Cargando…
LRR-RLK family from two Citrus species: genome-wide identification and evolutionary aspects
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 a...
Autores principales: | , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2016
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4982124/ https://www.ncbi.nlm.nih.gov/pubmed/27515968 http://dx.doi.org/10.1186/s12864-016-2930-9 |
_version_ | 1782447718498566144 |
---|---|
author | Magalhães, Diogo M. Scholte, Larissa L. S. Silva, Nicholas V. Oliveira, Guilherme C. Zipfel, Cyril Takita, Marco A. De Souza, Alessandra A. |
author_facet | Magalhães, Diogo M. Scholte, Larissa L. S. Silva, Nicholas V. Oliveira, Guilherme C. Zipfel, Cyril Takita, Marco A. De Souza, Alessandra A. |
author_sort | Magalhães, Diogo M. |
collection | PubMed |
description | 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. 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. 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-2930-9) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4982124 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-49821242016-08-13 LRR-RLK family from two Citrus species: genome-wide identification and evolutionary aspects Magalhães, Diogo M. Scholte, Larissa L. S. Silva, Nicholas V. Oliveira, Guilherme C. Zipfel, Cyril Takita, Marco A. De Souza, Alessandra A. BMC Genomics Research Article 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. 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. 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-2930-9) contains supplementary material, which is available to authorized users. BioMed Central 2016-08-12 /pmc/articles/PMC4982124/ /pubmed/27515968 http://dx.doi.org/10.1186/s12864-016-2930-9 Text en © The Author(s). 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Magalhães, Diogo M. Scholte, Larissa L. S. Silva, Nicholas V. Oliveira, Guilherme C. Zipfel, Cyril Takita, Marco A. De Souza, Alessandra A. LRR-RLK family from two Citrus species: genome-wide identification and evolutionary aspects |
title | LRR-RLK family from two Citrus species: genome-wide identification and evolutionary aspects |
title_full | LRR-RLK family from two Citrus species: genome-wide identification and evolutionary aspects |
title_fullStr | LRR-RLK family from two Citrus species: genome-wide identification and evolutionary aspects |
title_full_unstemmed | LRR-RLK family from two Citrus species: genome-wide identification and evolutionary aspects |
title_short | LRR-RLK family from two Citrus species: genome-wide identification and evolutionary aspects |
title_sort | lrr-rlk family from two citrus species: genome-wide identification and evolutionary aspects |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4982124/ https://www.ncbi.nlm.nih.gov/pubmed/27515968 http://dx.doi.org/10.1186/s12864-016-2930-9 |
work_keys_str_mv | AT magalhaesdiogom lrrrlkfamilyfromtwocitrusspeciesgenomewideidentificationandevolutionaryaspects AT scholtelarissals lrrrlkfamilyfromtwocitrusspeciesgenomewideidentificationandevolutionaryaspects AT silvanicholasv lrrrlkfamilyfromtwocitrusspeciesgenomewideidentificationandevolutionaryaspects AT oliveiraguilhermec lrrrlkfamilyfromtwocitrusspeciesgenomewideidentificationandevolutionaryaspects AT zipfelcyril lrrrlkfamilyfromtwocitrusspeciesgenomewideidentificationandevolutionaryaspects AT takitamarcoa lrrrlkfamilyfromtwocitrusspeciesgenomewideidentificationandevolutionaryaspects AT desouzaalessandraa lrrrlkfamilyfromtwocitrusspeciesgenomewideidentificationandevolutionaryaspects |