Resistance Gene Analogs in the Brassicaceae: Identification, Characterization, Distribution, and Evolution

Abstract

The Brassicaceae consists of a wide range of species, including important Brassica crop species and the model plant Arabidopsis (Arabidopsis thaliana). Brassica spp. crop diseases impose significant yield losses annually. A major way to reduce susceptibility to disease is the selection in breeding for resistance gene analogs (RGAs). Nucleotide binding site-leucine rich repeats (NLRs), receptor-like kinases (RLKs), and receptor-like proteins (RLPs) are the main types of RGAs; they contain conserved domains and motifs and play specific roles in resistance to pathogens. Here, all classes of RGAs have been identified using annotation and assembly-based pipelines in all available genome annotations from the Brassicaceae, including multiple genome assemblies of the same species where available (total of 32 genomes). The number of RGAs, based on genome annotations, varies within and between species. In total 34,065 RGAs were identified, with the majority being RLKs (21,691), then NLRs (8,588) and RLPs (3,786). Analysis of the RGA protein sequences revealed a high level of sequence identity, whereby 99.43% of RGAs fell into several orthogroups. This study establishes a resource for the identification and characterization of RGAs in the Brassicaceae and provides a framework for further studies of RGAs for an ultimate goal of assisting breeders in improving resistance to plant disease.

Figure 1.

Phylogeny of Brassicaceae genomes based on R genes. The colored bars show the percentages of RLKs and RLPs in each genome. Genes were identified using RGAugury.

Figure 2.

Phylogeny of Brassicaceae genomes based on R genes. The colored bars show the percentage of NLRs in each genome. Genes were identified using RGAugury. Boxes show the agreement of the presented results with the previously reported phylogenetic relationship of Brassicaceae by Huang et al. (2016). All species from clade A grouped and formed a separate clade, similar to species from clade B and F. Species from the Cleomaceae family formed a separate clade from all Brassicaceae family species.

Figure 3.

Comparing the NLR, RLK, and RLP ratios with assembled sizes of the genomes, illustrating no clear link between the genome size and the ratio of RGAs.

Figure 4.

Phylogeny of Brassicaceae genomes based on R genes. The colored bars show the percentage of NLRs in each genome. Genes were identified using NLR-Annotator.

Figure 5.

Distribution and density of RGAs in genomes of Brassica spp. RGAs are presented from B. oleracea (ending in o), B. rapa (ending in r), and B. napus (ending in n) genomes.

Figure 6.

Significance test of phylogenetic signals for RLKs, RLPs, and NLRs across the Brassicaceae using autocorrection (local Moran’s I) metrics. Red bars represent genomes with significant phylogenetic autocorrelation (P < 0.05).