Comparative analysis of evolutionary dynamics of genes encoding leucine-rich repeat receptor-like kinase between rice and Arabidopsis

Abstract

The leucine-rich repeat (LRR) receptor kinase (RLK) proteins constitute a large superfamily in the plant genome, and carry out key functions in a variety of biological pathways. In an effort to determine the evolutionary fate of members of a large gene family such as plant LRR RLK proteins we conducted in silico analysis using complete genome sequencing datasets, genome-wide transcriptome databases, and bioinformatics tools. A total of 292 and 165 LRR RLK genes were retrieved from the rice and Arabidopsis genomes, respectively, formed by diverse duplication events for gene expansion. The phylogenic analyses of the LRR RLK genes suggested combinations of LRR domains and RLK domains in the ancient plant genome prior to the divergence of rice and Arabidopsis, followed by massive independent expansions during speciation. The somewhat high frequencies (50-73%) of expressional divergence of members of duplicate gene pairs formed by whole/segmental genome duplication (W/SGD) and tandem duplication (TD) events of Arabidopsis and TD events of rice support the idea of their functional diversity for gene retention. By contrast, a relatively low degree (at least 20%) of members of rice LRR RLK gene pairs formed by W/SGD appear to be divergent in expression following the duplication event. At least 7 pairs of co-expressed gene clusters, including each of the tentative orthologous LRR RLK genes between rice and Arabidopsis, were enriched to an orthologous set between members of each of the pairs as compared to those of the random pairs, suggesting some degree of functional conservation of individual genes. These results may shed some light on the crucial functions of the plant LRR RLK genes with regard to a variety of biological processes.

Genome-wide identification, characterization and expression analysis of populusleucine-rich repeat receptor-like protein kinase genes

“…PtLRR-RLK genes were comprehensively distributed within the poplar genome and 22 genes are localized to unassembled genomic sequence scaffolds and thus could not be mapped to any particular chromosome (Figure 3). Approximately 82% (312 out of 379) PtLRR-RLK genes are located in the replicated region, which is different from rice and Arabidopsis in which the frequencies of genes generated by S/WGDs are much lower (11% in rice and 26% in Arabidopsis ) [45]. Among them, 140 genes lacked duplicates on the corresponding duplicated blocks, suggesting that dynamic rearrangement, mutation or segmental loss may have occurred following the segmental duplication.…”

Differential retention and expansion of the ancestral genes associated with the paleopolyploidies in modern rosid plants, as revealed by analysis of the extensins super-gene family

“…If the paralogous extensins had expanded neither through W/SGD nor TD, they were considered to have proliferated via other duplication strategies [33]. …”

Tackling Drought Stress: RECEPTOR-LIKE KINASES Present New Approaches

“…Whole-genome studies have further shown that genes encoding the largest RLK subfamily of LRR RLKs covary significantly between species in terms of numbers and structure and therefore have been predicted to possess similar functions (Hwang et al, 2011;. Their evolutionary conservation therefore circumvents the problematic genetic differences between model and crop species and allows global extrapolation after LRR RLK studies have been performed in model plants (Shiu et al, 2004).…”