Expansion and diversification of the SET domain gene family following whole-genome duplications in Populus trichocarpa.
Identifieur interne : 002A93 ( Main/Exploration ); précédent : 002A92; suivant : 002A94Expansion and diversification of the SET domain gene family following whole-genome duplications in Populus trichocarpa.
Auteurs : Li Lei [République populaire de Chine] ; Shi-Liang Zhou ; Hong Ma ; Liang-Sheng ZhangSource :
- BMC evolutionary biology [ 1471-2148 ] ; 2012.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Histone-Lysine N-Methyltransferase.
- genetics : Populus.
- Evolution, Molecular, Gene Duplication, Gene Expression Profiling, Genome, Plant, Multigene Family, Phylogeny, Sequence Alignment.
Abstract
BACKGROUND
Histone lysine methylation modifies chromatin structure and regulates eukaryotic gene transcription and a variety of developmental and physiological processes. SET domain proteins are lysine methyltransferases containing the evolutionarily-conserved SET domain, which is known to be the catalytic domain.
RESULTS
We identified 59 SET genes in the Populus genome. Phylogenetic analyses of 106 SET genes from Populus and Arabidopsis supported the clustering of SET genes into six distinct subfamilies and identified 19 duplicated gene pairs in Populus. The chromosome locations of these gene pairs and the distribution of synonymous substitution rates showed that the expansion of the SET gene family might be caused by large-scale duplications in Populus. Comparison of gene structures and domain architectures of each duplicate pair indicated that divergence took place at the 3'- and 5'-terminal transcribed regions and at the N- and C-termini of the predicted proteins, respectively. Expression profile analysis of Populus SET genes suggested that most Populus SET genes were expressed widely, many with the highest expression in young leaves. In particular, the expression profiles of 12 of the 19 duplicated gene pairs fell into two types of expression patterns.
CONCLUSIONS
The 19 duplicated SET genes could have originated from whole genome duplication events. The differences in SET gene structure, domain architecture, and expression profiles in various tissues of Populus suggest that members of the SET gene family have a variety of developmental and physiological functions. Our study provides clues about the evolution of epigenetic regulation of chromatin structure and gene expression.
DOI: 10.1186/1471-2148-12-51
PubMed: 22497662
PubMed Central: PMC3402991
Affiliations:
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trichocarpa.</title><author><name sortKey="Lei, Li" sort="Lei, Li" uniqKey="Lei L" first="Li" last="Lei">Li Lei</name><affiliation wicri:level="1"><nlm:affiliation>1State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>1State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Zhou, Shi Liang" sort="Zhou, Shi Liang" uniqKey="Zhou S" first="Shi-Liang" last="Zhou">Shi-Liang Zhou</name></author><author><name sortKey="Ma, Hong" sort="Ma, Hong" uniqKey="Ma H" first="Hong" last="Ma">Hong Ma</name></author><author><name sortKey="Zhang, Liang Sheng" sort="Zhang, Liang Sheng" uniqKey="Zhang L" first="Liang-Sheng" last="Zhang">Liang-Sheng Zhang</name></author></analytic><series><title level="j">BMC evolutionary biology</title><idno type="eISSN">1471-2148</idno><imprint><date when="2012" type="published">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Evolution, Molecular (MeSH)</term><term>Gene Duplication (MeSH)</term><term>Gene Expression Profiling (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Histone-Lysine N-Methyltransferase (genetics)</term><term>Multigene Family (MeSH)</term><term>Phylogeny (MeSH)</term><term>Populus (genetics)</term><term>Sequence Alignment (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Alignement de séquences (MeSH)</term><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Duplication de gène (MeSH)</term><term>Famille multigénique (MeSH)</term><term>Génome végétal (MeSH)</term><term>Histone-lysine N-methyltransferase (génétique)</term><term>Phylogenèse (MeSH)</term><term>Populus (génétique)</term><term>Évolution moléculaire (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Histone-Lysine N-Methyltransferase</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Histone-lysine N-methyltransferase</term><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Evolution, Molecular</term><term>Gene Duplication</term><term>Gene Expression Profiling</term><term>Genome, Plant</term><term>Multigene Family</term><term>Phylogeny</term><term>Sequence Alignment</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Alignement de séquences</term><term>Analyse de profil d'expression de gènes</term><term>Duplication de gène</term><term>Famille multigénique</term><term>Génome végétal</term><term>Phylogenèse</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>Histone lysine methylation modifies chromatin structure and regulates eukaryotic gene transcription and a variety of developmental and physiological processes. SET domain proteins are lysine methyltransferases containing the evolutionarily-conserved SET domain, which is known to be the catalytic domain.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>We identified 59 SET genes in the Populus genome. Phylogenetic analyses of 106 SET genes from Populus and Arabidopsis supported the clustering of SET genes into six distinct subfamilies and identified 19 duplicated gene pairs in Populus. The chromosome locations of these gene pairs and the distribution of synonymous substitution rates showed that the expansion of the SET gene family might be caused by large-scale duplications in Populus. Comparison of gene structures and domain architectures of each duplicate pair indicated that divergence took place at the 3'- and 5'-terminal transcribed regions and at the N- and C-termini of the predicted proteins, respectively. Expression profile analysis of Populus SET genes suggested that most Populus SET genes were expressed widely, many with the highest expression in young leaves. In particular, the expression profiles of 12 of the 19 duplicated gene pairs fell into two types of expression patterns.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>The 19 duplicated SET genes could have originated from whole genome duplication events. The differences in SET gene structure, domain architecture, and expression profiles in various tissues of Populus suggest that members of the SET gene family have a variety of developmental and physiological functions. Our study provides clues about the evolution of epigenetic regulation of chromatin structure and gene expression.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">22497662</PMID><DateCompleted><Year>2012</Year><Month>10</Month><Day>15</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2148</ISSN><JournalIssue CitedMedium="Internet"><Volume>12</Volume><PubDate><Year>2012</Year><Month>Apr</Month><Day>12</Day></PubDate></JournalIssue><Title>BMC evolutionary biology</Title><ISOAbbreviation>BMC Evol Biol</ISOAbbreviation></Journal><ArticleTitle>Expansion and diversification of the SET domain gene family following whole-genome duplications in Populus trichocarpa.</ArticleTitle><Pagination><MedlinePgn>51</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2148-12-51</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Histone lysine methylation modifies chromatin structure and regulates eukaryotic gene transcription and a variety of developmental and physiological processes. SET domain proteins are lysine methyltransferases containing the evolutionarily-conserved SET domain, which is known to be the catalytic domain.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We identified 59 SET genes in the Populus genome. Phylogenetic analyses of 106 SET genes from Populus and Arabidopsis supported the clustering of SET genes into six distinct subfamilies and identified 19 duplicated gene pairs in Populus. The chromosome locations of these gene pairs and the distribution of synonymous substitution rates showed that the expansion of the SET gene family might be caused by large-scale duplications in Populus. Comparison of gene structures and domain architectures of each duplicate pair indicated that divergence took place at the 3'- and 5'-terminal transcribed regions and at the N- and C-termini of the predicted proteins, respectively. Expression profile analysis of Populus SET genes suggested that most Populus SET genes were expressed widely, many with the highest expression in young leaves. In particular, the expression profiles of 12 of the 19 duplicated gene pairs fell into two types of expression patterns.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">The 19 duplicated SET genes could have originated from whole genome duplication events. The differences in SET gene structure, domain architecture, and expression profiles in various tissues of Populus suggest that members of the SET gene family have a variety of developmental and physiological functions. 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uniqKey="Zhou S" first="Shi-Liang" last="Zhou">Shi-Liang Zhou</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Lei, Li" sort="Lei, Li" uniqKey="Lei L" first="Li" last="Lei">Li Lei</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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