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

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.

Genome-Wide Analysis of Soybean JmjC Domain-Containing Proteins Suggests Evolutionary Conservation Following Whole-Genome Duplication

“…In this study, we have demonstrated that 16 soybean paralogous pairs derived from the second WGD, which suggests that the WGD duplication might be the main mechanism of JmjC gene family expansion and functional diversity during the evolution of soybean. This result is consistent with some other gene families not only AAT gene family (Cheng et al, 2016), GST supergene family (Liu et al, 2015), and receptor-like kinase genes (Zhou et al, 2016) in soybean, but also SET domain family in Populus trichocar (Lei et al, 2012; Zhang and Ma, 2012), and 14-3-3 family genes and AP2/ERF superfamily in M. truncatula (Qin et al, 2016; Shu et al, 2016). And in Arabidopsis , previous studies have proposed that more than 90% regulatory genes increased due to WGD (Maere et al, 2005).…”

Ca2+/Cation Antiporters (CaCA): Identification, Characterization and Expression Profiling in Bread Wheat (Triticum aestivum L.)

“…Several standard methods are reported for the characterization and comparison of different features of various genes in a gene family (Singh et al, 2015; Shumayla et al, 2016a,b; Zhou et al, 2016). The TaCaCA superfamily genes and proteins were analyzed in terms of various characteristic features like exon/intron organization, intron phase, length, molecular weight, pI, transmembrane, cytoplasmic loop size, cellular localization and domain architecture (Figure 3; Table 1; Files S4–S8).…”

Duplication and Divergence of Leucine-Rich Repeat Receptor-Like Protein Kinase (LRR-RLK) Genes in Basal Angiosperm Amborella trichopoda

“…Then, MapInspect software (http://mapinspect.software.informer.com/) was used to produce the schematic diagrams of physical locations of LRR-RLK genes in scaffolds. As previous literature, tandem duplication cluster in this study was defined as a region containing two or more genes within 200 kb (Zan et al, 2013; Zhou et al, 2016). Furthermore, tandem duplication genes should show close relationship in phylogenetic tree.…”

“…In eudicots, such as A. thaliana, Brassica rapa, Solanum lycopersicum and Populus trichocarpa , 213, 303, 234, and 379 LRR-RLK genes, respectively, have been identified from the analysis of genome sequences (Shiu and Bleecker, 2001; Zan et al, 2013; Rameneni et al, 2015; Wei et al, 2015). Based on the sequence similarity and domain conservation, as many as 467 genes were identified in the Glycine max genome (Zhou et al, 2016). In monocot Oryza sativa , 309 LRR-RLK genes were found via genome-wide identification (Sun and Wang, 2011).…”

“…A recent study showed that another monocot Triticum aestivum has the largest number of LRR-RLK genes (531) as far as we know (Shumayla et al, 2016). Tandem duplication and whole genome duplication are major mechanisms underlying expansion of the LRR-RLK family in these species (Shiu and Bleecker, 2001, 2003; Sun and Wang, 2011; Zan et al, 2013; Zhou et al, 2016). After duplication, duplicated genes often accumulate mutations that lead to functional divergence.…”