Genome-wide investigation of pentatricopeptide repeat gene family in poplar and their expression analysis in response to biotic and abiotic stresses.
Identifieur interne : 000E62 ( Main/Exploration ); précédent : 000E61; suivant : 000E63Genome-wide investigation of pentatricopeptide repeat gene family in poplar and their expression analysis in response to biotic and abiotic stresses.
Auteurs : Haitao Xing [République populaire de Chine] ; Xiaokang Fu [République populaire de Chine] ; Chen Yang [République populaire de Chine] ; Xiaofeng Tang [République populaire de Chine] ; Li Guo [République populaire de Chine] ; Chaofeng Li [République populaire de Chine] ; Changzheng Xu [République populaire de Chine] ; Keming Luo [République populaire de Chine]Source :
- Scientific reports [ 2045-2322 ] ; 2018.
Descripteurs français
- KwdFr :
- Analyse de profil d'expression de gènes (MeSH), Arabidopsis (génétique), Chromosomes de plante (métabolisme), Famille multigénique (génétique), Gènes de plante (génétique), Génome végétal (génétique), Motifs d'acides aminés (génétique), Oryza (génétique), Oryza (métabolisme), Phylogenèse (MeSH), Populus (génétique), Protéines d'Arabidopsis (génétique), Protéines d'Arabidopsis (métabolisme), Protéines végétales (génétique), Régulation de l'expression des gènes végétaux (génétique), Stress physiologique (génétique), Étude d'association pangénomique (MeSH).
- MESH :
- génétique : Arabidopsis, Famille multigénique, Gènes de plante, Génome végétal, Motifs d'acides aminés, Oryza, Populus, Protéines d'Arabidopsis, Protéines végétales, Régulation de l'expression des gènes végétaux, Stress physiologique.
- métabolisme : Chromosomes de plante, Oryza, Protéines d'Arabidopsis.
- Analyse de profil d'expression de gènes, Phylogenèse, Étude d'association pangénomique.
English descriptors
- KwdEn :
- Amino Acid Motifs (genetics), Arabidopsis (genetics), Arabidopsis Proteins (genetics), Arabidopsis Proteins (metabolism), Chromosomes, Plant (metabolism), Gene Expression Profiling (MeSH), Gene Expression Regulation, Plant (genetics), Genes, Plant (genetics), Genome, Plant (genetics), Genome-Wide Association Study (MeSH), Multigene Family (genetics), Oryza (genetics), Oryza (metabolism), Phylogeny (MeSH), Plant Proteins (genetics), Populus (genetics), Stress, Physiological (genetics).
- MESH :
- chemical , genetics : Arabidopsis Proteins, Plant Proteins.
- genetics : Amino Acid Motifs, Arabidopsis, Gene Expression Regulation, Plant, Genes, Plant, Genome, Plant, Multigene Family, Oryza, Populus, Stress, Physiological.
- chemical , metabolism : Arabidopsis Proteins, Chromosomes, Plant, Oryza.
- Gene Expression Profiling, Genome-Wide Association Study, Phylogeny.
Abstract
Pentatricopeptide repeat (PPR) proteins, which are characterized by tandem 30-40 amino acid sequence motifs, constitute of a large gene family in plants. Some PPR proteins have been identified to play important roles in organellar RNA metabolism and organ development in Arabidopsis and rice. However, functions of PPR genes in woody species remain largely unknown. Here, we identified and characterized a total of 626 PPR genes containing PPR motifs in the Populus trichocarpa genome. A comprehensive genome-wide analysis of the poplar PPR gene family was performed, including chromosomal location, phylogenetic relationships and gene duplication. Genome-wide transcriptomic analysis showed that 154 of the PtrPPR genes were induced by biotic and abiotic treatments, including Marssonina brunnea, salicylic acid (SA), methyl jasmonate (MeJA), mechanical wounding, cold and salinity stress. Quantitative RT-PCR analysis further investigated the expression profiles of 11 PtrPPR genes under different stresses. Our results contribute to a comprehensive understanding the roles of PPR proteins and provided an insight for improving the stress tolerance in poplar.
DOI: 10.1038/s41598-018-21269-1
PubMed: 29434322
PubMed Central: PMC5809412
Affiliations:
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Institute of Plateau Biology, Chinese Academy of Sciences, 810008, Xining</wicri:regionArea><wicri:noRegion>Xining</wicri:noRegion></affiliation></author><author><name sortKey="Xu, Changzheng" sort="Xu, Changzheng" uniqKey="Xu C" first="Changzheng" last="Xu">Changzheng Xu</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, 400715, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, 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uniqKey="Tang X" first="Xiaofeng" last="Tang">Xiaofeng Tang</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, 400715, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, 400715</wicri:regionArea><wicri:noRegion>400715</wicri:noRegion></affiliation></author><author><name sortKey="Guo, Li" sort="Guo, Li" uniqKey="Guo L" first="Li" last="Guo">Li Guo</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, 400715, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, 400715</wicri:regionArea><wicri:noRegion>400715</wicri:noRegion></affiliation></author><author><name sortKey="Li, Chaofeng" sort="Li, Chaofeng" uniqKey="Li C" first="Chaofeng" last="Li">Chaofeng Li</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 810008, Xining, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 810008, Xining</wicri:regionArea><wicri:noRegion>Xining</wicri:noRegion></affiliation></author><author><name sortKey="Xu, Changzheng" sort="Xu, Changzheng" uniqKey="Xu C" first="Changzheng" last="Xu">Changzheng Xu</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, 400715, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, 400715</wicri:regionArea><wicri:noRegion>400715</wicri:noRegion></affiliation></author><author><name sortKey="Luo, Keming" sort="Luo, Keming" uniqKey="Luo K" first="Keming" last="Luo">Keming Luo</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, 400715, China. kemingl@swu.edu.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, 400715</wicri:regionArea><wicri:noRegion>400715</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 810008, Xining, China. kemingl@swu.edu.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 810008, Xining</wicri:regionArea><wicri:noRegion>Xining</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>Amino Acid Motifs (genetics)</term><term>Arabidopsis (genetics)</term><term>Arabidopsis Proteins (genetics)</term><term>Arabidopsis Proteins (metabolism)</term><term>Chromosomes, Plant (metabolism)</term><term>Gene Expression Profiling (MeSH)</term><term>Gene Expression Regulation, Plant (genetics)</term><term>Genes, Plant (genetics)</term><term>Genome, Plant (genetics)</term><term>Genome-Wide Association Study (MeSH)</term><term>Multigene Family (genetics)</term><term>Oryza (genetics)</term><term>Oryza (metabolism)</term><term>Phylogeny (MeSH)</term><term>Plant Proteins (genetics)</term><term>Populus (genetics)</term><term>Stress, Physiological (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Arabidopsis (génétique)</term><term>Chromosomes de plante (métabolisme)</term><term>Famille multigénique (génétique)</term><term>Gènes de plante (génétique)</term><term>Génome végétal (génétique)</term><term>Motifs d'acides aminés (génétique)</term><term>Oryza (génétique)</term><term>Oryza (métabolisme)</term><term>Phylogenèse (MeSH)</term><term>Populus (génétique)</term><term>Protéines d'Arabidopsis (génétique)</term><term>Protéines d'Arabidopsis (métabolisme)</term><term>Protéines végétales (génétique)</term><term>Régulation de l'expression des gènes végétaux (génétique)</term><term>Stress physiologique (génétique)</term><term>Étude d'association pangénomique (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Arabidopsis Proteins</term><term>Plant Proteins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Amino Acid Motifs</term><term>Arabidopsis</term><term>Gene Expression Regulation, Plant</term><term>Genes, Plant</term><term>Genome, Plant</term><term>Multigene Family</term><term>Oryza</term><term>Populus</term><term>Stress, Physiological</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Arabidopsis</term><term>Famille multigénique</term><term>Gènes de plante</term><term>Génome végétal</term><term>Motifs d'acides aminés</term><term>Oryza</term><term>Populus</term><term>Protéines d'Arabidopsis</term><term>Protéines végétales</term><term>Régulation de l'expression des gènes végétaux</term><term>Stress physiologique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Arabidopsis Proteins</term><term>Chromosomes, Plant</term><term>Oryza</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Chromosomes de plante</term><term>Oryza</term><term>Protéines d'Arabidopsis</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Gene Expression Profiling</term><term>Genome-Wide Association Study</term><term>Phylogeny</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Phylogenèse</term><term>Étude d'association pangénomique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Pentatricopeptide repeat (PPR) proteins, which are characterized by tandem 30-40 amino acid sequence motifs, constitute of a large gene family in plants. Some PPR proteins have been identified to play important roles in organellar RNA metabolism and organ development in Arabidopsis and rice. However, functions of PPR genes in woody species remain largely unknown. Here, we identified and characterized a total of 626 PPR genes containing PPR motifs in the Populus trichocarpa genome. A comprehensive genome-wide analysis of the poplar PPR gene family was performed, including chromosomal location, phylogenetic relationships and gene duplication. Genome-wide transcriptomic analysis showed that 154 of the PtrPPR genes were induced by biotic and abiotic treatments, including Marssonina brunnea, salicylic acid (SA), methyl jasmonate (MeJA), mechanical wounding, cold and salinity stress. Quantitative RT-PCR analysis further investigated the expression profiles of 11 PtrPPR genes under different stresses. Our results contribute to a comprehensive understanding the roles of PPR proteins and provided an insight for improving the stress tolerance in poplar.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">29434322</PMID><DateCompleted><Year>2019</Year><Month>09</Month><Day>30</Day></DateCompleted><DateRevised><Year>2019</Year><Month>09</Month><Day>30</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>02</Month><Day>12</Day></PubDate></JournalIssue><Title>Scientific reports</Title><ISOAbbreviation>Sci Rep</ISOAbbreviation></Journal><ArticleTitle>Genome-wide investigation of pentatricopeptide repeat gene family in poplar and their expression analysis in response to biotic and abiotic stresses.</ArticleTitle><Pagination><MedlinePgn>2817</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1038/s41598-018-21269-1</ELocationID><Abstract><AbstractText>Pentatricopeptide repeat (PPR) proteins, which are characterized by tandem 30-40 amino acid sequence motifs, constitute of a large gene family in plants. Some PPR proteins have been identified to play important roles in organellar RNA metabolism and organ development in Arabidopsis and rice. However, functions of PPR genes in woody species remain largely unknown. Here, we identified and characterized a total of 626 PPR genes containing PPR motifs in the Populus trichocarpa genome. A comprehensive genome-wide analysis of the poplar PPR gene family was performed, including chromosomal location, phylogenetic relationships and gene duplication. Genome-wide transcriptomic analysis showed that 154 of the PtrPPR genes were induced by biotic and abiotic treatments, including Marssonina brunnea, salicylic acid (SA), methyl jasmonate (MeJA), mechanical wounding, cold and salinity stress. Quantitative RT-PCR analysis further investigated the expression profiles of 11 PtrPPR genes under different stresses. Our results contribute to a comprehensive understanding the roles of PPR proteins and provided an insight for improving the stress tolerance in poplar.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Xing</LastName><ForeName>Haitao</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, 400715, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fu</LastName><ForeName>Xiaokang</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, 400715, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Chen</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, 400715, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tang</LastName><ForeName>Xiaofeng</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, 400715, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Guo</LastName><ForeName>Li</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, 400715, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Chaofeng</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 810008, Xining, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Changzheng</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, 400715, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Luo</LastName><ForeName>Keming</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, 400715, China. kemingl@swu.edu.cn.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 810008, Xining, China. kemingl@swu.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>02</Month><Day>12</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Sci Rep</MedlineTA><NlmUniqueID>101563288</NlmUniqueID><ISSNLinking>2045-2322</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D029681">Arabidopsis Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="C538752">pentatricopeptide repeat protein, Arabidopsis</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D020816" MajorTopicYN="N">Amino Acid Motifs</DescriptorName><QualifierName UI="Q000235" 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UI="D017343" MajorTopicYN="N">Genes, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D055106" MajorTopicYN="N">Genome-Wide Association Study</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005810" MajorTopicYN="N">Multigene Family</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012275" MajorTopicYN="N">Oryza</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010940" 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uniqKey="Guo L" first="Li" last="Guo">Li Guo</name><name sortKey="Li, Chaofeng" sort="Li, Chaofeng" uniqKey="Li C" first="Chaofeng" last="Li">Chaofeng Li</name><name sortKey="Luo, Keming" sort="Luo, Keming" uniqKey="Luo K" first="Keming" last="Luo">Keming Luo</name><name sortKey="Luo, Keming" sort="Luo, Keming" uniqKey="Luo K" first="Keming" last="Luo">Keming Luo</name><name sortKey="Tang, Xiaofeng" sort="Tang, Xiaofeng" uniqKey="Tang X" first="Xiaofeng" last="Tang">Xiaofeng Tang</name><name sortKey="Xu, Changzheng" sort="Xu, Changzheng" uniqKey="Xu C" first="Changzheng" last="Xu">Changzheng Xu</name><name sortKey="Yang, Chen" sort="Yang, Chen" uniqKey="Yang C" first="Chen" last="Yang">Chen Yang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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