Computational Identification, Phylogenetic and Synteny Analysis of Receptor-Like Kinases “RLK” and Receptor-Like Proteins “RLP” in Legumes

Abstract

Legumes are considered the second most important family of crop plants after the grass family based on economic relevance. In recent years, the field of legume genomics has expanded due to advancements in high-throughput sequencing and genotyping technologies. To date, no published comparative genomic analysis explores receptor-like kinases “RLK” and receptor-like proteins “RLP” among legume genomes. Evaluating these RLK and RLP should provide a source of new information because extensive genetic and phenotypic studies have already discovered the diverse roles of RLK and RLP in cell development, disease resistance, and stress responses among other functions. This study demonstrates that a computational logical approach for classifying the RLK/RLP in legumes/non-legumes is statistically well supported and can be used in other plant species. The analysis of RLK/RLP of 7 legumes and 3 non-legume species evaluated suggests that about 2% are RLK and less than 1% of the proteins are RLP. The results suggest a dynamic evolution of RLK and RLP in the legume family. In fact, between 66% to 85% of RLK and 83% to 88% of RLP belong to orthologous clusters among the species evaluated. The remaining RLK and RLP proteins are classified as singletons. The ratio of the pairwise synteny blocks of RLK/RLP among legumes shows a 1:1 relationship. The exception is G. max, which shows an approximately 2:1 ratio due to its recent whole genome duplication (G. max vs. the other six legumes). The other legumes show evidence of a similar proportion of plasma membrane proteins among the legume pairwise synteny blocks.