PoplarV1, Main, Exploration, bibRecord, 001542

Adaptive evolution and functional innovation of Populus-specific recently evolved microRNAs.

Identifieur interne : 001542 ( Main/Exploration ); précédent : 001541; suivant : 001543

Adaptive evolution and functional innovation of Populus-specific recently evolved microRNAs.

Auteurs : Jianbo Xie [République populaire de Chine] ; Xiaohui Yang [République populaire de Chine] ; Yuepeng Song [République populaire de Chine] ; Qingzhang Du [République populaire de Chine] ; Ying Li [République populaire de Chine] ; Jinhui Chen [République populaire de Chine] ; Deqiang Zhang [République populaire de Chine]

Source :

The New phytologist [ 1469-8137 ] ; 2017.

RBID : pubmed:27277139

Descripteurs français

English descriptors

KwdEn :
- Adaptation, Physiological (MeSH), Base Sequence (MeSH), Biocatalysis (MeSH), Conserved Sequence (genetics), Evolution, Molecular (MeSH), Gene Dosage (MeSH), Gene Duplication (MeSH), Gene Frequency (genetics), Genes, Plant (MeSH), MicroRNAs (genetics), MicroRNAs (metabolism), Multigene Family (MeSH), Open Reading Frames (genetics), Populus (genetics), Species Specificity (MeSH).
MESH :
- chemical , genetics : MicroRNAs.
- genetics : Conserved Sequence, Gene Frequency, Open Reading Frames, Populus.
- chemical , metabolism : MicroRNAs.
- Adaptation, Physiological, Base Sequence, Biocatalysis, Evolution, Molecular, Gene Dosage, Gene Duplication, Genes, Plant, Multigene Family, Species Specificity.

Abstract

Lineage-specific microRNAs (miRNAs) undergo rapid turnover during evolution; however, their origin and functional importance have remained controversial. Here, we examine the origin, evolution, and potential roles in local adaptation of Populus-specific miRNAs, which originated after the recent salicoid-specific, whole-genome duplication. RNA sequencing was used to generate extensive, comparable miRNA and gene expression data for six tissues. A natural population of Populus trichocarpa and closely related species were used to study the divergence rates, evolution, and adaptive variation of miRNAs. MiRNAs that originated in 5' untranslated regions had higher expression levels and their expression showed high correlation with their host genes. Compared with conserved miRNAs, a significantly higher proportion of Populus-specific miRNAs appear to target genes that were duplicated in salicoids. Examination of single nucleotide polymorphisms in Populus-specific miRNA precursors showed high amounts of population differentiation. We also characterized the newly emerged MIR6445 family, which could trigger the production of phased small interfering RNAs from NAC mRNAs, which encode a transcription factor with primary roles in a variety of plant developmental processes. Together, these observations provide evolutionary insights into the birth and potential roles of Populus-specific miRNAs in genome maintenance, local adaptation, and functional innovation.

DOI: 10.1111/nph.14046
PubMed: 27277139

Affiliations:

République populaire de Chine

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

to stream Main, to step Corpus: 001757
to stream Main, to step Curation: 001757

Le document en format XML

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<author><name sortKey="Chen, Jinhui" sort="Chen, Jinhui" uniqKey="Chen J" first="Jinhui" last="Chen">Jinhui Chen</name>
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<author><name sortKey="Zhang, Deqiang" sort="Zhang, Deqiang" uniqKey="Zhang D" first="Deqiang" last="Zhang">Deqiang Zhang</name>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Adaptation, Physiological (MeSH)</term>
<term>Base Sequence (MeSH)</term>
<term>Biocatalysis (MeSH)</term>
<term>Conserved Sequence (genetics)</term>
<term>Evolution, Molecular (MeSH)</term>
<term>Gene Dosage (MeSH)</term>
<term>Gene Duplication (MeSH)</term>
<term>Gene Frequency (genetics)</term>
<term>Genes, Plant (MeSH)</term>
<term>MicroRNAs (genetics)</term>
<term>MicroRNAs (metabolism)</term>
<term>Multigene Family (MeSH)</term>
<term>Open Reading Frames (genetics)</term>
<term>Populus (genetics)</term>
<term>Species Specificity (MeSH)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Adaptation physiologique (MeSH)</term>
<term>Biocatalyse (MeSH)</term>
<term>Cadres ouverts de lecture (génétique)</term>
<term>Dosage génique (MeSH)</term>
<term>Duplication de gène (MeSH)</term>
<term>Famille multigénique (MeSH)</term>
<term>Fréquence d'allèle (génétique)</term>
<term>Gènes de plante (MeSH)</term>
<term>Populus (génétique)</term>
<term>Spécificité d'espèce (MeSH)</term>
<term>Séquence conservée (génétique)</term>
<term>Séquence nucléotidique (MeSH)</term>
<term>microARN (génétique)</term>
<term>microARN (métabolisme)</term>
<term>Évolution moléculaire (MeSH)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>MicroRNAs</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Conserved Sequence</term>
<term>Gene Frequency</term>
<term>Open Reading Frames</term>
<term>Populus</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Cadres ouverts de lecture</term>
<term>Fréquence d'allèle</term>
<term>Populus</term>
<term>Séquence conservée</term>
<term>microARN</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>MicroRNAs</term>
</keywords>
<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>microARN</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Adaptation, Physiological</term>
<term>Base Sequence</term>
<term>Biocatalysis</term>
<term>Evolution, Molecular</term>
<term>Gene Dosage</term>
<term>Gene Duplication</term>
<term>Genes, Plant</term>
<term>Multigene Family</term>
<term>Species Specificity</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Adaptation physiologique</term>
<term>Biocatalyse</term>
<term>Dosage génique</term>
<term>Duplication de gène</term>
<term>Famille multigénique</term>
<term>Gènes de plante</term>
<term>Spécificité d'espèce</term>
<term>Séquence nucléotidique</term>
<term>Évolution moléculaire</term>
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<front><div type="abstract" xml:lang="en">Lineage-specific microRNAs (miRNAs) undergo rapid turnover during evolution; however, their origin and functional importance have remained controversial. Here, we examine the origin, evolution, and potential roles in local adaptation of Populus-specific miRNAs, which originated after the recent salicoid-specific, whole-genome duplication. RNA sequencing was used to generate extensive, comparable miRNA and gene expression data for six tissues. A natural population of Populus trichocarpa and closely related species were used to study the divergence rates, evolution, and adaptive variation of miRNAs. MiRNAs that originated in 5' untranslated regions had higher expression levels and their expression showed high correlation with their host genes. Compared with conserved miRNAs, a significantly higher proportion of Populus-specific miRNAs appear to target genes that were duplicated in salicoids. Examination of single nucleotide polymorphisms in Populus-specific miRNA precursors showed high amounts of population differentiation. We also characterized the newly emerged MIR6445 family, which could trigger the production of phased small interfering RNAs from NAC mRNAs, which encode a transcription factor with primary roles in a variety of plant developmental processes. Together, these observations provide evolutionary insights into the birth and potential roles of Populus-specific miRNAs in genome maintenance, local adaptation, and functional innovation.</div>
</front>
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<Month>02</Month>
<Day>14</Day>
</DateCompleted>
<DateRevised><Year>2020</Year>
<Month>09</Month>
<Day>30</Day>
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<JournalIssue CitedMedium="Internet"><Volume>213</Volume>
<Issue>1</Issue>
<PubDate><Year>2017</Year>
<Month>01</Month>
</PubDate>
</JournalIssue>
<Title>The New phytologist</Title>
<ISOAbbreviation>New Phytol</ISOAbbreviation>
</Journal>
<ArticleTitle>Adaptive evolution and functional innovation of Populus-specific recently evolved microRNAs.</ArticleTitle>
<Pagination><MedlinePgn>206-219</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1111/nph.14046</ELocationID>
<Abstract><AbstractText>Lineage-specific microRNAs (miRNAs) undergo rapid turnover during evolution; however, their origin and functional importance have remained controversial. Here, we examine the origin, evolution, and potential roles in local adaptation of Populus-specific miRNAs, which originated after the recent salicoid-specific, whole-genome duplication. RNA sequencing was used to generate extensive, comparable miRNA and gene expression data for six tissues. A natural population of Populus trichocarpa and closely related species were used to study the divergence rates, evolution, and adaptive variation of miRNAs. MiRNAs that originated in 5' untranslated regions had higher expression levels and their expression showed high correlation with their host genes. Compared with conserved miRNAs, a significantly higher proportion of Populus-specific miRNAs appear to target genes that were duplicated in salicoids. Examination of single nucleotide polymorphisms in Populus-specific miRNA precursors showed high amounts of population differentiation. We also characterized the newly emerged MIR6445 family, which could trigger the production of phased small interfering RNAs from NAC mRNAs, which encode a transcription factor with primary roles in a variety of plant developmental processes. Together, these observations provide evolutionary insights into the birth and potential roles of Populus-specific miRNAs in genome maintenance, local adaptation, and functional innovation.</AbstractText>
<CopyrightInformation>© 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.</CopyrightInformation>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Xie</LastName>
<ForeName>Jianbo</ForeName>
<Initials>J</Initials>
<AffiliationInfo><Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Yang</LastName>
<ForeName>Xiaohui</ForeName>
<Initials>X</Initials>
<AffiliationInfo><Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Song</LastName>
<ForeName>Yuepeng</ForeName>
<Initials>Y</Initials>
<AffiliationInfo><Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Du</LastName>
<ForeName>Qingzhang</ForeName>
<Initials>Q</Initials>
<AffiliationInfo><Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Li</LastName>
<ForeName>Ying</ForeName>
<Initials>Y</Initials>
<AffiliationInfo><Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Chen</LastName>
<ForeName>Jinhui</ForeName>
<Initials>J</Initials>
<AffiliationInfo><Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Zhang</LastName>
<ForeName>Deqiang</ForeName>
<Initials>D</Initials>
<AffiliationInfo><Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.</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>2016</Year>
<Month>06</Month>
<Day>09</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo><Country>England</Country>
<MedlineTA>New Phytol</MedlineTA>
<NlmUniqueID>9882884</NlmUniqueID>
<ISSNLinking>0028-646X</ISSNLinking>
</MedlineJournalInfo>
<ChemicalList><Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D035683">MicroRNAs</NameOfSubstance>
</Chemical>
</ChemicalList>
<CitationSubset>IM</CitationSubset>
<CommentsCorrectionsList><CommentsCorrections RefType="ErratumIn"><RefSource>New Phytol. 2017 Jan;213(1):470</RefSource>
<PMID Version="1">27891641</PMID>
</CommentsCorrections>
</CommentsCorrectionsList>
<MeshHeadingList><MeshHeading><DescriptorName UI="D000222" MajorTopicYN="Y">Adaptation, Physiological</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D055162" MajorTopicYN="N">Biocatalysis</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D017124" MajorTopicYN="N">Conserved Sequence</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D019143" MajorTopicYN="Y">Evolution, Molecular</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D018628" MajorTopicYN="N">Gene Dosage</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D020440" MajorTopicYN="N">Gene Duplication</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D005787" MajorTopicYN="N">Gene Frequency</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D017343" MajorTopicYN="N">Genes, Plant</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D035683" MajorTopicYN="N">MicroRNAs</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D005810" MajorTopicYN="N">Multigene Family</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D016366" MajorTopicYN="N">Open Reading Frames</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D013045" MajorTopicYN="N">Species Specificity</DescriptorName>
</MeshHeading>
</MeshHeadingList>
<KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Populus-specific</Keyword>
<Keyword MajorTopicYN="Y">functional innovation</Keyword>
<Keyword MajorTopicYN="Y">local adaptation</Keyword>
<Keyword MajorTopicYN="Y">micro-RNA (miRNA)</Keyword>
<Keyword MajorTopicYN="Y">whole-genome duplication (WGD)</Keyword>
</KeywordList>
</MedlineCitation>
<PubmedData><History><PubMedPubDate PubStatus="received"><Year>2016</Year>
<Month>04</Month>
<Day>11</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="accepted"><Year>2016</Year>
<Month>05</Month>
<Day>03</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="pubmed"><Year>2016</Year>
<Month>6</Month>
<Day>10</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline"><Year>2018</Year>
<Month>2</Month>
<Day>15</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="entrez"><Year>2016</Year>
<Month>6</Month>
<Day>10</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>ppublish</PublicationStatus>
<ArticleIdList><ArticleId IdType="pubmed">27277139</ArticleId>
<ArticleId IdType="doi">10.1111/nph.14046</ArticleId>
</ArticleIdList>
</PubmedData>
</pubmed>
<affiliations><list><country><li>République populaire de Chine</li>
</country>
</list>
<tree><country name="République populaire de Chine"><noRegion><name sortKey="Xie, Jianbo" sort="Xie, Jianbo" uniqKey="Xie J" first="Jianbo" last="Xie">Jianbo Xie</name>
</noRegion>
<name sortKey="Chen, Jinhui" sort="Chen, Jinhui" uniqKey="Chen J" first="Jinhui" last="Chen">Jinhui Chen</name>
<name sortKey="Chen, Jinhui" sort="Chen, Jinhui" uniqKey="Chen J" first="Jinhui" last="Chen">Jinhui Chen</name>
<name sortKey="Du, Qingzhang" sort="Du, Qingzhang" uniqKey="Du Q" first="Qingzhang" last="Du">Qingzhang Du</name>
<name sortKey="Du, Qingzhang" sort="Du, Qingzhang" uniqKey="Du Q" first="Qingzhang" last="Du">Qingzhang Du</name>
<name sortKey="Li, Ying" sort="Li, Ying" uniqKey="Li Y" first="Ying" last="Li">Ying Li</name>
<name sortKey="Li, Ying" sort="Li, Ying" uniqKey="Li Y" first="Ying" last="Li">Ying Li</name>
<name sortKey="Song, Yuepeng" sort="Song, Yuepeng" uniqKey="Song Y" first="Yuepeng" last="Song">Yuepeng Song</name>
<name sortKey="Song, Yuepeng" sort="Song, Yuepeng" uniqKey="Song Y" first="Yuepeng" last="Song">Yuepeng Song</name>
<name sortKey="Xie, Jianbo" sort="Xie, Jianbo" uniqKey="Xie J" first="Jianbo" last="Xie">Jianbo Xie</name>
<name sortKey="Yang, Xiaohui" sort="Yang, Xiaohui" uniqKey="Yang X" first="Xiaohui" last="Yang">Xiaohui Yang</name>
<name sortKey="Yang, Xiaohui" sort="Yang, Xiaohui" uniqKey="Yang X" first="Xiaohui" last="Yang">Xiaohui Yang</name>
<name sortKey="Zhang, Deqiang" sort="Zhang, Deqiang" uniqKey="Zhang D" first="Deqiang" last="Zhang">Deqiang Zhang</name>
<name sortKey="Zhang, Deqiang" sort="Zhang, Deqiang" uniqKey="Zhang D" first="Deqiang" last="Zhang">Deqiang Zhang</name>
</country>
</tree>
</affiliations>
</record>

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Adaptive evolution and functional innovation of Populus-specific recently evolved microRNAs.

Adaptive evolution and functional innovation of Populus-specific recently evolved microRNAs.

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