LRR-RLK family from two Citrus species: genome-wide identification and evolutionary aspects
Identifieur interne : 000151 ( Main/Exploration ); précédent : 000150; suivant : 000152LRR-RLK family from two Citrus species: genome-wide identification and evolutionary aspects
Auteurs : Diogo M. Magalhães ; Larissa L. S. Scholte ; Nicholas V. Silva ; Guilherme C. Oliveira ; Cyril Zipfel ; Marco A. Takita ; Alessandra A. De SouzaSource :
- BMC Genomics [ 1471-2164 ] ; 2016.
Abstract
Leucine-rich repeat receptor-like kinases (LRR-RLKs) represent the largest subfamily of plant RLKs. The functions of most LRR-RLKs have remained undiscovered, and a few that have been experimentally characterized have been shown to have important roles in growth and development as well as in defense responses. Although RLK subfamilies have been previously studied in many plants, no comprehensive study has been performed on this gene family in
We built integrative protein signature databases for
This work provided the first comprehensive evolutionary analysis of the LRR-RLKs in
The online version of this article (doi:10.1186/s12864-016-2930-9) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12864-016-2930-9
PubMed: 27515968
PubMed Central: 4982124
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">LRR-RLK family from two <italic>Citrus</italic> species: genome-wide identification and evolutionary aspects</title><author><name sortKey="Magalhaes, Diogo M" sort="Magalhaes, Diogo M" uniqKey="Magalhaes D" first="Diogo M." last="Magalhães">Diogo M. Magalhães</name><affiliation><nlm:aff id="Aff1">Instituto Agronômico, Centro de Citricultura Sylvio Moreira, Cordeirópolis, São Paulo Brazil</nlm:aff><wicri:noCountry code="subfield">São Paulo Brazil</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff2">Departamento de Genética e Biologia Molecular, Universidade Estadual de Campinas, Campinas, São Paulo Brazil</nlm:aff><wicri:noCountry code="subfield">São Paulo Brazil</wicri:noCountry></affiliation></author><author><name sortKey="Scholte, Larissa L S" sort="Scholte, Larissa L S" uniqKey="Scholte L" first="Larissa L. S." last="Scholte">Larissa L. S. Scholte</name><affiliation><nlm:aff id="Aff3">Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais, Grupo de Genômica e Biologia Computacional, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais Brazil</nlm:aff><wicri:noCountry code="subfield">Minas Gerais Brazil</wicri:noCountry></affiliation></author><author><name sortKey="Silva, Nicholas V" sort="Silva, Nicholas V" uniqKey="Silva N" first="Nicholas V." last="Silva">Nicholas V. Silva</name><affiliation><nlm:aff id="Aff1">Instituto Agronômico, Centro de Citricultura Sylvio Moreira, Cordeirópolis, São Paulo Brazil</nlm:aff><wicri:noCountry code="subfield">São Paulo Brazil</wicri:noCountry></affiliation></author><author><name sortKey="Oliveira, Guilherme C" sort="Oliveira, Guilherme C" uniqKey="Oliveira G" first="Guilherme C." last="Oliveira">Guilherme C. Oliveira</name><affiliation><nlm:aff id="Aff3">Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais, Grupo de Genômica e Biologia Computacional, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais Brazil</nlm:aff><wicri:noCountry code="subfield">Minas Gerais Brazil</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff4">Instituto Tecnológico Vale – ITV, Belém, Pará Brazil</nlm:aff><wicri:noCountry code="subfield">Pará Brazil</wicri:noCountry></affiliation></author><author><name sortKey="Zipfel, Cyril" sort="Zipfel, Cyril" uniqKey="Zipfel C" first="Cyril" last="Zipfel">Cyril Zipfel</name><affiliation><nlm:aff id="Aff5">The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH UK</nlm:aff><wicri:noCountry code="subfield">NR4 7UH UK</wicri:noCountry></affiliation></author><author><name sortKey="Takita, Marco A" sort="Takita, Marco A" uniqKey="Takita M" first="Marco A." last="Takita">Marco A. Takita</name><affiliation><nlm:aff id="Aff1">Instituto Agronômico, Centro de Citricultura Sylvio Moreira, Cordeirópolis, São Paulo Brazil</nlm:aff><wicri:noCountry code="subfield">São Paulo Brazil</wicri:noCountry></affiliation></author><author><name sortKey="De Souza, Alessandra A" sort="De Souza, Alessandra A" uniqKey="De Souza A" first="Alessandra A." last="De Souza">Alessandra A. De Souza</name><affiliation><nlm:aff id="Aff1">Instituto Agronômico, Centro de Citricultura Sylvio Moreira, Cordeirópolis, São Paulo Brazil</nlm:aff><wicri:noCountry code="subfield">São Paulo Brazil</wicri:noCountry></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27515968</idno><idno type="pmc">4982124</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4982124</idno><idno type="RBID">PMC:4982124</idno><idno type="doi">10.1186/s12864-016-2930-9</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000609</idno><idno type="wicri:Area/Pmc/Curation">000608</idno><idno type="wicri:Area/Pmc/Checkpoint">000124</idno><idno type="wicri:source">PubMed</idno><idno type="wicri:Area/PubMed/Corpus">000023</idno><idno type="wicri:Area/PubMed/Curation">000023</idno><idno type="wicri:Area/PubMed/Checkpoint">000023</idno><idno type="wicri:Area/Ncbi/Merge">002143</idno><idno type="wicri:Area/Ncbi/Curation">002143</idno><idno type="wicri:Area/Ncbi/Checkpoint">002143</idno><idno type="wicri:Area/Main/Merge">000151</idno><idno type="wicri:Area/Main/Curation">000151</idno><idno type="wicri:Area/Main/Exploration">000151</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">LRR-RLK family from two <italic>Citrus</italic> species: genome-wide identification and evolutionary aspects</title><author><name sortKey="Magalhaes, Diogo M" sort="Magalhaes, Diogo M" uniqKey="Magalhaes D" first="Diogo M." last="Magalhães">Diogo M. Magalhães</name><affiliation><nlm:aff id="Aff1">Instituto Agronômico, Centro de Citricultura Sylvio Moreira, Cordeirópolis, São Paulo Brazil</nlm:aff><wicri:noCountry code="subfield">São Paulo Brazil</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff2">Departamento de Genética e Biologia Molecular, Universidade Estadual de Campinas, Campinas, São Paulo Brazil</nlm:aff><wicri:noCountry code="subfield">São Paulo Brazil</wicri:noCountry></affiliation></author><author><name sortKey="Scholte, Larissa L S" sort="Scholte, Larissa L S" uniqKey="Scholte L" first="Larissa L. S." last="Scholte">Larissa L. S. Scholte</name><affiliation><nlm:aff id="Aff3">Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais, Grupo de Genômica e Biologia Computacional, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais Brazil</nlm:aff><wicri:noCountry code="subfield">Minas Gerais Brazil</wicri:noCountry></affiliation></author><author><name sortKey="Silva, Nicholas V" sort="Silva, Nicholas V" uniqKey="Silva N" first="Nicholas V." last="Silva">Nicholas V. Silva</name><affiliation><nlm:aff id="Aff1">Instituto Agronômico, Centro de Citricultura Sylvio Moreira, Cordeirópolis, São Paulo Brazil</nlm:aff><wicri:noCountry code="subfield">São Paulo Brazil</wicri:noCountry></affiliation></author><author><name sortKey="Oliveira, Guilherme C" sort="Oliveira, Guilherme C" uniqKey="Oliveira G" first="Guilherme C." last="Oliveira">Guilherme C. Oliveira</name><affiliation><nlm:aff id="Aff3">Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais, Grupo de Genômica e Biologia Computacional, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais Brazil</nlm:aff><wicri:noCountry code="subfield">Minas Gerais Brazil</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff4">Instituto Tecnológico Vale – ITV, Belém, Pará Brazil</nlm:aff><wicri:noCountry code="subfield">Pará Brazil</wicri:noCountry></affiliation></author><author><name sortKey="Zipfel, Cyril" sort="Zipfel, Cyril" uniqKey="Zipfel C" first="Cyril" last="Zipfel">Cyril Zipfel</name><affiliation><nlm:aff id="Aff5">The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH UK</nlm:aff><wicri:noCountry code="subfield">NR4 7UH UK</wicri:noCountry></affiliation></author><author><name sortKey="Takita, Marco A" sort="Takita, Marco A" uniqKey="Takita M" first="Marco A." last="Takita">Marco A. Takita</name><affiliation><nlm:aff id="Aff1">Instituto Agronômico, Centro de Citricultura Sylvio Moreira, Cordeirópolis, São Paulo Brazil</nlm:aff><wicri:noCountry code="subfield">São Paulo Brazil</wicri:noCountry></affiliation></author><author><name sortKey="De Souza, Alessandra A" sort="De Souza, Alessandra A" uniqKey="De Souza A" first="Alessandra A." last="De Souza">Alessandra A. De Souza</name><affiliation><nlm:aff id="Aff1">Instituto Agronômico, Centro de Citricultura Sylvio Moreira, Cordeirópolis, São Paulo Brazil</nlm:aff><wicri:noCountry code="subfield">São Paulo Brazil</wicri:noCountry></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Leucine-rich repeat receptor-like kinases (LRR-RLKs) represent the largest subfamily of plant RLKs. The functions of most LRR-RLKs have remained undiscovered, and a few that have been experimentally characterized have been shown to have important roles in growth and development as well as in defense responses. Although RLK subfamilies have been previously studied in many plants, no comprehensive study has been performed on this gene family in <italic>Citrus</italic> species, which have high economic importance and are frequent targets for emerging pathogens. In this study, we performed <italic>in silico</italic> analysis to identify and classify LRR-RLK homologues in the predicted proteomes of <italic>Citrus clementina</italic> (clementine) and <italic>Citrus sinensis</italic> (sweet orange). In addition, we used large-scale phylogenetic approaches to elucidate the evolutionary relationships of the LRR-RLKs and further narrowed the analysis to the LRR-XII group, which contains several previously described cell surface immune receptors.</p></sec><sec><title>Results</title><p>We built integrative protein signature databases for <italic>Citrus clementina</italic> and <italic>Citrus sinensis</italic> using all predicted protein sequences obtained from whole genomes. A total of 300 and 297 proteins were identified as LRR-RLKs in <italic>C. clementina</italic> and <italic>C. sinensis</italic>, respectively. Maximum-likelihood phylogenetic trees were estimated using <italic>Arabidopsis</italic> LRR-RLK as a template and they allowed us to classify <italic>Citrus</italic> LRR-RLKs into 16 groups. The LRR-XII group showed a remarkable expansion, containing approximately 150 paralogs encoded in each <italic>Citrus</italic> genome. Phylogenetic analysis also demonstrated the existence of two distinct LRR-XII clades, each one constituted mainly by RD and non-RD kinases. We identified 68 orthologous pairs from the <italic>C. clementina</italic> and <italic>C. sinensis</italic> LRR-XII genes. In addition, among the paralogs, we identified a subset of 78 and 62 clustered genes probably derived from tandem duplication events in the genomes of <italic>C. clementina</italic> and <italic>C. sinensis</italic>, respectively.</p></sec><sec><title>Conclusions</title><p>This work provided the first comprehensive evolutionary analysis of the LRR-RLKs in <italic>Citrus</italic>. A large expansion of LRR-XII in <italic>Citrus</italic> genomes suggests that it might play a key role in adaptive responses in host-pathogen co-evolution, related to the perennial life cycle and domestication of the citrus crop species.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12864-016-2930-9) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Osakabe, Y" uniqKey="Osakabe Y">Y Osakabe</name></author><author><name sortKey="Yamaguchi Shinozaki, K" uniqKey="Yamaguchi Shinozaki K">K Yamaguchi-Shinozaki</name></author><author><name sortKey="Shinozaki, K" uniqKey="Shinozaki K">K Shinozaki</name></author><author><name sortKey="Tran, L Sp" uniqKey="Tran L">L-SP Tran</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shiu, Sh" uniqKey="Shiu S">SH 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Rodier-goud</name></author><author><name sortKey="Barbosa Neto, Jf" uniqKey="Barbosa Neto J">JF Barbosa-neto</name></author><author><name sortKey="Sabot, F" uniqKey="Sabot F">F Sabot</name></author><author><name sortKey="Kudrna, D" uniqKey="Kudrna D">D Kudrna</name></author><author><name sortKey="Ammiraju, Jss" uniqKey="Ammiraju J">JSS Ammiraju</name></author><author><name sortKey="Schuster, Sc" uniqKey="Schuster S">SC Schuster</name></author><author><name sortKey="Carlson, Je" uniqKey="Carlson J">JE Carlson</name></author><author><name sortKey="Sallet, E" uniqKey="Sallet E">E Sallet</name></author><author><name sortKey="Schiex, T" uniqKey="Schiex T">T Schiex</name></author><author><name sortKey="Dievart, A" uniqKey="Dievart A">A Dievart</name></author><author><name sortKey="Kramer, M" uniqKey="Kramer M">M Kramer</name></author><author><name sortKey="Gelley, L" uniqKey="Gelley L">L Gelley</name></author><author><name sortKey="Shi, Z" uniqKey="Shi Z">Z Shi</name></author><author><name sortKey="Berard, A" uniqKey="Berard A">A Bérard</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list></list><tree><noCountry><name sortKey="De Souza, Alessandra A" sort="De Souza, Alessandra A" uniqKey="De Souza A" first="Alessandra A." last="De Souza">Alessandra A. De Souza</name><name sortKey="Magalhaes, Diogo M" sort="Magalhaes, Diogo M" uniqKey="Magalhaes D" first="Diogo M." last="Magalhães">Diogo M. Magalhães</name><name sortKey="Oliveira, Guilherme C" sort="Oliveira, Guilherme C" uniqKey="Oliveira G" first="Guilherme C." last="Oliveira">Guilherme C. Oliveira</name><name sortKey="Scholte, Larissa L S" sort="Scholte, Larissa L S" uniqKey="Scholte L" first="Larissa L. S." last="Scholte">Larissa L. S. Scholte</name><name sortKey="Silva, Nicholas V" sort="Silva, Nicholas V" uniqKey="Silva N" first="Nicholas V." last="Silva">Nicholas V. Silva</name><name sortKey="Takita, Marco A" sort="Takita, Marco A" uniqKey="Takita M" first="Marco A." last="Takita">Marco A. Takita</name><name sortKey="Zipfel, Cyril" sort="Zipfel, Cyril" uniqKey="Zipfel C" first="Cyril" last="Zipfel">Cyril Zipfel</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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