Comparative Analysis of the Receptor-Like Kinase Family in Arabidopsis and Rice[W]

TLDR

Receptor‑like kinases (RLKs) form a large RLK/Pelle gene family, with Arabidopsis thaliana harboring over 600 members that are key to plant growth, development, and defense. Rice possesses nearly twice as many RLK/Pelle members as Arabidopsis, a difference not attributable to overall gene number, and phylogenetic analysis shows that the common ancestor had >440 members, with lineage‑specific expansions—especially of defense‑related RLKs via tandem duplication—driven by domain fusions and higher nonsynonymous rates in extracellular domains.

Abstract

Abstract Receptor-like kinases (RLKs) belong to the large RLK/Pelle gene family, and it is known that the Arabidopsis thaliana genome contains >600 such members, which play important roles in plant growth, development, and defense responses. Surprisingly, we found that rice (Oryza sativa) has nearly twice as many RLK/Pelle members as Arabidopsis does, and it is not simply a consequence of a larger predicted gene number in rice. From the inferred phylogeny of all Arabidopsis and rice RLK/Pelle members, we estimated that the common ancestor of Arabidopsis and rice had >440 RLK/Pelles and that large-scale expansions of certain RLK/Pelle members and fusions of novel domains have occurred in both the Arabidopsis and rice lineages since their divergence. In addition, the extracellular domains have higher nonsynonymous substitution rates than the intracellular domains, consistent with the role of extracellular domains in sensing diverse signals. The lineage-specific expansions in Arabidopsis can be attributed to both tandem and large-scale duplications, whereas tandem duplication seems to be the major mechanism for recent expansions in rice. Interestingly, although the RLKs that are involved in development seem to have rarely been duplicated after the Arabidopsis–rice split, those that are involved in defense/disease resistance apparently have undergone many duplication events. These findings led us to hypothesize that most of the recent expansions of the RLK/Pelle family have involved defense/resistance-related genes.