PoplarV1, Main, Exploration, bibRecord, 000682

The developmental dynamics of the Populus stem transcriptome.

Identifieur interne : 000682 ( Main/Exploration ); précédent : 000681; suivant : 000683

The developmental dynamics of the Populus stem transcriptome.

Auteurs : Qing Chao [République populaire de Chine] ; Zhi-Fang Gao [République populaire de Chine] ; Dong Zhang [République populaire de Chine] ; Biligen-Gaowa Zhao [République populaire de Chine] ; Feng-Qin Dong [République populaire de Chine] ; Chun-Xiang Fu [République populaire de Chine] ; Li-Jun Liu [République populaire de Chine] ; Bai-Chen Wang [République populaire de Chine]

Source :

Plant biotechnology journal [ 1467-7652 ] ; 2019.

RBID : pubmed:29851301

Descripteurs français

KwdFr :
- ARN long non codant (génétique), Analyse de profil d'expression de gènes (MeSH), Phylogenèse (MeSH), Populus (croissance et développement), Populus (génétique), Populus (métabolisme), Régulation de l'expression des gènes végétaux (génétique), Tiges de plante (anatomie et histologie), Tiges de plante (croissance et développement), Tiges de plante (métabolisme), Transcriptome (génétique), Épissage alternatif (génétique).
MESH :
- anatomie et histologie : Tiges de plante.
- croissance et développement : Populus, Tiges de plante.
- génétique : ARN long non codant, Populus, Régulation de l'expression des gènes végétaux, Transcriptome, Épissage alternatif.
- métabolisme : Populus, Tiges de plante.
- Analyse de profil d'expression de gènes, Phylogenèse.

English descriptors

KwdEn :
- Alternative Splicing (genetics), Gene Expression Profiling (MeSH), Gene Expression Regulation, Plant (genetics), Phylogeny (MeSH), Plant Stems (anatomy & histology), Plant Stems (growth & development), Plant Stems (metabolism), Populus (genetics), Populus (growth & development), Populus (metabolism), RNA, Long Noncoding (genetics), Transcriptome (genetics).
MESH :
- chemical , genetics : RNA, Long Noncoding.
- anatomy & histology : Plant Stems.
- genetics : Alternative Splicing, Gene Expression Regulation, Plant, Populus, Transcriptome.
- growth & development : Plant Stems, Populus.
- metabolism : Plant Stems, Populus.
- Gene Expression Profiling, Phylogeny.

Abstract

The Populus shoot undergoes primary growth (longitudinal growth) followed by secondary growth (radial growth), which produces biomass that is an important source of energy worldwide. We adopted joint PacBio Iso-Seq and RNA-seq analysis to identify differentially expressed transcripts along a developmental gradient from the shoot apex to the fifth internode of Populus Nanlin895. We obtained 87 150 full-length transcripts, including 2081 new isoforms and 62 058 new alternatively spliced isoforms, most of which were produced by intron retention, that were used to update the Populus annotation. Among these novel isoforms, there are 1187 long non-coding RNAs and 356 fusion genes. Using this annotation, we found 15 838 differentially expressed transcripts along the shoot developmental gradient, of which 1216 were transcription factors (TFs). Only a few of these genes were reported previously. The differential expression of these TFs suggests that they may play important roles in primary and secondary growth. AP2, ARF, YABBY and GRF TFs are highly expressed in the apex, whereas NAC, bZIP, PLATZ and HSF TFs are likely to be important for secondary growth. Overall, our findings provide evidence that long-read sequencing can complement short-read sequencing for cataloguing and quantifying eukaryotic transcripts and increase our understanding of the vital and dynamic process of shoot development.

DOI: 10.1111/pbi.12958
PubMed: 29851301
PubMed Central: PMC6330540

Affiliations:

Links toward previous steps (curation, corpus...)

to stream Main, to step Corpus: 000E07
to stream Main, to step Curation: 000E07

Le document en format XML

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<term>Gene Expression Profiling (MeSH)</term>
<term>Gene Expression Regulation, Plant (genetics)</term>
<term>Phylogeny (MeSH)</term>
<term>Plant Stems (anatomy & histology)</term>
<term>Plant Stems (growth & development)</term>
<term>Plant Stems (metabolism)</term>
<term>Populus (genetics)</term>
<term>Populus (growth & development)</term>
<term>Populus (metabolism)</term>
<term>RNA, Long Noncoding (genetics)</term>
<term>Transcriptome (genetics)</term>
</keywords>
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<term>Analyse de profil d'expression de gènes (MeSH)</term>
<term>Phylogenèse (MeSH)</term>
<term>Populus (croissance et développement)</term>
<term>Populus (génétique)</term>
<term>Populus (métabolisme)</term>
<term>Régulation de l'expression des gènes végétaux (génétique)</term>
<term>Tiges de plante (anatomie et histologie)</term>
<term>Tiges de plante (croissance et développement)</term>
<term>Tiges de plante (métabolisme)</term>
<term>Transcriptome (génétique)</term>
<term>Épissage alternatif (génétique)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA, Long Noncoding</term>
</keywords>
<keywords scheme="MESH" qualifier="anatomie et histologie" xml:lang="fr"><term>Tiges de plante</term>
</keywords>
<keywords scheme="MESH" qualifier="anatomy & histology" xml:lang="en"><term>Plant Stems</term>
</keywords>
<keywords scheme="MESH" qualifier="croissance et développement" xml:lang="fr"><term>Populus</term>
<term>Tiges de plante</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Alternative Splicing</term>
<term>Gene Expression Regulation, Plant</term>
<term>Populus</term>
<term>Transcriptome</term>
</keywords>
<keywords scheme="MESH" qualifier="growth & development" xml:lang="en"><term>Plant Stems</term>
<term>Populus</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN long non codant</term>
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<term>Régulation de l'expression des gènes végétaux</term>
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<term>Épissage alternatif</term>
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<keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Plant Stems</term>
<term>Populus</term>
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<term>Tiges de plante</term>
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<term>Phylogeny</term>
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<front><div type="abstract" xml:lang="en">The Populus shoot undergoes primary growth (longitudinal growth) followed by secondary growth (radial growth), which produces biomass that is an important source of energy worldwide. We adopted joint PacBio Iso-Seq and RNA-seq analysis to identify differentially expressed transcripts along a developmental gradient from the shoot apex to the fifth internode of Populus Nanlin895. We obtained 87 150 full-length transcripts, including 2081 new isoforms and 62 058 new alternatively spliced isoforms, most of which were produced by intron retention, that were used to update the Populus annotation. Among these novel isoforms, there are 1187 long non-coding RNAs and 356 fusion genes. Using this annotation, we found 15 838 differentially expressed transcripts along the shoot developmental gradient, of which 1216 were transcription factors (TFs). Only a few of these genes were reported previously. The differential expression of these TFs suggests that they may play important roles in primary and secondary growth. AP2, ARF, YABBY and GRF TFs are highly expressed in the apex, whereas NAC, bZIP, PLATZ and HSF TFs are likely to be important for secondary growth. Overall, our findings provide evidence that long-read sequencing can complement short-read sequencing for cataloguing and quantifying eukaryotic transcripts and increase our understanding of the vital and dynamic process of shoot development.</div>
</front>
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<Month>04</Month>
<Day>15</Day>
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<DateRevised><Year>2020</Year>
<Month>03</Month>
<Day>06</Day>
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<Month>01</Month>
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<Title>Plant biotechnology journal</Title>
<ISOAbbreviation>Plant Biotechnol J</ISOAbbreviation>
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<ArticleTitle>The developmental dynamics of the Populus stem transcriptome.</ArticleTitle>
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<Abstract><AbstractText>The Populus shoot undergoes primary growth (longitudinal growth) followed by secondary growth (radial growth), which produces biomass that is an important source of energy worldwide. We adopted joint PacBio Iso-Seq and RNA-seq analysis to identify differentially expressed transcripts along a developmental gradient from the shoot apex to the fifth internode of Populus Nanlin895. We obtained 87 150 full-length transcripts, including 2081 new isoforms and 62 058 new alternatively spliced isoforms, most of which were produced by intron retention, that were used to update the Populus annotation. Among these novel isoforms, there are 1187 long non-coding RNAs and 356 fusion genes. Using this annotation, we found 15 838 differentially expressed transcripts along the shoot developmental gradient, of which 1216 were transcription factors (TFs). Only a few of these genes were reported previously. The differential expression of these TFs suggests that they may play important roles in primary and secondary growth. AP2, ARF, YABBY and GRF TFs are highly expressed in the apex, whereas NAC, bZIP, PLATZ and HSF TFs are likely to be important for secondary growth. Overall, our findings provide evidence that long-read sequencing can complement short-read sequencing for cataloguing and quantifying eukaryotic transcripts and increase our understanding of the vital and dynamic process of shoot development.</AbstractText>
<CopyrightInformation>© 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.</CopyrightInformation>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Chao</LastName>
<ForeName>Qing</ForeName>
<Initials>Q</Initials>
<AffiliationInfo><Affiliation>Key Laboratory of Photobiology, Photosynthesis Research Center, Institute of Botany, Chinese Academy of Sciences, Beijing, China.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Gao</LastName>
<ForeName>Zhi-Fang</ForeName>
<Initials>ZF</Initials>
<AffiliationInfo><Affiliation>Key Laboratory of Photobiology, Photosynthesis Research Center, Institute of Botany, Chinese Academy of Sciences, Beijing, China.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>University of Chinese Academy of Sciences, Beijing, China.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Zhang</LastName>
<ForeName>Dong</ForeName>
<Initials>D</Initials>
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</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Zhao</LastName>
<ForeName>Biligen-Gaowa</ForeName>
<Initials>BG</Initials>
<AffiliationInfo><Affiliation>Key Laboratory of Photobiology, Photosynthesis Research Center, Institute of Botany, Chinese Academy of Sciences, Beijing, China.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>University of Chinese Academy of Sciences, Beijing, China.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Dong</LastName>
<ForeName>Feng-Qin</ForeName>
<Initials>FQ</Initials>
<AffiliationInfo><Affiliation>The Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Fu</LastName>
<ForeName>Chun-Xiang</ForeName>
<Initials>CX</Initials>
<Identifier Source="ORCID">0000-0003-2378-5122</Identifier>
<AffiliationInfo><Affiliation>Key Laboratory of Biofuels, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Liu</LastName>
<ForeName>Li-Jun</ForeName>
<Initials>LJ</Initials>
<AffiliationInfo><Affiliation>College of Forestry, Shandong Agricultural University, Tai-An, Shandong, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Wang</LastName>
<ForeName>Bai-Chen</ForeName>
<Initials>BC</Initials>
<Identifier Source="ORCID">0000-0003-0169-4393</Identifier>
<AffiliationInfo><Affiliation>Key Laboratory of Photobiology, Photosynthesis Research Center, Institute of Botany, Chinese Academy of Sciences, Beijing, China.</Affiliation>
</AffiliationInfo>
</Author>
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<Language>eng</Language>
<GrantList CompleteYN="Y"><Grant><GrantID>2013AA102701</GrantID>
<Agency>National High Technology Research and Development Program of China</Agency>
<Country>International</Country>
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<ArticleDate DateType="Electronic"><Year>2018</Year>
<Month>06</Month>
<Day>25</Day>
</ArticleDate>
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The developmental dynamics of the Populus stem transcriptome.

The developmental dynamics of the Populus stem transcriptome.

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