Molecular characterization of the SPL gene family in Populus trichocarpa.
Identifieur interne : 002131 ( Main/Exploration ); précédent : 002130; suivant : 002132Molecular characterization of the SPL gene family in Populus trichocarpa.
Auteurs : Caili Li ; Shanfa Lu [République populaire de Chine]Source :
- BMC plant biology [ 1471-2229 ] ; 2014.
Descripteurs français
- KwdFr :
- Alignement de séquences (MeSH), Analyse de profil d'expression de gènes (MeSH), Arabidopsis (génétique), Chromosomes de plante (génétique), Données de séquences moléculaires (MeSH), Exons (génétique), Famille multigénique (MeSH), Gènes de plante (MeSH), Introns (génétique), Masse moléculaire (MeSH), Modèles génétiques (MeSH), Motifs d'acides aminés (MeSH), Phylogenèse (MeSH), Populus (génétique), Protéines végétales (composition chimique), Protéines végétales (génétique), Régulation de l'expression des gènes végétaux (MeSH), Structure tertiaire des protéines (MeSH), Séquence conservée (génétique), Séquence d'acides aminés (MeSH), Séquence nucléotidique (MeSH), Transcription génétique (MeSH), microARN (génétique), microARN (métabolisme).
- MESH :
- composition chimique : Protéines végétales.
- génétique : Arabidopsis, Chromosomes de plante, Exons, Introns, Populus, Protéines végétales, Séquence conservée, microARN.
- métabolisme : microARN.
- Alignement de séquences, Analyse de profil d'expression de gènes, Données de séquences moléculaires, Famille multigénique, Gènes de plante, Masse moléculaire, Modèles génétiques, Motifs d'acides aminés, Phylogenèse, Régulation de l'expression des gènes végétaux, Structure tertiaire des protéines, Séquence d'acides aminés, Séquence nucléotidique, Transcription génétique.
English descriptors
- KwdEn :
- Amino Acid Motifs (MeSH), Amino Acid Sequence (MeSH), Arabidopsis (genetics), Base Sequence (MeSH), Chromosomes, Plant (genetics), Conserved Sequence (genetics), Exons (genetics), Gene Expression Profiling (MeSH), Gene Expression Regulation, Plant (MeSH), Genes, Plant (MeSH), Introns (genetics), MicroRNAs (genetics), MicroRNAs (metabolism), Models, Genetic (MeSH), Molecular Sequence Data (MeSH), Molecular Weight (MeSH), Multigene Family (MeSH), Phylogeny (MeSH), Plant Proteins (chemistry), Plant Proteins (genetics), Populus (genetics), Protein Structure, Tertiary (MeSH), Sequence Alignment (MeSH), Transcription, Genetic (MeSH).
- MESH :
- chemical , chemistry : Plant Proteins.
- chemical , genetics : MicroRNAs, Plant Proteins.
- genetics : Arabidopsis, Chromosomes, Plant, Conserved Sequence, Exons, Introns, Populus.
- chemical , metabolism : MicroRNAs.
- Amino Acid Motifs, Amino Acid Sequence, Base Sequence, Gene Expression Profiling, Gene Expression Regulation, Plant, Genes, Plant, Models, Genetic, Molecular Sequence Data, Molecular Weight, Multigene Family, Phylogeny, Protein Structure, Tertiary, Sequence Alignment, Transcription, Genetic.
Abstract
BACKGROUND
SPLs, a family of transcription factors specific to plants, play vital roles in plant growth and development through regulation of various physiological and biochemical processes. Although Populus trichocarpa is a model forest tree, the PtSPL gene family has not been systematically studied.
RESULTS
Here we report the identification of 28 full-length PtSPLs, which distribute on 14 P. trichocarpa chromosomes. Based on the phylogenetic relationships of SPLs in P. trichocarpa and Arabidopsis, plant SPLs can be classified into 6 groups. Each group contains at least a PtSPL and an AtSPL. The N-terminal zinc finger 1 (Zn1) of SBP domain in group 6 SPLs has four cysteine residues (CCCC-type), while Zn1 of SPLs in the other groups mainly contains three cysteine and one histidine residues (C2HC-type). Comparative analyses of gene structures, conserved motifs and expression patterns of PtSPLs and AtSPLs revealed the conservation of plant SPLs within a group, whereas among groups, the P. trichocarpa and Arabidopsis SPLs were significantly different. Various conserved motifs were identified in PtSPLs but not found in AtSPLs, suggesting the diversity of plant SPLs. A total of 11 pairs of intrachromosome-duplicated PtSPLs were identified, suggesting the importance of gene duplication in SPL gene expansion in P. trichocarpa. In addition, 18 of the 28 PtSPLs, belonging to G1, G2 and G5, were found to be targets of miR156. Consistently, all of the AtSPLs in these groups are regulated by miR156. It suggests the conservation of miR156-mediated posttranscriptional regulation in plants.
CONCLUSIONS
A total of 28 full-length SPLs were identified from the whole genome sequence of P. trichocarpa. Through comprehensive analyses of gene structures, phylogenetic relationships, chromosomal locations, conserved motifs, expression patterns and miR156-mediated posttranscriptional regulation, the PtSPL gene family was characterized. Our results provide useful information for evolution and biological function of plant SPLs.
DOI: 10.1186/1471-2229-14-131
PubMed: 24884654
PubMed Central: PMC4035897
Affiliations:
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first="Shanfa" last="Lu">Shanfa Lu</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No,151, Malianwa North Road, Haidian District, Beijing 100193, China. sflu@implad.ac.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No,151, Malianwa North Road, Haidian District, Beijing 100193</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author></analytic><series><title level="j">BMC plant biology</title><idno type="eISSN">1471-2229</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Motifs (MeSH)</term><term>Amino Acid Sequence 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nucléotidique</term><term>Transcription génétique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>SPLs, a family of transcription factors specific to plants, play vital roles in plant growth and development through regulation of various physiological and biochemical processes. Although Populus trichocarpa is a model forest tree, the PtSPL gene family has not been systematically studied.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>Here we report the identification of 28 full-length PtSPLs, which distribute on 14 P. trichocarpa chromosomes. Based on the phylogenetic relationships of SPLs in P. trichocarpa and Arabidopsis, plant SPLs can be classified into 6 groups. Each group contains at least a PtSPL and an AtSPL. The N-terminal zinc finger 1 (Zn1) of SBP domain in group 6 SPLs has four cysteine residues (CCCC-type), while Zn1 of SPLs in the other groups mainly contains three cysteine and one histidine residues (C2HC-type). Comparative analyses of gene structures, conserved motifs and expression patterns of PtSPLs and AtSPLs revealed the conservation of plant SPLs within a group, whereas among groups, the P. trichocarpa and Arabidopsis SPLs were significantly different. Various conserved motifs were identified in PtSPLs but not found in AtSPLs, suggesting the diversity of plant SPLs. A total of 11 pairs of intrachromosome-duplicated PtSPLs were identified, suggesting the importance of gene duplication in SPL gene expansion in P. trichocarpa. In addition, 18 of the 28 PtSPLs, belonging to G1, G2 and G5, were found to be targets of miR156. Consistently, all of the AtSPLs in these groups are regulated by miR156. It suggests the conservation of miR156-mediated posttranscriptional regulation in plants.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>A total of 28 full-length SPLs were identified from the whole genome sequence of P. trichocarpa. Through comprehensive analyses of gene structures, phylogenetic relationships, chromosomal locations, conserved motifs, expression patterns and miR156-mediated posttranscriptional regulation, the PtSPL gene family was characterized. Our results provide useful information for evolution and biological function of plant SPLs.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24884654</PMID><DateCompleted><Year>2015</Year><Month>01</Month><Day>16</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2229</ISSN><JournalIssue CitedMedium="Internet"><Volume>14</Volume><PubDate><Year>2014</Year><Month>May</Month><Day>15</Day></PubDate></JournalIssue><Title>BMC plant biology</Title><ISOAbbreviation>BMC Plant Biol</ISOAbbreviation></Journal><ArticleTitle>Molecular characterization of the SPL gene family in Populus trichocarpa.</ArticleTitle><Pagination><MedlinePgn>131</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2229-14-131</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">SPLs, a family of transcription factors specific to plants, play vital roles in plant growth and development through regulation of various physiological and biochemical processes. Although Populus trichocarpa is a model forest tree, the PtSPL gene family has not been systematically studied.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">Here we report the identification of 28 full-length PtSPLs, which distribute on 14 P. trichocarpa chromosomes. Based on the phylogenetic relationships of SPLs in P. trichocarpa and Arabidopsis, plant SPLs can be classified into 6 groups. Each group contains at least a PtSPL and an AtSPL. The N-terminal zinc finger 1 (Zn1) of SBP domain in group 6 SPLs has four cysteine residues (CCCC-type), while Zn1 of SPLs in the other groups mainly contains three cysteine and one histidine residues (C2HC-type). Comparative analyses of gene structures, conserved motifs and expression patterns of PtSPLs and AtSPLs revealed the conservation of plant SPLs within a group, whereas among groups, the P. trichocarpa and Arabidopsis SPLs were significantly different. Various conserved motifs were identified in PtSPLs but not found in AtSPLs, suggesting the diversity of plant SPLs. A total of 11 pairs of intrachromosome-duplicated PtSPLs were identified, suggesting the importance of gene duplication in SPL gene expansion in P. trichocarpa. In addition, 18 of the 28 PtSPLs, belonging to G1, G2 and G5, were found to be targets of miR156. Consistently, all of the AtSPLs in these groups are regulated by miR156. It suggests the conservation of miR156-mediated posttranscriptional regulation in plants.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">A total of 28 full-length SPLs were identified from the whole genome sequence of P. trichocarpa. Through comprehensive analyses of gene structures, phylogenetic relationships, chromosomal locations, conserved motifs, expression patterns and miR156-mediated posttranscriptional regulation, the PtSPL gene family was characterized. Our results provide useful information for evolution and biological function of plant SPLs.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Caili</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Lu</LastName><ForeName>Shanfa</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No,151, Malianwa North Road, Haidian District, Beijing 100193, China. sflu@implad.ac.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>2014</Year><Month>05</Month><Day>15</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Plant 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