion></affiliation></author><author><name sortKey="Rao, Pian" sort="Rao, Pian" uniqKey="Rao P" first="Pian" last="Rao">Pian Rao</name><affiliation wicri:level="1"><nlm:affiliation>National 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Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083</wicri:regionArea><wicri:noRegion>100083</wicri:noRegion></affiliation></author><author><name sortKey="Su, Xiaoxing" sort="Su, Xiaoxing" uniqKey="Su X" first="Xiaoxing" last="Su">Xiaoxing Su</name><affiliation wicri:level="1"><nlm:affiliation>Berry Genomics Co., Ltd, Beijing, 100015, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Berry Genomics Co., Ltd, Beijing, 100015</wicri:regionArea><wicri:noRegion>100015</wicri:noRegion></affiliation></author><author><name sortKey="Zhao, Tianyun" sort="Zhao, Tianyun" uniqKey="Zhao T" first="Tianyun" last="Zhao">Tianyun Zhao</name><affiliation wicri:level="1"><nlm:affiliation>National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083</wicri:regionArea><wicri:noRegion>100083</wicri:noRegion></affiliation></author><author><name sortKey="Gao, Kai" sort="Gao, Kai" uniqKey="Gao K" first="Kai" last="Gao">Kai Gao</name><affiliation wicri:level="1"><nlm:affiliation>National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083</wicri:regionArea><wicri:noRegion>100083</wicri:noRegion></affiliation></author><author><name sortKey="Yang, Xiong" sort="Yang, Xiong" uniqKey="Yang X" first="Xiong" last="Yang">Xiong Yang</name><affiliation wicri:level="1"><nlm:affiliation>National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083</wicri:regionArea><wicri:noRegion>100083</wicri:noRegion></affiliation></author><author><name sortKey="An, Xinmin" sort="An, Xinmin" uniqKey="An X" first="Xinmin" last="An">Xinmin An</name><affiliation wicri:level="1"><nlm:affiliation>National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China. anxinmin@bjfu.edu.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083</wicri:regionArea><wicri:noRegion>100083</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, 97331, USA. anxinmin@bjfu.edu.cn.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, 97331</wicri:regionArea><wicri:noRegion>97331</wicri:noRegion></affiliation></author></analytic><series><title level="j">Scientific reports</title><idno type="eISSN">2045-2322</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Flowers (growth & development)</term><term>Gene Expression Profiling (MeSH)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Gene Regulatory Networks (MeSH)</term><term>High-Throughput Nucleotide Sequencing (MeSH)</term><term>Populus (growth & development)</term><term>Sequence Analysis, RNA (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Analyse de séquence d'ARN (MeSH)</term><term>Fleurs (croissance et développement)</term><term>Populus (croissance et développement)</term><term>Régulation de l'expression des gènes végétaux (MeSH)</term><term>Réseaux de régulation génique (MeSH)</term><term>Séquençage nucléotidique à haut débit (MeSH)</term></keywords><keywords scheme="MESH" qualifier="croissance et développement" xml:lang="fr"><term>Fleurs</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="growth & development" xml:lang="en"><term>Flowers</term><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Gene Expression Profiling</term><term>Gene Expression Regulation, Plant</term><term>Gene Regulatory Networks</term><term>High-Throughput Nucleotide Sequencing</term><term>Sequence Analysis, RNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Analyse de séquence d'ARN</term><term>Régulation de l'expression des gènes végétaux</term><term>Réseaux de régulation génique</term><term>Séquençage nucléotidique à haut débit</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">To obtain a comprehensive overview of the dynamic transcriptome during male floral bud development in Populus tomentosa, high-throughput RNA-seq was conducted during eight flowering-related stages. Among the 109,212 de novo assembled unigenes, 6,959 were differentially expressed during the eight stages. The overrepresented classed of genes identified by Gene Ontology (GO) enrichment included 'response to environmental stimuli' and 'plant-type spore development'. One-third of the differentially expressed genes were transcription factors (TFs). Several genes and gene families were analyzed in depth, including MADS-box TFs, Squamosa promoter binding protein-like family, receptor-like kinases, FLOWERING LOCUS T/TERMINAL-FLOWER-LIKE 1 family, key genes involved in anther and tapetum development, as well as LEAFY, WUSCHEL and CONSTANS. The results provided new insights into the roles of these and other well known gene families during the annual flowering cycle. To explore the mechanisms regulating poplar flowering, a weighted gene co-expression network was constructed using 98 floral-related genes involved in flower meristem identity and flower development. Many modules of co-expressed genes and hub genes were identified, such as APETALA1 and HUA1. This work provides many new insights on the annual flowering cycle in a perennial plant, and a major new resource for plant biology and biotechnology.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">29335419</PMID><DateCompleted><Year>2018</Year><Month>11</Month><Day>20</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>20</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">2045-2322</ISSN><JournalIssue CitedMedium="Internet"><Volume>8</Volume><Issue>1</Issue><PubDate><Year>2018</Year><Month>01</Month><Day>15</Day></PubDate></JournalIssue><Title>Scientific reports</Title><ISOAbbreviation>Sci Rep</ISOAbbreviation></Journal><ArticleTitle>A Global View of Transcriptome Dynamics During Male Floral Bud Development in Populus tomentosa.</ArticleTitle><Pagination><MedlinePgn>722</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1038/s41598-017-18084-5</ELocationID><Abstract><AbstractText>To obtain a comprehensive overview of the dynamic transcriptome during male floral bud development in Populus tomentosa, high-throughput RNA-seq was conducted during eight flowering-related stages. Among the 109,212 de novo assembled unigenes, 6,959 were differentially expressed during the eight stages. The overrepresented classed of genes identified by Gene Ontology (GO) enrichment included 'response to environmental stimuli' and 'plant-type spore development'. One-third of the differentially expressed genes were transcription factors (TFs). Several genes and gene families were analyzed in depth, including MADS-box TFs, Squamosa promoter binding protein-like family, receptor-like kinases, FLOWERING LOCUS T/TERMINAL-FLOWER-LIKE 1 family, key genes involved in anther and tapetum development, as well as LEAFY, WUSCHEL and CONSTANS. The results provided new insights into the roles of these and other well known gene families during the annual flowering cycle. To explore the mechanisms regulating poplar flowering, a weighted gene co-expression network was constructed using 98 floral-related genes involved in flower meristem identity and flower development. Many modules of co-expressed genes and hub genes were identified, such as APETALA1 and HUA1. This work provides many new insights on the annual flowering cycle in a perennial plant, and a major new resource for plant biology and biotechnology.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Zhong</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, 100083, China. zhongchen@bjfu.edu.cn.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China. zhongchen@bjfu.edu.cn.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rao</LastName><ForeName>Pian</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Xiaoyu</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Su</LastName><ForeName>Xiaoxing</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Berry Genomics Co., Ltd, Beijing, 100015, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhao</LastName><ForeName>Tianyun</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gao</LastName><ForeName>Kai</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Xiong</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>An</LastName><ForeName>Xinmin</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China. anxinmin@bjfu.edu.cn.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, 97331, USA. anxinmin@bjfu.edu.cn.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2018</Year><Month>01</Month><Day>15</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Sci Rep</MedlineTA><NlmUniqueID>101563288</NlmUniqueID><ISSNLinking>2045-2322</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D035264" MajorTopicYN="N">Flowers</DescriptorName><QualifierName UI="Q000254" MajorTopicYN="Y">growth & development</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="Y">Gene Expression Regulation, 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