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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.

LRR-RLK family from two Citrus species: genome-wide identification and evolutionary aspects