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

Abstract

The LysM receptor-like kinases (LysM-RLKs) play a crucial role in plant symbiosis and response to environmental stresses. Brassica napus, B. rapa, and B. oleracea are utilized as valuable vegetables. Different biotic and abiotic stressors affect these crops, resulting in yield losses. Therefore, genome-wide analysis of the LysM-RLK gene family was conducted. From the genome of the examined species, 33 LysM-RLK have been found. The conserved domains of Brassica LysM-RLKs were divided into three groups: LYK, LYP, and LysMn. In the BrassicaLysM-RLK gene family, only segmental duplication has occurred. The Ka/Ks ratio for the duplicated pair of genes was less than one indicating that the genes' function had not changed over time. The BrassicaLysM-RLKs contain 70 cis-elements, indicating that they are involved in stress response. 39 miRNA molecules were responsible for the post-transcriptional regulation of 12 Brassica LysM-RLKs. A total of 22 SSR loci were discovered in 16 Brassica LysM-RLKs. According to RNA-seq data, the highest expression in response to biotic stresses was related to BnLYP6. According to the docking simulations, several residues in the active sites of BnLYP6 are in direct contact with the docked chitin and could be useful in future studies to develop pathogen-resistant B. napus. This research reveals comprehensive information that could lead to the identification of potential genes for Brassica species genetic manipulation.

Keywords: bioinformatics; codon usage bias; expression pattern; in silico study; modeling; molecular docking.

Figure 1

Phylogenetic relationships of LysM-RLK genes from Brassica napus (Bn), Brassica rapa (Br), Brassica oleracea (Bo), Oryza sativa (Os), Arabidopsis thaliana (At), Vitis vinifera (Vv), and Brachypodium distachyon (Bd). Colored branches have been used to depict various subfamilies. The phylogenetic dendrogram was constructed using MEGA 7 software and the neighbor-joining (NJ) method with 1000 bootstraps.

Figure 2

The chromosomal location of LysM-RLK genes and the duplication relationship between them. Colored boxes represent chromosomes. Curves are used to show gene duplications.

Figure 3

The conserved motifs (A) and exon-intron structure (B) of LysM-RLK genes in Brassica species. Exons and introns were represented by green boxes and black lines, respectively. Different motifs are shown by different colors Exon-intron structure and Motifs were determined using gene structure display server (GSDS) and MEME online tool, respectively.

Figure 4

The expression pattern of LysM-RLK genes in different tissues. The color boxes indicate expression values, the lowest (green), medium (black), and the highest (red).

Figure 5

The expression pattern of LysM-RLK genes under abiotic stresses. The color boxes indicate expression values, the lowest (green), medium (black), and the highest (red).

Figure 6

The expression pattern of LysM-RLK genes in response to Sclerotinia clerotiorum infection. The color boxes indicate expression values, the lowest (green), medium (black), and the highest (red). R, S, and C indicate resistant (J964), susceptible (J902), and control plants, respectively.

Figure 7

The expression pattern of LysM-RLK genes in response to Leptosphaeria maculans infection. The color boxes indicate expression values, the lowest (green), medium (black), and the highest (red). R, S, C, and T indicate resistant (DF78), susceptible (Westar), control, and treatment plants, respectively.

Figure 8

The BnLYP6 protein features. Secondary and three-dimensional model structure (A,B). The residues involved in the BnLYP6-chitin interaction (C). Docking studies of the three-dimensional structure of chitin onto the predicted model of BnLYP6 (D). AutoDock v4.2.6 has been used to analyze ligand-protein interaction.

Figure 9

Relative synonymous codon usage analysis (RSCU) values of Brassica LysM-RLKs are represented as a heat map. The color boxes represent RSCU values, with the lowest (blue) and maximum (red) codon usage. TBtools was used to construct the heatmap.