LRR-RLK family from two Citrus species: genome-wide identification and evolutionary aspects.
Identifieur interne : 000035 ( PubMed/Checkpoint ); précédent : 000034; suivant : 000036LRR-RLK family from two Citrus species: genome-wide identification and evolutionary aspects.
Auteurs : Diogo M. Magalhães [Brésil] ; Larissa L S. Scholte [Brésil] ; Nicholas V. Silva [Brésil] ; Guilherme C. Oliveira [Brésil] ; Cyril Zipfel [Royaume-Uni] ; Marco A. Takita [Brésil] ; Alessandra A. De Souza [Brésil]Source :
- 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 Citrus species, which have high economic importance and are frequent targets for emerging pathogens. In this study, we performed in silico analysis to identify and classify LRR-RLK homologues in the predicted proteomes of Citrus clementina (clementine) and Citrus sinensis (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.
DOI: 10.1186/s12864-016-2930-9
PubMed: 27515968
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De Souza</name><affiliation wicri:level="3"><nlm:affiliation>Instituto Agronômico, Centro de Citricultura Sylvio Moreira, Cordeirópolis, São Paulo, Brazil. alessandra@centrodecitricultura.br.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Instituto Agronômico, Centro de Citricultura Sylvio Moreira, Cordeirópolis, São Paulo</wicri:regionArea><placeName><settlement type="city">São Paulo</settlement><region type="state">État de São Paulo</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2016">2016</date><idno type="RBID">pubmed:27515968</idno><idno type="pmid">27515968</idno><idno type="doi">10.1186/s12864-016-2930-9</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></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">LRR-RLK family from two Citrus 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 wicri:level="3"><nlm:affiliation>Instituto Agronômico, Centro de Citricultura Sylvio Moreira, Cordeirópolis, São Paulo, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Instituto Agronômico, Centro de Citricultura Sylvio Moreira, Cordeirópolis, São Paulo</wicri:regionArea><placeName><settlement type="city">São Paulo</settlement><region type="state">État de São Paulo</region></placeName></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 wicri:level="2"><nlm:affiliation>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:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>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</wicri:regionArea><placeName><region type="state">Minas Gerais</region></placeName></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 wicri:level="3"><nlm:affiliation>Instituto Agronômico, Centro de Citricultura Sylvio Moreira, Cordeirópolis, São Paulo, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Instituto Agronômico, Centro de Citricultura Sylvio Moreira, Cordeirópolis, São Paulo</wicri:regionArea><placeName><settlement type="city">São Paulo</settlement><region type="state">État de São Paulo</region></placeName></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 wicri:level="2"><nlm:affiliation>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:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>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</wicri:regionArea><placeName><region type="state">Minas Gerais</region></placeName></affiliation></author><author><name sortKey="Zipfel, Cyril" sort="Zipfel, Cyril" uniqKey="Zipfel C" first="Cyril" last="Zipfel">Cyril Zipfel</name><affiliation wicri:level="1"><nlm:affiliation>The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH</wicri:regionArea><wicri:noRegion>NR4 7UH</wicri:noRegion></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 wicri:level="3"><nlm:affiliation>Instituto Agronômico, Centro de Citricultura Sylvio Moreira, Cordeirópolis, São Paulo, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Instituto Agronômico, Centro de Citricultura Sylvio Moreira, Cordeirópolis, São Paulo</wicri:regionArea><placeName><settlement type="city">São Paulo</settlement><region type="state">État de São Paulo</region></placeName></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 wicri:level="3"><nlm:affiliation>Instituto Agronômico, Centro de Citricultura Sylvio Moreira, Cordeirópolis, São Paulo, Brazil. alessandra@centrodecitricultura.br.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Instituto Agronômico, Centro de Citricultura Sylvio Moreira, Cordeirópolis, São Paulo</wicri:regionArea><placeName><settlement type="city">São Paulo</settlement><region type="state">État de São Paulo</region></placeName></affiliation></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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 Citrus species, which have high economic importance and are frequent targets for emerging pathogens. In this study, we performed in silico analysis to identify and classify LRR-RLK homologues in the predicted proteomes of Citrus clementina (clementine) and Citrus sinensis (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.</div></front></TEI><pubmed><MedlineCitation Status="In-Data-Review" Owner="NLM"><PMID Version="1">27515968</PMID><DateCreated><Year>2016</Year><Month>8</Month><Day>12</Day></DateCreated><DateRevised><Year>2016</Year><Month>8</Month><Day>17</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>17</Volume><Issue>1</Issue><PubDate><Year>2016</Year><Month>Aug</Month><Day>12</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>LRR-RLK family from two Citrus species: genome-wide identification and evolutionary aspects.</ArticleTitle><Pagination><MedlinePgn>623</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12864-016-2930-9</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">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 Citrus species, which have high economic importance and are frequent targets for emerging pathogens. In this study, we performed in silico analysis to identify and classify LRR-RLK homologues in the predicted proteomes of Citrus clementina (clementine) and Citrus sinensis (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.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We built integrative protein signature databases for Citrus clementina and Citrus sinensis using all predicted protein sequences obtained from whole genomes. A total of 300 and 297 proteins were identified as LRR-RLKs in C. clementina and C. sinensis, respectively. Maximum-likelihood phylogenetic trees were estimated using Arabidopsis LRR-RLK as a template and they allowed us to classify Citrus LRR-RLKs into 16 groups. The LRR-XII group showed a remarkable expansion, containing approximately 150 paralogs encoded in each Citrus 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 C. clementina and C. sinensis 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 C. clementina and C. sinensis, respectively.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">This work provided the first comprehensive evolutionary analysis of the LRR-RLKs in Citrus. A large expansion of LRR-XII in Citrus 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.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Magalhães</LastName><ForeName>Diogo M</ForeName><Initials>DM</Initials><AffiliationInfo><Affiliation>Instituto Agronômico, Centro de Citricultura Sylvio Moreira, Cordeirópolis, São Paulo, Brazil.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Departamento de Genética e Biologia Molecular, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Scholte</LastName><ForeName>Larissa L S</ForeName><Initials>LL</Initials><AffiliationInfo><Affiliation>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.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Silva</LastName><ForeName>Nicholas V</ForeName><Initials>NV</Initials><AffiliationInfo><Affiliation>Instituto Agronômico, Centro de Citricultura Sylvio Moreira, Cordeirópolis, São Paulo, Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Oliveira</LastName><ForeName>Guilherme C</ForeName><Initials>GC</Initials><AffiliationInfo><Affiliation>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.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Instituto Tecnológico Vale - ITV, Belém, Pará, Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zipfel</LastName><ForeName>Cyril</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Takita</LastName><ForeName>Marco A</ForeName><Initials>MA</Initials><AffiliationInfo><Affiliation>Instituto Agronômico, Centro de Citricultura Sylvio Moreira, Cordeirópolis, São Paulo, Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>De Souza</LastName><ForeName>Alessandra A</ForeName><Initials>AA</Initials><AffiliationInfo><Affiliation>Instituto Agronômico, Centro de Citricultura Sylvio Moreira, Cordeirópolis, São Paulo, Brazil. alessandra@centrodecitricultura.br.</Affiliation></AffiliationInfo></Author></AuthorList><Language>ENG</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>Aug</Month><Day>12</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Genomics</MedlineTA><NlmUniqueID>100965258</NlmUniqueID><ISSNLinking>1471-2164</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><OtherID Source="NLM">PMC4982124</OtherID><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Citrus clementina</Keyword><Keyword MajorTopicYN="N">Citrus sinensis</Keyword><Keyword MajorTopicYN="N">Leucine-rich repeat receptor-like kinase</Keyword><Keyword MajorTopicYN="N">Phylogeny</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2016</Year><Month>1</Month><Day>22</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2016</Year><Month>7</Month><Day>12</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>8</Month><Day>13</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>8</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>8</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">27515968</ArticleId><ArticleId IdType="doi">10.1186/s12864-016-2930-9</ArticleId><ArticleId IdType="pii">10.1186/s12864-016-2930-9</ArticleId><ArticleId IdType="pmc">PMC4982124</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Brésil</li><li>Royaume-Uni</li></country><region><li>Minas Gerais</li><li>État de São Paulo</li></region><settlement><li>São Paulo</li></settlement></list><tree><country name="Brésil"><region name="État de São Paulo"><name sortKey="Magalhaes, Diogo M" sort="Magalhaes, Diogo M" uniqKey="Magalhaes D" first="Diogo M" last="Magalhães">Diogo M. 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Takita</name></country><country name="Royaume-Uni"><noRegion><name sortKey="Zipfel, Cyril" sort="Zipfel, Cyril" uniqKey="Zipfel C" first="Cyril" last="Zipfel">Cyril Zipfel</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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