Genome-wide analysis of NBS-encoding disease resistance genes in Cucumis sativusand phylogenetic study of NBS-encoding genes in Cucurbitaceae crops

Abstract

BackgroundPlant nucleotide-binding site (NBS)-leucine-rich repeat (LRR) proteins encoded by resistance genes play an important role in the responses of plants to various pathogens, including viruses, bacteria, fungi, and nematodes. In this study, a comprehensive analysis of NBS-encoding genes within the whole cucumber genome was performed, and the phylogenetic relationships of NBS-encoding resistance gene homologues (RGHs) belonging to six species in five genera of Cucurbitaceae crops were compared.ResultsCucumber has relatively few NBS-encoding genes. Nevertheless, cucumber maintains genes belonging to both Toll/interleukine-1 receptor (TIR) and CC (coiled-coil) families. Eight commonly conserved motifs have been established in these two families which support the grouping into TIR and CC families. Moreover, three additional conserved motifs, namely, CNBS-1, CNBS-2 and TNBS-1, have been identified in sequences from CC and TIR families. Analyses of exon/intron configurations revealed that some intron loss or gain events occurred during the structural evolution between the two families. Phylogenetic analyses revealed that gene duplication, sequence divergence, and gene loss were proposed as the major modes of evolution of NBS-encoding genes in Cucurbitaceae species. Compared with NBS-encoding sequences from the Arabidopsis thaliana genome, the remaining seven TIR familes of NBS proteins and RGHs from Cucurbitaceae species have been shown to be phylogenetically distinct from the TIR family of NBS-encoding genes in Arabidopsis, except for two subfamilies (TIR4 and TIR9). On the other hand, in the CC-NBS family, they grouped closely with the CC family of NBS-encoding genes in Arabidopsis. Thus, the NBS-encoding genes in Cucurbitaceae crops are shown to be ancient, and NBS-encoding gene expansions (especially the TIR family) may have occurred before the divergence of Cucurbitaceae and Arabidopsis.ConclusionThe results of this paper will provide a genomic framework for the further isolation of candidate disease resistance NBS-encoding genes in cucumber, and contribute to the understanding of the evolutionary mode of NBS-encoding genes in Cucurbitaceae crops.

Plant Nucleotide Binding Site–Leucine-Rich Repeat (NBS-LRR) Genes: Active Guardians in Host Defense Responses

“…To date, a large number of NBS-encoding sequences have been isolated from various plant species through genome-wide analyses: from about 50 in papaya and Cucumis sativus [12,13], to 653 in Oryza sativa [14]. More details are shown in Table 1, that reports the number of NBS-encoding genes identified in different species up to now.…”

Identification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrass

“…A few plant species, such as cucumber [28] and papaya [29], have considerably less than 0.5 % NB-LRR genes. Additionally, NB-LRR genes in grass species have been calculated to make up anywhere from 0.4 to 1.35 % the total number of predicted proteins [25].…”

Distinct Patterns of Gene Gain and Loss: Diverse Evolutionary Modes of NBS-Encoding Genes in Three Solanaceae Crop Species

“…Li et al 2010; X. Li et al 2010; Lozano et al 2012; Luo et al 2012; Meyers et al 2003; Monosi et al 2004; Mun et al 2009; Porter et al 2009; Tan and Wu 2012; Wan et al 2013; Wei et al 2013; Wu et al 2014; Yang et al 2006, 2008; Zhou et al 2004). Additionally, comparative genomic studies of the evolutionary history of NBS-encoding genes have identified evolutionary characteristics and patterns of NBS-encoding genes in a number of clades.…”