Evolution and divergence of SBP-box genes in land plants.
Identifieur interne : 001D84 ( Main/Exploration ); précédent : 001D83; suivant : 001D85Evolution and divergence of SBP-box genes in land plants.
Auteurs : Shu-Dong Zhang [République populaire de Chine] ; Li-Zhen Ling [République populaire de Chine] ; Ting-Shuang Yi [République populaire de Chine]Source :
- BMC genomics [ 1471-2164 ] ; 2015.
Descripteurs français
- KwdFr :
- Arabidopsis (génétique), Bryophyta (génétique), Duplication de gène (MeSH), Embryophyta (génétique), Famille multigénique (génétique), Génome végétal (MeSH), Oryza (génétique), Phylogenèse (MeSH), Populus (génétique), Protéines végétales (biosynthèse), Protéines végétales (génétique), Régulation de l'expression des gènes végétaux (MeSH), Séquence d'acides aminés (génétique), Zea mays (génétique), Évolution moléculaire (MeSH).
- MESH :
English descriptors
- KwdEn :
- Amino Acid Sequence (genetics), Arabidopsis (genetics), Bryophyta (genetics), Embryophyta (genetics), Evolution, Molecular (MeSH), Gene Duplication (MeSH), Gene Expression Regulation, Plant (MeSH), Genome, Plant (MeSH), Multigene Family (genetics), Oryza (genetics), Phylogeny (MeSH), Plant Proteins (biosynthesis), Plant Proteins (genetics), Populus (genetics), Zea mays (genetics).
- MESH :
- chemical , biosynthesis : Plant Proteins.
- genetics : Amino Acid Sequence, Arabidopsis, Bryophyta, Embryophyta, Multigene Family, Oryza, Plant Proteins, Populus, Zea mays.
- Evolution, Molecular, Gene Duplication, Gene Expression Regulation, Plant, Genome, Plant, Phylogeny.
Abstract
BACKGROUND
Squamosa promoter binding protein (SBP)-box family genes encode plant-specific transcription factors that control many important biological functions, including phase transition, inflorescence branching, fruit ripening, and copper homeostasis. Nevertheless, the evolutionary patterns of SBP-box genes and evolutionary forces driving them are still not well understood.
METHODS
104 SBP-box gene candidates of five representative land plants were obtained from Phytozome database (v10.3). Phylogenetic combined with gene structure analyses were used to identify SBP-box gene lineages in land plants. Gene copy number and the sequence and structure features were then compared among these different SBP-box lineages. Selection analysis, relative rate tests and expression divergence were finally used to interpret the evolutionary relationships and divergence of SBP-box genes in land plants.
RESULTS
We investigated 104 SBP-box genes from moss, Arabidopsis, poplar, rice, and maize. These genes are divided into group I and II, and the latter is further divided into two subgroups (subgroup II-1 and II-2) based on phylogenetic analysis. Interestingly, subgroup II-1 genes have similar sequence and structural features to group I genes, whereas subgroup II-2 genes exhibit intrinsic differences on these features, including high copy numbers and the presence of miR156/miR529 regulation. Further analyses indicate that subgroup II-1 genes are constrained by stronger purifying selection and evolve at a lower substitution rate than II-2 genes, just as group I genes do when compared to II genes. Among subgroup II-2 genes, miR156 targets evolve more rapidly than miR529 targets and experience comparatively relaxed purifying selection. These results suggest that group I and subgroup II-1 genes under strong selective constraint are conserved. By contrast, subgroup II-2 genes evolve under relaxed purifying selection and have diversified through gene copy duplications and changes in miR156/529 regulation, which might contribute to morphological diversifications of land plants.
CONCLUSIONS
Our results indicate that different evolutionary rates and selection strengths lead to differing evolutionary patterns in SBP-box genes in land plants, providing a guide for future functional diversity analyses of these genes.
DOI: 10.1186/s12864-015-1998-y
PubMed: 26467431
PubMed Central: PMC4606839
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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tingshuangyi@mail.kib.ac.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Germplasm Bank of Wild Species, Kunming Institute of Botany of the Chinese Academy of Sciences, Kunming, 650201</wicri:regionArea><wicri:noRegion>650201</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence (genetics)</term><term>Arabidopsis (genetics)</term><term>Bryophyta (genetics)</term><term>Embryophyta (genetics)</term><term>Evolution, Molecular (MeSH)</term><term>Gene Duplication (MeSH)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Multigene Family (genetics)</term><term>Oryza (genetics)</term><term>Phylogeny (MeSH)</term><term>Plant Proteins (biosynthesis)</term><term>Plant Proteins (genetics)</term><term>Populus (genetics)</term><term>Zea mays (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Arabidopsis (génétique)</term><term>Bryophyta (génétique)</term><term>Duplication de gène (MeSH)</term><term>Embryophyta (génétique)</term><term>Famille multigénique (génétique)</term><term>Génome végétal (MeSH)</term><term>Oryza (génétique)</term><term>Phylogenèse (MeSH)</term><term>Populus (génétique)</term><term>Protéines végétales (biosynthèse)</term><term>Protéines végétales (génétique)</term><term>Régulation de l'expression des gènes végétaux (MeSH)</term><term>Séquence d'acides aminés (génétique)</term><term>Zea mays (génétique)</term><term>Évolution moléculaire (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="biosynthesis" xml:lang="en"><term>Plant Proteins</term></keywords><keywords scheme="MESH" qualifier="biosynthèse" xml:lang="fr"><term>Protéines végétales</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Amino Acid Sequence</term><term>Arabidopsis</term><term>Bryophyta</term><term>Embryophyta</term><term>Multigene Family</term><term>Oryza</term><term>Plant Proteins</term><term>Populus</term><term>Zea mays</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Arabidopsis</term><term>Bryophyta</term><term>Embryophyta</term><term>Famille multigénique</term><term>Oryza</term><term>Populus</term><term>Protéines végétales</term><term>Séquence d'acides aminés</term><term>Zea mays</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Evolution, Molecular</term><term>Gene Duplication</term><term>Gene Expression Regulation, Plant</term><term>Genome, Plant</term><term>Phylogeny</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Duplication de gène</term><term>Génome végétal</term><term>Phylogenèse</term><term>Régulation de l'expression des gènes végétaux</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>Squamosa promoter binding protein (SBP)-box family genes encode plant-specific transcription factors that control many important biological functions, including phase transition, inflorescence branching, fruit ripening, and copper homeostasis. Nevertheless, the evolutionary patterns of SBP-box genes and evolutionary forces driving them are still not well understood.</p></div><div type="abstract" xml:lang="en"><p><b>METHODS</b></p><p>104 SBP-box gene candidates of five representative land plants were obtained from Phytozome database (v10.3). Phylogenetic combined with gene structure analyses were used to identify SBP-box gene lineages in land plants. Gene copy number and the sequence and structure features were then compared among these different SBP-box lineages. Selection analysis, relative rate tests and expression divergence were finally used to interpret the evolutionary relationships and divergence of SBP-box genes in land plants.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>We investigated 104 SBP-box genes from moss, Arabidopsis, poplar, rice, and maize. These genes are divided into group I and II, and the latter is further divided into two subgroups (subgroup II-1 and II-2) based on phylogenetic analysis. Interestingly, subgroup II-1 genes have similar sequence and structural features to group I genes, whereas subgroup II-2 genes exhibit intrinsic differences on these features, including high copy numbers and the presence of miR156/miR529 regulation. Further analyses indicate that subgroup II-1 genes are constrained by stronger purifying selection and evolve at a lower substitution rate than II-2 genes, just as group I genes do when compared to II genes. Among subgroup II-2 genes, miR156 targets evolve more rapidly than miR529 targets and experience comparatively relaxed purifying selection. These results suggest that group I and subgroup II-1 genes under strong selective constraint are conserved. By contrast, subgroup II-2 genes evolve under relaxed purifying selection and have diversified through gene copy duplications and changes in miR156/529 regulation, which might contribute to morphological diversifications of land plants.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>Our results indicate that different evolutionary rates and selection strengths lead to differing evolutionary patterns in SBP-box genes in land plants, providing a guide for future functional diversity analyses of these genes.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26467431</PMID><DateCompleted><Year>2016</Year><Month>07</Month><Day>01</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>16</Volume><PubDate><Year>2015</Year><Month>Oct</Month><Day>14</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Evolution and divergence of SBP-box genes in land plants.</ArticleTitle><Pagination><MedlinePgn>787</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12864-015-1998-y</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Squamosa promoter binding protein (SBP)-box family genes encode plant-specific transcription factors that control many important biological functions, including phase transition, inflorescence branching, fruit ripening, and copper homeostasis. Nevertheless, the evolutionary patterns of SBP-box genes and evolutionary forces driving them are still not well understood.</AbstractText><AbstractText Label="METHODS" NlmCategory="METHODS">104 SBP-box gene candidates of five representative land plants were obtained from Phytozome database (v10.3). Phylogenetic combined with gene structure analyses were used to identify SBP-box gene lineages in land plants. Gene copy number and the sequence and structure features were then compared among these different SBP-box lineages. Selection analysis, relative rate tests and expression divergence were finally used to interpret the evolutionary relationships and divergence of SBP-box genes in land plants.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We investigated 104 SBP-box genes from moss, Arabidopsis, poplar, rice, and maize. These genes are divided into group I and II, and the latter is further divided into two subgroups (subgroup II-1 and II-2) based on phylogenetic analysis. Interestingly, subgroup II-1 genes have similar sequence and structural features to group I genes, whereas subgroup II-2 genes exhibit intrinsic differences on these features, including high copy numbers and the presence of miR156/miR529 regulation. Further analyses indicate that subgroup II-1 genes are constrained by stronger purifying selection and evolve at a lower substitution rate than II-2 genes, just as group I genes do when compared to II genes. Among subgroup II-2 genes, miR156 targets evolve more rapidly than miR529 targets and experience comparatively relaxed purifying selection. These results suggest that group I and subgroup II-1 genes under strong selective constraint are conserved. By contrast, subgroup II-2 genes evolve under relaxed purifying selection and have diversified through gene copy duplications and changes in miR156/529 regulation, which might contribute to morphological diversifications of land plants.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">Our results indicate that different evolutionary rates and selection strengths lead to differing evolutionary patterns in SBP-box genes in land plants, providing a guide for future functional diversity analyses of these genes.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Shu-Dong</ForeName><Initials>SD</Initials><AffiliationInfo><Affiliation>Germplasm Bank of Wild Species, Kunming Institute of Botany of the Chinese Academy of Sciences, Kunming, 650201, China. sdchang@mail.kib.ac.cn.</Affiliation></AffiliationInfo></Author><Author 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Zhang</name></noRegion><name sortKey="Ling, Li Zhen" sort="Ling, Li Zhen" uniqKey="Ling L" first="Li-Zhen" last="Ling">Li-Zhen Ling</name><name sortKey="Yi, Ting Shuang" sort="Yi, Ting Shuang" uniqKey="Yi T" first="Ting-Shuang" last="Yi">Ting-Shuang Yi</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:26467431" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a PoplarV1
| This area was generated with Dilib version V0.6.37. |  |