Cysteine-Rich Receptor-Like Kinase Gene Family Identification in the Phaseolus Genome and Comparative Analysis of Their Expression Profiles Specific to Mycorrhizal and Rhizobial Symbiosis

Abstract

Receptor-like kinases (RLKs) are conserved upstream signaling molecules that regulate several biological processes, including plant development and stress adaptation. Cysteine (C)-rich receptor-like kinases (CRKs) are an important class of RLK that play vital roles in disease resistance and cell death in plants. Genome-wide analyses of CRK genes have been carried out in Arabidopsis and rice, while functional characterization of some CRKs has been carried out in wheat and tomato in addition to Arabidopsis. A comprehensive analysis of the CRK gene family in leguminous crops has not yet been conducted, and our understanding of their roles in symbiosis is rather limited. Here, we report the comprehensive analysis of the Phaseolus CRK gene family, including identification, sequence similarity, phylogeny, chromosomal localization, gene structures, transcript expression profiles, and in silico promoter analysis. Forty-six CRK homologs were identified and phylogenetically clustered into five groups. Expression analysis suggests that PvCRK genes are differentially expressed in both vegetative and reproductive tissues. Further, transcriptomic analysis revealed that shared and unique CRK genes were upregulated during arbuscular mycorrhizal and rhizobial symbiosis. Overall, the systematic analysis of the PvCRK gene family provides valuable information for further studies on the biological roles of CRKs in various Phaseolus tissues during diverse biological processes, including Phaseolus-mycorrhiza/rhizobia symbiosis.

Genetics of nodulation in Aeschynomene evenia uncovers mechanisms of the rhizobium–legume symbiosis

“…Finding that the core Nod signaling pathway, but not the upstream Nod factor receptors, is conserved in A. evenia suggests that one main difference with other legumes comes from the symbiotic receptor plugged-in in the pathway 41 . In line with this idea, a receptor-like-kinase belonging to the large CRK family 38 was discovered as being required to trigger nodulation in A. evenia . In the legume phylogeny, this gene is present only in Papilionoid lineages using an intercellular infection process and also in the Caesalpinioid legumes, C. fasciculata and Mimosa pudica .…”

“…7b ). Analysis of the region containing the symbiotic locus identified mutations in a gene that encodes a cysteine-rich receptor-like kinase (CRK) 38 , henceforth named AeCRK (Supplementary Table 23 ). The predicted 658-aa-long protein harbors a signal peptide, two extracellular DUF26 (domains of unknown function) domains, a transmembrane domain (TM), and an intracellular serine/threonine kinase domain (Fig.…”

“…Nodulation-related genes were collected from recent studies in M. truncatula and L. japonicus 1 , 3 , 24 and the protein sequences were retrieved from orthogroups generated with OrthoFinder for the 12 Aeschynomene taxa and the 14 other legume species. Important gene families or processes, such as the LysM-RLK/RLPs 24 , components of the Topoisomerase VI complex 29 – 32 , NCRs 33 – 35 , Lbs/Glbs 36 , 37 , and CRK receptors 38 were analyzed in greater detail ( Supplementary Notes 2 and 3). For phylogenetic tree reconstructions, protein sequences were aligned with MAFFT v7.407_1 and processed with FastME v2.1.6.1_1 (model of sequence evolution: LG, gamma distribution: 1 and bootstrap value: ×1000) or PhyML v3.1_1 (model of sequence evolution: LG, gamma model: ML estimate, bootstrap value: ×100) using the NGPhylogeny online tool 60 ( https://ngphylogeny.fr/ ).…”

Genetics of nodulation in Aeschynomene evenia uncovers new mechanisms of the rhizobium-legume symbiosis

“…7b). Analysis of the region containing the symbiotic locus identified mutations in a gene that encodes a Cysteine-rich Receptorlike Kinase (CRK) 38 , henceforth named AeCRK (Supplementary, Table 22). The predicted 658 aa-long protein harbors a signal peptide, two extracellular DUF26 domains, a transmembrane domain, and an intracellular serine/threonine kinase domain ( Fig.…”

“…Nodulation-related genes were collected from recent studies in M. truncatula and L. japonicus 1,3,24 and the protein sequences were retrieved from orthogroups generated with OrthoFinder for the 12 Aeschynomene taxa and the 14 other legume species. Important gene families or processes, such as the LysM-RLK/RLPs 24 , components of the Topoisomerase VI complex [29][30][31][32] , NCRs [33][34][35] , Lbs/Glbs [36][37] , and CRK receptors 38 were analyzed in greater detail (SI Appendix, Supplementary Methods). For phylogenetic tree reconstructions, protein sequences were aligned with MAFFT v7.407_1 and processed with FastME v2.1.6.1_1 (model of sequence evolution: LG, gamma distribution: 1 and Bootstrap value: x1000) or PhyML v3.1_1 (model of sequence evolution: LG, Gamma model: ML estimate, Bootstrap value: x100) using the NGPhylogeny online tool 60 (https://ngphylogeny.fr/).…”