Genome-wide identification and evolutionary analysis of leucine-rich repeat receptor-like protein kinase genes in soybean.

Fulai Zhou,Li-Juan Qiu,Yong Guo

doi:10.1186/s12870-016-0744-1

Abstract

BackgroundLeucine-rich repeat receptor-like kinases (LRR-RLKs) constitute the largest subfamily of receptor-like kinases in plant. A number of reports have demonstrated that plant LRR-RLKs play important roles in growth, development, differentiation, and stress responses. However, no comprehensive analysis of this gene family has been carried out in legume species.ResultsBased on the principles of sequence similarity and domain conservation, a total of 467 LRR-RLK genes were identified in soybean genome. The GmLRR-RLKs are non-randomly distributed across all 20 chromosomes of soybean and about 73.3 % of them are located in segmental duplicated regions. The analysis of synonymous substitutions for putative paralogous gene pairs indicated that most of these gene pairs resulted from segmental duplications in soybean genome. Furthermore, the exon/intron organization, motif composition and arrangements were considerably conserved among members of the same groups or subgroups in the constructed phylogenetic tree. The close phylogenetic relationship between soybean LRR-RLK genes with identified Arabidopsis genes in the same group also provided insight into their putative functions. Expression profiling analysis of GmLRR-RLKs suggested that they appeared to be differentially expressed among different tissues and some of duplicated genes exhibited divergent expression patterns. In addition, artificial selected GmLRR-RLKs were also identified by comparing the SNPs between wild and cultivated soybeans and 17 genes were detected in regions previously reported to contain domestication-related QTLs.ConclusionsComprehensive and evolutionary analysis of soybean LRR-RLK gene family was performed at whole genome level. The data provides valuable tools in future efforts to identify functional divergence of this gene family and gene diversity among different genotypes in legume species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0744-1) contains supplementary material, which is available to authorized users.

Highlights

Leucine-rich repeat receptor-like kinases (LRR-Receptor-like kinases (RLKs)) constitute the largest subfamily of receptor-like kinases in plant
Identification and genome distribution of leucine-rich repeat (LRR)-RLK gene family in soybean In order to identify all members of Leucine-rich repeat receptor-like kinase (LRR-RLK) in soybean genome, a batch BLAST search was performed against soybean protein database using the amino acid sequences of all Arabidopsis LRR-RLKs as queries
Comparing with LRR-RLK genes identified in Arabidopsis, rice and populus genome (213, 309 and 379 members respectively) [26,27,28], soybean LRR-RLK gene family identified in this study is the largest one in plant so far

Summary

Introduction

Leucine-rich repeat receptor-like kinases (LRR-RLKs) constitute the largest subfamily of receptor-like kinases in plant. Receptor-like kinases (RLKs) are a diverse group of transmembrane proteins characterized with a ligand-binding domain to receive signal molecules, a membranespanning domain to anchor the protein, and a cytoplasmic protein kinase domain to transduce signals downstream [1]. In both plants and animals, RLKs mediate plenty of signaling messages at the cell surface and act as key regulators during developmental processes [2,3,4]. According to the divergence of extracellular domains, RLKs can be further classified into 17 subgroups, including leucine-rich repeat (LRR) RLKs, S-domain RLKs, and so on [8, 9]. LRR-RLK is the largest one in plants by far, the members of which contain several tandem repeats of about 24 amino acids with conserved leucine residues in the extracellular regions [7, 10]

Methods

Results

Conclusion