Characterization and evolution of conserved MicroRNA through duplication events in date palm (Phoenix dactylifera).
Identifieur interne : 002768 ( Main/Exploration ); précédent : 002767; suivant : 002769Characterization and evolution of conserved MicroRNA through duplication events in date palm (Phoenix dactylifera).
Auteurs : Yong Xiao [République populaire de Chine] ; Wei Xia ; Yaodong Yang ; Annaliese S. Mason ; Xintao Lei ; Zilong MaSource :
- PloS one [ 1932-6203 ] ; 2013.
Descripteurs français
- KwdFr :
- ARN des plantes (génétique), Alignement de séquences (MeSH), Arecaceae (génétique), Données de séquences moléculaires (MeSH), Duplications génomiques segmentaires (MeSH), Gènes de plante (MeSH), Génome végétal (MeSH), Phylogenèse (MeSH), Séquence nucléotidique (MeSH), microARN (génétique), Évolution moléculaire (MeSH).
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : MicroRNAs, RNA, Plant.
- genetics : Arecaceae.
- Base Sequence, Evolution, Molecular, Genes, Plant, Genome, Plant, Molecular Sequence Data, Phylogeny, Segmental Duplications, Genomic, Sequence Alignment.
Abstract
MicroRNAs (miRNAs) are important regulators of gene expression at the post-transcriptional level in a wide range of species. Highly conserved miRNAs regulate ancestral transcription factors common to all plants, and control important basic processes such as cell division and meristem function. We selected 21 conserved miRNA families to analyze the distribution and maintenance of miRNAs. Recently, the first genome sequence in Palmaceae was released: date palm (Phoenix dactylifera). We conducted a systematic miRNA analysis in date palm, computationally identifying and characterizing the distribution and duplication of conserved miRNAs in this species compared to other published plant genomes. A total of 81 miRNAs belonging to 18 miRNA families were identified in date palm. The majority of miRNAs in date palm and seven other well-studied plant species were located in intergenic regions and located 4 to 5 kb away from the nearest protein-coding genes. Sequence comparison showed that 67% of date palm miRNA members were present in duplicated segments, and that 135 pairs of miRNA-containing segments were duplicated in Arabidopsis, tomato, orange, rice, apple, poplar and soybean with a high similarity of non coding sequences between duplicated segments, indicating genomic duplication was a major force for expansion of conserved miRNAs. Duplicated miRNA pairs in date palm showed divergence in pre-miRNA sequence and in number of promoters, implying that these duplicated pairs may have undergone divergent evolution. Comparisons between date palm and the seven other plant species for the gain/loss of miR167 loci in an ancient segment shared between monocots and dicots suggested that these conserved miRNAs were highly influenced by and diverged as a result of genomic duplication events.
DOI: 10.1371/journal.pone.0071435
PubMed: 23951162
PubMed Central: PMC3738527
Affiliations:
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Mason</name></author><author><name sortKey="Lei, Xintao" sort="Lei, Xintao" uniqKey="Lei X" first="Xintao" last="Lei">Xintao Lei</name></author><author><name sortKey="Ma, Zilong" sort="Ma, Zilong" uniqKey="Ma Z" first="Zilong" last="Ma">Zilong Ma</name></author></analytic><series><title level="j">PloS one</title><idno type="eISSN">1932-6203</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Arecaceae (genetics)</term><term>Base Sequence (MeSH)</term><term>Evolution, Molecular (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Genome, Plant (MeSH)</term><term>MicroRNAs (genetics)</term><term>Molecular Sequence Data (MeSH)</term><term>Phylogeny (MeSH)</term><term>RNA, Plant (genetics)</term><term>Segmental Duplications, Genomic (MeSH)</term><term>Sequence Alignment (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN des plantes (génétique)</term><term>Alignement de séquences (MeSH)</term><term>Arecaceae (génétique)</term><term>Données de séquences moléculaires (MeSH)</term><term>Duplications génomiques segmentaires (MeSH)</term><term>Gènes de plante (MeSH)</term><term>Génome végétal (MeSH)</term><term>Phylogenèse (MeSH)</term><term>Séquence nucléotidique (MeSH)</term><term>microARN (génétique)</term><term>Évolution moléculaire (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>MicroRNAs</term><term>RNA, Plant</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arecaceae</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN des plantes</term><term>Arecaceae</term><term>microARN</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Evolution, Molecular</term><term>Genes, Plant</term><term>Genome, Plant</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Segmental Duplications, Genomic</term><term>Sequence Alignment</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Alignement de séquences</term><term>Données de séquences moléculaires</term><term>Duplications génomiques segmentaires</term><term>Gènes de plante</term><term>Génome végétal</term><term>Phylogenèse</term><term>Séquence nucléotidique</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">MicroRNAs (miRNAs) are important regulators of gene expression at the post-transcriptional level in a wide range of species. Highly conserved miRNAs regulate ancestral transcription factors common to all plants, and control important basic processes such as cell division and meristem function. We selected 21 conserved miRNA families to analyze the distribution and maintenance of miRNAs. Recently, the first genome sequence in Palmaceae was released: date palm (Phoenix dactylifera). We conducted a systematic miRNA analysis in date palm, computationally identifying and characterizing the distribution and duplication of conserved miRNAs in this species compared to other published plant genomes. A total of 81 miRNAs belonging to 18 miRNA families were identified in date palm. The majority of miRNAs in date palm and seven other well-studied plant species were located in intergenic regions and located 4 to 5 kb away from the nearest protein-coding genes. Sequence comparison showed that 67% of date palm miRNA members were present in duplicated segments, and that 135 pairs of miRNA-containing segments were duplicated in Arabidopsis, tomato, orange, rice, apple, poplar and soybean with a high similarity of non coding sequences between duplicated segments, indicating genomic duplication was a major force for expansion of conserved miRNAs. Duplicated miRNA pairs in date palm showed divergence in pre-miRNA sequence and in number of promoters, implying that these duplicated pairs may have undergone divergent evolution. Comparisons between date palm and the seven other plant species for the gain/loss of miR167 loci in an ancient segment shared between monocots and dicots suggested that these conserved miRNAs were highly influenced by and diverged as a result of genomic duplication events. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">23951162</PMID><DateCompleted><Year>2014</Year><Month>04</Month><Day>30</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>8</Volume><Issue>8</Issue><PubDate><Year>2013</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS One</ISOAbbreviation></Journal><ArticleTitle>Characterization and evolution of conserved MicroRNA through duplication events in date palm (Phoenix dactylifera).</ArticleTitle><Pagination><MedlinePgn>e71435</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0071435</ELocationID><Abstract><AbstractText>MicroRNAs (miRNAs) are important regulators of gene expression at the post-transcriptional level in a wide range of species. Highly conserved miRNAs regulate ancestral transcription factors common to all plants, and control important basic processes such as cell division and meristem function. We selected 21 conserved miRNA families to analyze the distribution and maintenance of miRNAs. Recently, the first genome sequence in Palmaceae was released: date palm (Phoenix dactylifera). We conducted a systematic miRNA analysis in date palm, computationally identifying and characterizing the distribution and duplication of conserved miRNAs in this species compared to other published plant genomes. A total of 81 miRNAs belonging to 18 miRNA families were identified in date palm. The majority of miRNAs in date palm and seven other well-studied plant species were located in intergenic regions and located 4 to 5 kb away from the nearest protein-coding genes. Sequence comparison showed that 67% of date palm miRNA members were present in duplicated segments, and that 135 pairs of miRNA-containing segments were duplicated in Arabidopsis, tomato, orange, rice, apple, poplar and soybean with a high similarity of non coding sequences between duplicated segments, indicating genomic duplication was a major force for expansion of conserved miRNAs. Duplicated miRNA pairs in date palm showed divergence in pre-miRNA sequence and in number of promoters, implying that these duplicated pairs may have undergone divergent evolution. Comparisons between date palm and the seven other plant species for the gain/loss of miR167 loci in an ancient segment shared between monocots and dicots suggested that these conserved miRNAs were highly influenced by and diverged as a result of genomic duplication events. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Xiao</LastName><ForeName>Yong</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Hainan Key Laboratory of Tropical Oil Crops Biology/Coconuts Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xia</LastName><ForeName>Wei</ForeName><Initials>W</Initials></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Yaodong</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Mason</LastName><ForeName>Annaliese S</ForeName><Initials>AS</Initials></Author><Author ValidYN="Y"><LastName>Lei</LastName><ForeName>Xintao</ForeName><Initials>X</Initials></Author><Author ValidYN="Y"><LastName>Ma</LastName><ForeName>Zilong</ForeName><Initials>Z</Initials></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>2013</Year><Month>08</Month><Day>08</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PLoS One</MedlineTA><NlmUniqueID>101285081</NlmUniqueID><ISSNLinking>1932-6203</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D035683">MicroRNAs</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018749">RNA, 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Mason</name><name sortKey="Xia, Wei" sort="Xia, Wei" uniqKey="Xia W" first="Wei" last="Xia">Wei Xia</name><name sortKey="Yang, Yaodong" sort="Yang, Yaodong" uniqKey="Yang Y" first="Yaodong" last="Yang">Yaodong Yang</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Xiao, Yong" sort="Xiao, Yong" uniqKey="Xiao Y" first="Yong" last="Xiao">Yong Xiao</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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