PoplarV1, Main, Exploration, bibRecord, 001D31

Genome-wide identification, phylogeny and expression analysis of GRAS gene family in tomato.

Identifieur interne : 001D31 ( Main/Exploration ); précédent : 001D30; suivant : 001D32

Genome-wide identification, phylogeny and expression analysis of GRAS gene family in tomato.

Auteurs : Wei Huang [Oman] ; Zhiqiang Xian [Oman] ; Xia Kang [Oman] ; Ning Tang [Oman] ; Zhengguo Li [République populaire de Chine]

Source :

BMC plant biology [ 1471-2229 ] ; 2015.

RBID : pubmed:26302743

Descripteurs français

KwdFr :
- Alignement de séquences (MeSH), Analyse de profil d'expression de gènes (MeSH), Analyse de séquence d'ADN (MeSH), Arabidopsis (effets des médicaments et des substances chimiques), Arabidopsis (génétique), Données de séquences moléculaires (MeSH), Facteur de croissance végétal (pharmacologie), Famille multigénique (MeSH), Fruit (croissance et développement), Fruit (génétique), Gènes de plante (MeSH), Génome végétal (MeSH), Lycopersicon esculentum (croissance et développement), Lycopersicon esculentum (effets des médicaments et des substances chimiques), Lycopersicon esculentum (génétique), Phylogenèse (MeSH), Protéines végétales (composition chimique), Protéines végétales (génétique), Protéines végétales (métabolisme), Régulation de l'expression des gènes végétaux (effets des médicaments et des substances chimiques), Spécificité d'organe (effets des médicaments et des substances chimiques), Spécificité d'organe (génétique), Structure tertiaire des protéines (MeSH), Séquence d'acides aminés (MeSH), Séquence nucléotidique (MeSH), microARN (génétique), microARN (métabolisme).
MESH :
- composition chimique : Protéines végétales.
- croissance et développement : Fruit, Lycopersicon esculentum.
- effets des médicaments et des substances chimiques : Arabidopsis, Lycopersicon esculentum, Régulation de l'expression des gènes végétaux, Spécificité d'organe.
- génétique : Arabidopsis, Fruit, Lycopersicon esculentum, Protéines végétales, Spécificité d'organe, microARN.
- métabolisme : Protéines végétales, microARN.
- pharmacologie : Facteur de croissance végétal.
- Alignement de séquences, Analyse de profil d'expression de gènes, Analyse de séquence d'ADN, Données de séquences moléculaires, Famille multigénique, Gènes de plante, Génome végétal, Phylogenèse, Structure tertiaire des protéines, Séquence d'acides aminés, Séquence nucléotidique.

English descriptors

KwdEn :
- Amino Acid Sequence (MeSH), Arabidopsis (drug effects), Arabidopsis (genetics), Base Sequence (MeSH), Fruit (genetics), Fruit (growth & development), Gene Expression Profiling (MeSH), Gene Expression Regulation, Plant (drug effects), Genes, Plant (MeSH), Genome, Plant (MeSH), Lycopersicon esculentum (drug effects), Lycopersicon esculentum (genetics), Lycopersicon esculentum (growth & development), MicroRNAs (genetics), MicroRNAs (metabolism), Molecular Sequence Data (MeSH), Multigene Family (MeSH), Organ Specificity (drug effects), Organ Specificity (genetics), Phylogeny (MeSH), Plant Growth Regulators (pharmacology), Plant Proteins (chemistry), Plant Proteins (genetics), Plant Proteins (metabolism), Protein Structure, Tertiary (MeSH), Sequence Alignment (MeSH), Sequence Analysis, DNA (MeSH).
MESH :
- chemical , chemistry : Plant Proteins.
- chemical , genetics : MicroRNAs, Plant Proteins.
- drug effects : Arabidopsis, Gene Expression Regulation, Plant, Lycopersicon esculentum, Organ Specificity.
- genetics : Arabidopsis, Fruit, Lycopersicon esculentum, Organ Specificity.
- growth & development : Fruit, Lycopersicon esculentum.
- chemical , metabolism : MicroRNAs, Plant Proteins.
- chemical , pharmacology : Plant Growth Regulators.
- Amino Acid Sequence, Base Sequence, Gene Expression Profiling, Genes, Plant, Genome, Plant, Molecular Sequence Data, Multigene Family, Phylogeny, Protein Structure, Tertiary, Sequence Alignment, Sequence Analysis, DNA.

Abstract

BACKGROUND

GRAS transcription factors usually act as integrators of multiple growth regulatory and environmental signals, including axillary shoot meristem formation, root radial pattering, phytohormones, light signaling, and abiotic/biotic stress. However, little is known about this gene family in tomato (Solanum lycopersicum), the most important model plant for crop species with fleshy fruits.

RESULTS

In this study, 53 GRAS genes were identified and renamed based on tomato whole-genome sequence and their respective chromosome distribution except 19 members were kept as their already existed name. Multiple sequence alignment showed typical GRAS domain in these proteins. Phylogenetic analysis of GRAS proteins from tomato, Arabidopsis, Populus, P.mume, and Rice revealed that SlGRAS proteins could be divided into at least 13 subfamilies. SlGRAS24 and SlGRAS40 were identified as target genes of miR171 using5'-RACE (Rapid amplification of cDNA ends). qRT-PCR analysis revealed tissue-/organ- and development stage-specific expression patterns of SlGRAS genes. Moreover, their expression patterns in response to different hormone and abiotic stress treatments were also investigated.

CONCLUSIONS

This study provides the first comprehensive analysis of GRAS gene family in the tomato genome. The data will undoubtedly be useful for better understanding the potential functions of GRAS genes, and their possible roles in mediating hormone cross-talk and abiotic stress in tomato as well as in some other relative species.

DOI: 10.1186/s12870-015-0590-6
PubMed: 26302743
PubMed Central: PMC4549011

Affiliations:

Oman, République populaire de Chine

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

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Le document en format XML

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<term>Arabidopsis (genetics)</term>
<term>Base Sequence (MeSH)</term>
<term>Fruit (genetics)</term>
<term>Fruit (growth & development)</term>
<term>Gene Expression Profiling (MeSH)</term>
<term>Gene Expression Regulation, Plant (drug effects)</term>
<term>Genes, Plant (MeSH)</term>
<term>Genome, Plant (MeSH)</term>
<term>Lycopersicon esculentum (drug effects)</term>
<term>Lycopersicon esculentum (genetics)</term>
<term>Lycopersicon esculentum (growth & development)</term>
<term>MicroRNAs (genetics)</term>
<term>MicroRNAs (metabolism)</term>
<term>Molecular Sequence Data (MeSH)</term>
<term>Multigene Family (MeSH)</term>
<term>Organ Specificity (drug effects)</term>
<term>Organ Specificity (genetics)</term>
<term>Phylogeny (MeSH)</term>
<term>Plant Growth Regulators (pharmacology)</term>
<term>Plant Proteins (chemistry)</term>
<term>Plant Proteins (genetics)</term>
<term>Plant Proteins (metabolism)</term>
<term>Protein Structure, Tertiary (MeSH)</term>
<term>Sequence Alignment (MeSH)</term>
<term>Sequence Analysis, DNA (MeSH)</term>
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<term>Analyse de séquence d'ADN (MeSH)</term>
<term>Arabidopsis (effets des médicaments et des substances chimiques)</term>
<term>Arabidopsis (génétique)</term>
<term>Données de séquences moléculaires (MeSH)</term>
<term>Facteur de croissance végétal (pharmacologie)</term>
<term>Famille multigénique (MeSH)</term>
<term>Fruit (croissance et développement)</term>
<term>Fruit (génétique)</term>
<term>Gènes de plante (MeSH)</term>
<term>Génome végétal (MeSH)</term>
<term>Lycopersicon esculentum (croissance et développement)</term>
<term>Lycopersicon esculentum (effets des médicaments et des substances chimiques)</term>
<term>Lycopersicon esculentum (génétique)</term>
<term>Phylogenèse (MeSH)</term>
<term>Protéines végétales (composition chimique)</term>
<term>Protéines végétales (génétique)</term>
<term>Protéines végétales (métabolisme)</term>
<term>Régulation de l'expression des gènes végétaux (effets des médicaments et des substances chimiques)</term>
<term>Spécificité d'organe (effets des médicaments et des substances chimiques)</term>
<term>Spécificité d'organe (génétique)</term>
<term>Structure tertiaire des protéines (MeSH)</term>
<term>Séquence d'acides aminés (MeSH)</term>
<term>Séquence nucléotidique (MeSH)</term>
<term>microARN (génétique)</term>
<term>microARN (métabolisme)</term>
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<term>Lycopersicon esculentum</term>
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<term>Gene Expression Regulation, Plant</term>
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<term>Lycopersicon esculentum</term>
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<term>Fruit</term>
<term>Lycopersicon esculentum</term>
<term>Protéines végétales</term>
<term>Spécificité d'organe</term>
<term>microARN</term>
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<term>microARN</term>
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<keywords scheme="MESH" qualifier="pharmacologie" xml:lang="fr"><term>Facteur de croissance végétal</term>
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<keywords scheme="MESH" type="chemical" qualifier="pharmacology" xml:lang="en"><term>Plant Growth Regulators</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term>
<term>Base Sequence</term>
<term>Gene Expression Profiling</term>
<term>Genes, Plant</term>
<term>Genome, Plant</term>
<term>Molecular Sequence Data</term>
<term>Multigene Family</term>
<term>Phylogeny</term>
<term>Protein Structure, Tertiary</term>
<term>Sequence Alignment</term>
<term>Sequence Analysis, DNA</term>
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<term>Analyse de profil d'expression de gènes</term>
<term>Analyse de séquence d'ADN</term>
<term>Données de séquences moléculaires</term>
<term>Famille multigénique</term>
<term>Gènes de plante</term>
<term>Génome végétal</term>
<term>Phylogenèse</term>
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<front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b>
</p>
<p>GRAS transcription factors usually act as integrators of multiple growth regulatory and environmental signals, including axillary shoot meristem formation, root radial pattering, phytohormones, light signaling, and abiotic/biotic stress. However, little is known about this gene family in tomato (Solanum lycopersicum), the most important model plant for crop species with fleshy fruits.</p>
</div>
<div type="abstract" xml:lang="en"><p><b>RESULTS</b>
</p>
<p>In this study, 53 GRAS genes were identified and renamed based on tomato whole-genome sequence and their respective chromosome distribution except 19 members were kept as their already existed name. Multiple sequence alignment showed typical GRAS domain in these proteins. Phylogenetic analysis of GRAS proteins from tomato, Arabidopsis, Populus, P.mume, and Rice revealed that SlGRAS proteins could be divided into at least 13 subfamilies. SlGRAS24 and SlGRAS40 were identified as target genes of miR171 using5'-RACE (Rapid amplification of cDNA ends). qRT-PCR analysis revealed tissue-/organ- and development stage-specific expression patterns of SlGRAS genes. Moreover, their expression patterns in response to different hormone and abiotic stress treatments were also investigated.</p>
</div>
<div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b>
</p>
<p>This study provides the first comprehensive analysis of GRAS gene family in the tomato genome. The data will undoubtedly be useful for better understanding the potential functions of GRAS genes, and their possible roles in mediating hormone cross-talk and abiotic stress in tomato as well as in some other relative species.</p>
</div>
</front>
</TEI>
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<DateCompleted><Year>2016</Year>
<Month>01</Month>
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<Title>BMC plant biology</Title>
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<ArticleTitle>Genome-wide identification, phylogeny and expression analysis of GRAS gene family in tomato.</ArticleTitle>
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<Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">GRAS transcription factors usually act as integrators of multiple growth regulatory and environmental signals, including axillary shoot meristem formation, root radial pattering, phytohormones, light signaling, and abiotic/biotic stress. However, little is known about this gene family in tomato (Solanum lycopersicum), the most important model plant for crop species with fleshy fruits.</AbstractText>
<AbstractText Label="RESULTS" NlmCategory="RESULTS">In this study, 53 GRAS genes were identified and renamed based on tomato whole-genome sequence and their respective chromosome distribution except 19 members were kept as their already existed name. Multiple sequence alignment showed typical GRAS domain in these proteins. Phylogenetic analysis of GRAS proteins from tomato, Arabidopsis, Populus, P.mume, and Rice revealed that SlGRAS proteins could be divided into at least 13 subfamilies. SlGRAS24 and SlGRAS40 were identified as target genes of miR171 using5'-RACE (Rapid amplification of cDNA ends). qRT-PCR analysis revealed tissue-/organ- and development stage-specific expression patterns of SlGRAS genes. Moreover, their expression patterns in response to different hormone and abiotic stress treatments were also investigated.</AbstractText>
<AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">This study provides the first comprehensive analysis of GRAS gene family in the tomato genome. The data will undoubtedly be useful for better understanding the potential functions of GRAS genes, and their possible roles in mediating hormone cross-talk and abiotic stress in tomato as well as in some other relative species.</AbstractText>
</Abstract>
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<ForeName>Wei</ForeName>
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<AffiliationInfo><Affiliation>Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China. huanghaowei1988@126.com.</Affiliation>
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<ForeName>Zhiqiang</ForeName>
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<AffiliationInfo><Affiliation>Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China. shane19851@gmail.com.</Affiliation>
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<Author ValidYN="Y"><LastName>Kang</LastName>
<ForeName>Xia</ForeName>
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<AffiliationInfo><Affiliation>Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China. 1060530628@qq.com.</Affiliation>
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<Author ValidYN="Y"><LastName>Tang</LastName>
<ForeName>Ning</ForeName>
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<AffiliationInfo><Affiliation>Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China. sabrina-0810@hotmail.com.</Affiliation>
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<ForeName>Zhengguo</ForeName>
<Initials>Z</Initials>
<AffiliationInfo><Affiliation>Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China. zhengguoli@cqu.edu.cn.</Affiliation>
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<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
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Genome-wide identification, phylogeny and expression analysis of GRAS gene family in tomato.

Genome-wide identification, phylogeny and expression analysis of GRAS gene family in tomato.

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