Genome-wide analysis of the MADS-box gene family in polyploid cotton (Gossypium hirsutum) and in its diploid parental species (Gossypium arboreum and Gossypium raimondii).
Identifieur interne : 000E98 ( Main/Corpus ); précédent : 000E97; suivant : 000E99Genome-wide analysis of the MADS-box gene family in polyploid cotton (Gossypium hirsutum) and in its diploid parental species (Gossypium arboreum and Gossypium raimondii).
Auteurs : Sarah Muniz Nardeli ; Sinara Artico ; Gustavo Mitsunori Aoyagi ; Stéfanie Menezes De Moura ; Tatiane Da Franca Silva ; Maria Fatima Grossi-De-Sa ; Elisson Romanel ; Marcio Alves-FerreiraSource :
- Plant physiology and biochemistry : PPB [ 1873-2690 ] ; 2018.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Plant Proteins, Transcription Factors.
- genetics : Gossypium.
- metabolism : Gossypium, Plant Proteins, Transcription Factors.
- physiology : Gene Expression Regulation, Plant.
- Diploidy, Genome-Wide Association Study, Polyploidy.
Abstract
The MADS-box gene family encodes transcription factors that share a highly conserved domain known to bind to DNA. Members of this family control various processes of development in plants, from root formation to fruit ripening. In this work, a survey of diploid (Gossypium raimondii and Gossypium arboreum) and tetraploid (Gossypium hirsutum) cotton genomes found a total of 147, 133 and 207 MADS-box genes, respectively, distributed in the MIKC, Mα, Mβ, Mγ, and Mδ subclades. A comparative phylogenetic analysis among cotton species, Arabidopsis, poplar and grapevine MADS-box homologous genes allowed us to evaluate the evolution of each MADS-box lineage in cotton plants and identify sequences within well-established subfamilies. Chromosomal localization and phylogenetic analysis revealed that G. raimondii and G. arboreum showed a conserved evolution of the MIKC subclade and a distinct pattern of duplication events in the Mα, Mγ and Mδ subclades. Additionally, G. hirsutum showed a combination of its parental subgenomes followed by a distinct evolutionary history including gene gain and loss in each subclade. qPCR analysis revealed the expression patterns of putative homologs in the AP1, AP3, AGL6, SEP4, AGL15, AG, AGL17, TM8, SVP, SOC and TT16 subfamilies of G. hirsutum. The identification of putative cotton orthologs is discussed in the light of evolution and gene expression data from other plants. This analysis of the MADS-box genes in Gossypium species opens an avenue to understanding the origin and evolution of each gene subfamily within diploid and polyploid species and paves the way for functional studies in cotton species.
DOI: 10.1016/j.plaphy.2018.03.019
PubMed: 29604523
Links to Exploration step
pubmed:29604523Le document en format XML
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<author><name sortKey="Nardeli, Sarah Muniz" sort="Nardeli, Sarah Muniz" uniqKey="Nardeli S" first="Sarah Muniz" last="Nardeli">Sarah Muniz Nardeli</name>
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<author><name sortKey="De Moura, Stefanie Menezes" sort="De Moura, Stefanie Menezes" uniqKey="De Moura S" first="Stéfanie Menezes" last="De Moura">Stéfanie Menezes De Moura</name>
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<author><name sortKey="Grossi De Sa, Maria Fatima" sort="Grossi De Sa, Maria Fatima" uniqKey="Grossi De Sa M" first="Maria Fatima" last="Grossi-De-Sa">Maria Fatima Grossi-De-Sa</name>
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<author><name sortKey="Romanel, Elisson" sort="Romanel, Elisson" uniqKey="Romanel E" first="Elisson" last="Romanel">Elisson Romanel</name>
<affiliation><nlm:affiliation>Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo (EEL-USP), CEP 12602-810, Lorena, SP, Brazil. Electronic address: romanel@usp.br.</nlm:affiliation>
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<author><name sortKey="Alves Ferreira, Marcio" sort="Alves Ferreira, Marcio" uniqKey="Alves Ferreira M" first="Marcio" last="Alves-Ferreira">Marcio Alves-Ferreira</name>
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<author><name sortKey="Nardeli, Sarah Muniz" sort="Nardeli, Sarah Muniz" uniqKey="Nardeli S" first="Sarah Muniz" last="Nardeli">Sarah Muniz Nardeli</name>
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<author><name sortKey="Aoyagi, Gustavo Mitsunori" sort="Aoyagi, Gustavo Mitsunori" uniqKey="Aoyagi G" first="Gustavo Mitsunori" last="Aoyagi">Gustavo Mitsunori Aoyagi</name>
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<author><name sortKey="De Moura, Stefanie Menezes" sort="De Moura, Stefanie Menezes" uniqKey="De Moura S" first="Stéfanie Menezes" last="De Moura">Stéfanie Menezes De Moura</name>
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<author><name sortKey="Da Franca Silva, Tatiane" sort="Da Franca Silva, Tatiane" uniqKey="Da Franca Silva T" first="Tatiane" last="Da Franca Silva">Tatiane Da Franca Silva</name>
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<author><name sortKey="Grossi De Sa, Maria Fatima" sort="Grossi De Sa, Maria Fatima" uniqKey="Grossi De Sa M" first="Maria Fatima" last="Grossi-De-Sa">Maria Fatima Grossi-De-Sa</name>
<affiliation><nlm:affiliation>Embrapa Recursos Genéticos e Biotecnologia (Cenargen), CEP 70770-917, Brasília, DF, Brazil. Electronic address: fatima.grossi@embrapa.br.</nlm:affiliation>
</affiliation>
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<author><name sortKey="Romanel, Elisson" sort="Romanel, Elisson" uniqKey="Romanel E" first="Elisson" last="Romanel">Elisson Romanel</name>
<affiliation><nlm:affiliation>Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo (EEL-USP), CEP 12602-810, Lorena, SP, Brazil. Electronic address: romanel@usp.br.</nlm:affiliation>
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<author><name sortKey="Alves Ferreira, Marcio" sort="Alves Ferreira, Marcio" uniqKey="Alves Ferreira M" first="Marcio" last="Alves-Ferreira">Marcio Alves-Ferreira</name>
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<series><title level="j">Plant physiology and biochemistry : PPB</title>
<idno type="eISSN">1873-2690</idno>
<imprint><date when="2018" type="published">2018</date>
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<term>Gene Expression Regulation, Plant (physiology)</term>
<term>Genome-Wide Association Study (MeSH)</term>
<term>Gossypium (genetics)</term>
<term>Gossypium (metabolism)</term>
<term>Plant Proteins (genetics)</term>
<term>Plant Proteins (metabolism)</term>
<term>Polyploidy (MeSH)</term>
<term>Transcription Factors (genetics)</term>
<term>Transcription Factors (metabolism)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Plant Proteins</term>
<term>Transcription Factors</term>
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<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Gossypium</term>
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<term>Plant Proteins</term>
<term>Transcription Factors</term>
</keywords>
<keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Gene Expression Regulation, Plant</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Diploidy</term>
<term>Genome-Wide Association Study</term>
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<front><div type="abstract" xml:lang="en">The MADS-box gene family encodes transcription factors that share a highly conserved domain known to bind to DNA. Members of this family control various processes of development in plants, from root formation to fruit ripening. In this work, a survey of diploid (Gossypium raimondii and Gossypium arboreum) and tetraploid (Gossypium hirsutum) cotton genomes found a total of 147, 133 and 207 MADS-box genes, respectively, distributed in the MIKC, Mα, Mβ, Mγ, and Mδ subclades. A comparative phylogenetic analysis among cotton species, Arabidopsis, poplar and grapevine MADS-box homologous genes allowed us to evaluate the evolution of each MADS-box lineage in cotton plants and identify sequences within well-established subfamilies. Chromosomal localization and phylogenetic analysis revealed that G. raimondii and G. arboreum showed a conserved evolution of the MIKC subclade and a distinct pattern of duplication events in the Mα, Mγ and Mδ subclades. Additionally, G. hirsutum showed a combination of its parental subgenomes followed by a distinct evolutionary history including gene gain and loss in each subclade. qPCR analysis revealed the expression patterns of putative homologs in the AP1, AP3, AGL6, SEP4, AGL15, AG, AGL17, TM8, SVP, SOC and TT16 subfamilies of G. hirsutum. The identification of putative cotton orthologs is discussed in the light of evolution and gene expression data from other plants. This analysis of the MADS-box genes in Gossypium species opens an avenue to understanding the origin and evolution of each gene subfamily within diploid and polyploid species and paves the way for functional studies in cotton species.</div>
</front>
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<Abstract><AbstractText>The MADS-box gene family encodes transcription factors that share a highly conserved domain known to bind to DNA. Members of this family control various processes of development in plants, from root formation to fruit ripening. In this work, a survey of diploid (Gossypium raimondii and Gossypium arboreum) and tetraploid (Gossypium hirsutum) cotton genomes found a total of 147, 133 and 207 MADS-box genes, respectively, distributed in the MIKC, Mα, Mβ, Mγ, and Mδ subclades. A comparative phylogenetic analysis among cotton species, Arabidopsis, poplar and grapevine MADS-box homologous genes allowed us to evaluate the evolution of each MADS-box lineage in cotton plants and identify sequences within well-established subfamilies. Chromosomal localization and phylogenetic analysis revealed that G. raimondii and G. arboreum showed a conserved evolution of the MIKC subclade and a distinct pattern of duplication events in the Mα, Mγ and Mδ subclades. Additionally, G. hirsutum showed a combination of its parental subgenomes followed by a distinct evolutionary history including gene gain and loss in each subclade. qPCR analysis revealed the expression patterns of putative homologs in the AP1, AP3, AGL6, SEP4, AGL15, AG, AGL17, TM8, SVP, SOC and TT16 subfamilies of G. hirsutum. The identification of putative cotton orthologs is discussed in the light of evolution and gene expression data from other plants. This analysis of the MADS-box genes in Gossypium species opens an avenue to understanding the origin and evolution of each gene subfamily within diploid and polyploid species and paves the way for functional studies in cotton species.</AbstractText>
<CopyrightInformation>Copyright © 2018 Elsevier Masson SAS. All rights reserved.</CopyrightInformation>
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<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Nardeli</LastName>
<ForeName>Sarah Muniz</ForeName>
<Initials>SM</Initials>
<AffiliationInfo><Affiliation>Laboratório de Genética Molecular Vegetal, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), CEP 21941-617, Rio de Janeiro, RJ, Brazil. Electronic address: snardeli@gmail.com.</Affiliation>
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<Initials>GM</Initials>
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<Initials>SM</Initials>
<AffiliationInfo><Affiliation>Laboratório de Genética Molecular Vegetal, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), CEP 21941-617, Rio de Janeiro, RJ, Brazil. Electronic address: stefanieshalom@gmail.com.</Affiliation>
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<ForeName>Tatiane</ForeName>
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