Genome-Wide Identification and Evolution of Receptor-Like Kinases (RLKs) and Receptor like Proteins (RLPs) in Brassica juncea

Abstract

Brassica juncea, an allotetraploid species, is an important germplasm resource for canola improvement, due to its many beneficial agronomic traits, such as heat and drought tolerance and blackleg resistance. Receptor-like kinase (RLK) and receptor-like protein (RLP) genes are two types of resistance gene analogues (RGA) that play important roles in plant innate immunity, stress response and various development processes. In this study, genome wide analysis of RLKs and RLPs is performed in B. juncea. In total, 493 RLKs (LysM-RLKs and LRR-RLKs) and 228 RLPs (LysM-RLPs and LRR-RLPs) are identified in the genome of B. juncea, using RGAugury. Only 13.54% RLKs and 11.79% RLPs are observed to be grouped within gene clusters. The majority of RLKs (90.17%) and RLPs (52.83%) are identified as duplicates, indicating that gene duplications significantly contribute to the expansion of RLK and RLP families. Comparative analysis between B. juncea and its progenitor species, B. rapa and B. nigra, indicate that 83.62% RLKs and 41.98% RLPs are conserved in B. juncea, and RLPs are likely to have a faster evolution than RLKs. This study provides a valuable resource for the identification and characterisation of candidate RLK and RLP genes.

Mining of Cloned Disease Resistance Gene Homologs (CDRHs) in Brassica Species and Arabidopsis thaliana

“…The fewer RGAs in the individual sub-genomes of the Brassica polyploids compared to their diploid genome progenitor that we found in this study is consistent with the other Brassica RGA studies [ 11 , 96 , 109 , 110 , 111 , 112 ]. Duplicated disease R genes or RGAs are favourably lost in the sub-genomes of polyploid Brassicas after a duplication event compared to their diploid genome progenitors [ 109 , 110 , 113 , 114 ].…”

“…To perform the homology search, the protein sequence of each of the cloned genes was aligned across the seven genomes using translated Basic Local Alignment Search Tool (tBLASTn) using CoGeBlast [ 93 ]. Following the criteria used by previous studies identifying homologous genes in plants, tBLASTn hits with an E value range outside E0 to E-45 [ 94 , 95 , 96 ] or which did not have >70% similarity [ 96 , 97 , 98 , 99 ] were removed from further analyses. Since the smallest reference gene used in the study, At_Rpw8.1 , has 148 aa [ 75 ], any tBLASTn hits with <148 aa, were also removed from further analyses.…”

Analyses of Lysin-motif Receptor-like Kinase (LysM-RLK) Gene Family in Allotetraploid Brassica napus L. and Its Progenitor Species: An In Silico Study

“…Study of RGAs of 30 species of Brassicaceae showed that between 5 and 14 LysM-RLK genes are present in the different assembly versions of B. napus [ 4 ]. The study of RLK and RLP in Brassica juncea also showed that the number of LysM-RLK genes in this plant is low and in contrast, LRR-RLK genes have a high frequency [ 4 , 81 ].The observed difference in the number of LysM-RLK genes identified in this study may be due to differences in detection criteria and differences in B. napus assembly versions. RLKs has been identified in many plants such as Arabidopsis thaliana , Oryza sativa , Brachypodium distachyon , Citrus sinensis , Triticum aestivum , Gossypium hirsutum , Pyrus bretschneideri , Malus domestica, Solanum tuberosum and B .…”

“…RLKs has been identified in many plants such as Arabidopsis thaliana , Oryza sativa , Brachypodium distachyon , Citrus sinensis , Triticum aestivum , Gossypium hirsutum , Pyrus bretschneideri , Malus domestica, Solanum tuberosum and B . juncea that containing 14, 20, 11, 9, 117, 60, 18, 21, 10 and 11 RLKs genes, respectively [ 16 , 17 , 39 , 40 , 43 , 78 , 81 , 82 ]. Due to the variability of the number of genes in different plant species, it can be concluded that the expansion of the LysM-RLK gene family is species-specific resulted from gene duplication events [ 83 ].…”

Tissue-Specific RNA-Seq Analysis and Identification of Receptor-Like Proteins Related to Plant Growth in Capsicum annuum

“…The RNA-seq has been widely applied to research including the analysis of gene expression and prediction of gene function since next-generation sequencing has been easily available to use. Several studies have reported the genome-wide identification of RLP genes in Arabidopsis, rice, tomato, Brassica, and legumes [ 24 , 29 , 30 , 31 , 32 , 33 ]. However, no previous study has reported the genome-wide transcriptional profiles in organ-specific of RLPs in pepper.…”