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Comprehensive dissection of transcript and metabolite shifts during seed germination and post-germination stages in poplar.

Identifieur interne : 000A59 ( Main/Exploration ); précédent : 000A58; suivant : 000A60

Comprehensive dissection of transcript and metabolite shifts during seed germination and post-germination stages in poplar.

Auteurs : Chunpu Qu [République populaire de Chine] ; Zhuang Zuo [République populaire de Chine] ; Lina Cao [République populaire de Chine] ; Jiahuan Huang [République populaire de Chine] ; Xue Sun [République populaire de Chine] ; Peng Zhang [République populaire de Chine] ; Chengjun Yang [République populaire de Chine] ; Lixin Li [République populaire de Chine] ; Zhiru Xu [République populaire de Chine] ; Guanjun Liu [République populaire de Chine]

Source :

RBID : pubmed:31242858

Descripteurs français

English descriptors

Abstract

BACKGROUND

Seed germination, a complex, physiological-morphogenetic process, is a critical stage in the life cycle of plants. Biological changes in germinating seeds have not been investigated in poplar, a model woody plant.

RESULTS

In this study, we exploited next-generation sequencing and metabolomics analysis and uncovered a series of significantly different genes and metabolites at various stages of seed germination and post germination. The K-means method was used to identify multiple transcription factors, including AP2/EREBP, DOF, and YABBY, involved in specific seed germination and post-germination stages. A weighted gene coexpression network analysis revealed that cell wall, amino acid metabolism, and transport-related pathways were significantly enriched during stages 3 and 5, with no significant enrichment observed in primary metabolic processes such as glycolysis and the tricarboxylic acid cycle. A metabolomics analysis detected significant changes in intermediate metabolites in these primary metabolic processes, while a targeted correlation network analysis identified the gene family members most relevant to these changing metabolites.

CONCLUSIONS

Taken together, our results provide important insights into the molecular networks underlying poplar seed germination and post-germination processes. The targeted correlation network analysis approach developed in this study can be applied to search for key candidate genes in specific biochemical reactions and represents a new strategy for joint multiomics analyses.


DOI: 10.1186/s12870-019-1862-3
PubMed: 31242858
PubMed Central: PMC6595626


Affiliations:


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Le document en format XML

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<name sortKey="Sun, Xue" sort="Sun, Xue" uniqKey="Sun X" first="Xue" last="Sun">Xue Sun</name>
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<name sortKey="Zhang, Peng" sort="Zhang, Peng" uniqKey="Zhang P" first="Peng" last="Zhang">Peng Zhang</name>
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<nlm:affiliation>School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.</nlm:affiliation>
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<wicri:regionArea>School of Forestry, Northeast Forestry University, Harbin, 150040</wicri:regionArea>
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<name sortKey="Yang, Chengjun" sort="Yang, Chengjun" uniqKey="Yang C" first="Chengjun" last="Yang">Chengjun Yang</name>
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<nlm:affiliation>School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.</nlm:affiliation>
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<name sortKey="Li, Lixin" sort="Li, Lixin" uniqKey="Li L" first="Lixin" last="Li">Lixin Li</name>
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<name sortKey="Xu, Zhiru" sort="Xu, Zhiru" uniqKey="Xu Z" first="Zhiru" last="Xu">Zhiru Xu</name>
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<name sortKey="Liu, Guanjun" sort="Liu, Guanjun" uniqKey="Liu G" first="Guanjun" last="Liu">Guanjun Liu</name>
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<title level="j">BMC plant biology</title>
<idno type="eISSN">1471-2229</idno>
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<date when="2019" type="published">2019</date>
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<term>Gene Expression Profiling (MeSH)</term>
<term>Gene Expression Regulation, Plant (MeSH)</term>
<term>Germination (genetics)</term>
<term>Plant Proteins (genetics)</term>
<term>Plant Proteins (metabolism)</term>
<term>Populus (genetics)</term>
<term>Populus (growth & development)</term>
<term>Seeds (genetics)</term>
<term>Seeds (growth & development)</term>
<term>Transcription Factors (genetics)</term>
<term>Transcription Factors (metabolism)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr">
<term>Analyse de profil d'expression de gènes (MeSH)</term>
<term>Facteurs de transcription (génétique)</term>
<term>Facteurs de transcription (métabolisme)</term>
<term>Germination (génétique)</term>
<term>Graines (croissance et développement)</term>
<term>Graines (génétique)</term>
<term>Populus (croissance et développement)</term>
<term>Populus (génétique)</term>
<term>Protéines végétales (génétique)</term>
<term>Protéines végétales (métabolisme)</term>
<term>Régulation de l'expression des gènes végétaux (MeSH)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en">
<term>Plant Proteins</term>
<term>Transcription Factors</term>
</keywords>
<keywords scheme="MESH" qualifier="croissance et développement" xml:lang="fr">
<term>Graines</term>
<term>Populus</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en">
<term>Germination</term>
<term>Populus</term>
<term>Seeds</term>
</keywords>
<keywords scheme="MESH" qualifier="growth & development" xml:lang="en">
<term>Populus</term>
<term>Seeds</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr">
<term>Facteurs de transcription</term>
<term>Germination</term>
<term>Graines</term>
<term>Populus</term>
<term>Protéines végétales</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en">
<term>Plant Proteins</term>
<term>Transcription Factors</term>
</keywords>
<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr">
<term>Facteurs de transcription</term>
<term>Protéines végétales</term>
</keywords>
<keywords scheme="MESH" xml:lang="en">
<term>Gene Expression Profiling</term>
<term>Gene Expression Regulation, Plant</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr">
<term>Analyse de profil d'expression de gènes</term>
<term>Régulation de l'expression des gènes végétaux</term>
</keywords>
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<front>
<div type="abstract" xml:lang="en">
<p>
<b>BACKGROUND</b>
</p>
<p>Seed germination, a complex, physiological-morphogenetic process, is a critical stage in the life cycle of plants. Biological changes in germinating seeds have not been investigated in poplar, a model woody plant.</p>
</div>
<div type="abstract" xml:lang="en">
<p>
<b>RESULTS</b>
</p>
<p>In this study, we exploited next-generation sequencing and metabolomics analysis and uncovered a series of significantly different genes and metabolites at various stages of seed germination and post germination. The K-means method was used to identify multiple transcription factors, including AP2/EREBP, DOF, and YABBY, involved in specific seed germination and post-germination stages. A weighted gene coexpression network analysis revealed that cell wall, amino acid metabolism, and transport-related pathways were significantly enriched during stages 3 and 5, with no significant enrichment observed in primary metabolic processes such as glycolysis and the tricarboxylic acid cycle. A metabolomics analysis detected significant changes in intermediate metabolites in these primary metabolic processes, while a targeted correlation network analysis identified the gene family members most relevant to these changing metabolites.</p>
</div>
<div type="abstract" xml:lang="en">
<p>
<b>CONCLUSIONS</b>
</p>
<p>Taken together, our results provide important insights into the molecular networks underlying poplar seed germination and post-germination processes. The targeted correlation network analysis approach developed in this study can be applied to search for key candidate genes in specific biochemical reactions and represents a new strategy for joint multiomics analyses.</p>
</div>
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<Month>Jun</Month>
<Day>26</Day>
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<Title>BMC plant biology</Title>
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<AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Seed germination, a complex, physiological-morphogenetic process, is a critical stage in the life cycle of plants. Biological changes in germinating seeds have not been investigated in poplar, a model woody plant.</AbstractText>
<AbstractText Label="RESULTS" NlmCategory="RESULTS">In this study, we exploited next-generation sequencing and metabolomics analysis and uncovered a series of significantly different genes and metabolites at various stages of seed germination and post germination. The K-means method was used to identify multiple transcription factors, including AP2/EREBP, DOF, and YABBY, involved in specific seed germination and post-germination stages. A weighted gene coexpression network analysis revealed that cell wall, amino acid metabolism, and transport-related pathways were significantly enriched during stages 3 and 5, with no significant enrichment observed in primary metabolic processes such as glycolysis and the tricarboxylic acid cycle. A metabolomics analysis detected significant changes in intermediate metabolites in these primary metabolic processes, while a targeted correlation network analysis identified the gene family members most relevant to these changing metabolites.</AbstractText>
<AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">Taken together, our results provide important insights into the molecular networks underlying poplar seed germination and post-germination processes. The targeted correlation network analysis approach developed in this study can be applied to search for key candidate genes in specific biochemical reactions and represents a new strategy for joint multiomics analyses.</AbstractText>
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<ForeName>Chunpu</ForeName>
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<AffiliationInfo>
<Affiliation>School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.</Affiliation>
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<AffiliationInfo>
<Affiliation>School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.</Affiliation>
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<AffiliationInfo>
<Affiliation>School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.</Affiliation>
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<LastName>Sun</LastName>
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<AffiliationInfo>
<Affiliation>School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.</Affiliation>
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<ForeName>Lixin</ForeName>
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<LastName>Xu</LastName>
<ForeName>Zhiru</ForeName>
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<AffiliationInfo>
<Affiliation>School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China. liuguanjun2013@nefu.edu.cn.</Affiliation>
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<Language>eng</Language>
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<Grant>
<GrantID>2572017CA01</GrantID>
<Agency>the Fundamental Research Funds for the Central Universities</Agency>
<Country></Country>
</Grant>
<Grant>
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<Agency>National Natural Science Foundation of China</Agency>
<Country></Country>
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<Grant>
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<Country></Country>
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<name sortKey="Zuo, Zhuang" sort="Zuo, Zhuang" uniqKey="Zuo Z" first="Zhuang" last="Zuo">Zhuang Zuo</name>
<name sortKey="Zuo, Zhuang" sort="Zuo, Zhuang" uniqKey="Zuo Z" first="Zhuang" last="Zuo">Zhuang Zuo</name>
</country>
</tree>
</affiliations>
</record>

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