Exploring Cloned Disease Resistance Gene Homologues and Resistance Gene Analogues in Brassica nigra, Sinapis arvensis, and Sinapis alba: Identification, Characterisation, Distribution, and Evolution

Abstract

This study identifies and classifies resistance gene analogues (RGAs) in the genomes of Brassica nigra, Sinapis arvensis and Sinapis alba using the RGAugury pipeline. RGAs were categorised into four main classes: receptor-like kinases (RLKs), receptor-like proteins (RLPs), nucleotide-binding leucine-rich repeat (NLR) proteins and transmembrane-coiled-coil (TM-CC) genes. A total of 4499 candidate RGAs were detected, with species-specific proportions. RLKs were the most abundant across all genomes, followed by TM-CCs and RLPs. The sub-classification of RLKs and RLPs identified LRR-RLKs, LRR-RLPs, LysM-RLKs, and LysM-RLPs. Atypical NLRs were more frequent than typical ones in all species. Atypical NLRs were more frequent than typical ones in all species. We explored the relationship between chromosome size and RGA count using regression analysis. In B. nigra and S. arvensis, larger chromosomes generally harboured more RGAs, while S. alba displayed the opposite trend. Exceptions were observed in all species, where some larger chromosomes contained fewer RGAs in B. nigra and S. arvensis, or more RGAs in S. alba. The distribution and density of RGAs across chromosomes were examined. RGA distribution was skewed towards chromosomal ends, with patterns differing across RGA types. Sequence hierarchical pairwise similarity analysis revealed distinct gene clusters, suggesting evolutionary relationships. The study also identified homologous genes among RGAs and non-RGAs in each species, providing insights into disease resistance mechanisms. Finally, RLKs and RLPs were co-localised with reported disease resistance loci in Brassica, indicating significant associations. Phylogenetic analysis of cloned RGAs and QTL-mapped RLKs and RLPs identified distinct clusters, enhancing our understanding of their evolutionary trajectories. These findings provide a comprehensive view of RGA diversity and genomics in these Brassicaceae species, providing valuable insights for future research in plant disease resistance and crop improvement.

Keywords: Brassicaceae; homologues; phylogenetic; resistance gene analogues; weed.

Figure 1

(a–c): Chromosomal distribution: RGAs are primarily located towards the ends of each chromosome. (d–f): Differential distribution: Different types of RGAs show varying distribution patterns along the chromosomes, with a notable absence near the centromeres.

Figure 2

Distribution and count of cloned disease resistance gene homologues identified from 49 cloned R genes across the genomes of B. nigra, S. arvensis, and S. alba. The figure illustrates the presence of various resistance domains, including RLK, RLP, CNL, TNL, RNL, TN, CN, RN, NL, TX, OTHER, and RPW8, highlighting the number and distribution of CDRHs containing these domains within each species.

Figure 3

The number and distribution of cloned disease resistance gene homologues associated with resistance to various diseases, including Alternaria black spot (ABS), blackleg (BL), bacterial leaf spot (BLS), clubroot (CR), downy mildew (DM), Fusarium wilt (FW), grey mould (GM), powdery mildew (PM), Sclerotinia stem rot (SSR), and white rust (WR) in the genomes of B. nigra, S. arvensis, and S. alba. The data presented reflects the analysis of 205 CDRHs associated with the 49 cloned R genes, highlighting their contributions to disease resistance across these Brassicaceae species.