Abstract
Plant disease resistance genes are a key component of defending plants from a range of pathogens. The majority of these resistance genes belong to the super-family that harbors a Nucleotide-binding site (NBS). A number of studies have focused on NBS-encoding genes in disease resistant breeding programs for diverse plants. However, little information has been reported with an emphasis on systematic analysis and comparison of NBS-encoding genes in cotton. To fill this gap of knowledge, in this study, we identified and investigated the NBS-encoding resistance genes in cotton using the whole genome sequence information of Gossypium raimondii. Totally, 355 NBS-encoding resistance genes were identified. Analyses of the conserved motifs and structural diversity showed that the most two distinct features for these genes are the high proportion of non-regular NBS genes and the high diversity of N-termini domains. Analyses of the physical locations and duplications of NBS-encoding genes showed that gene duplication of disease resistance genes could play an important role in cotton by leading to an increase in the functional diversity of the cotton NBS-encoding genes. Analyses of phylogenetic comparisons indicated that, in cotton, the NBS-encoding genes with TIR domain not only have their own evolution pattern different from those of genes without TIR domain, but also have their own species-specific pattern that differs from those of TIR genes in other plants. Analyses of the correlation between disease resistance QTL and NBS-encoding resistance genes showed that there could be more than half of the disease resistance QTL associated to the NBS-encoding genes in cotton, which agrees with previous studies establishing that more than half of plant resistance genes are NBS-encoding genes.
Highlights
Plant diseases can dramatically reduce crop yield and quality
To identify nucleotide binding sites (NBS)-encoding resistance genes in the diploid cotton, first, a set of 113 manually curated reference disease resistance genes was selected from plant resistance gene database [32] (Table S3), and the protein sequence of the 40,976 protein-coding genes were subsequently checked for sequence homology with at least one resistance protein contained in the reference dataset using the BLAST algorithm with a stringent e-value cut-off of 1610215; in the second step, domain analysis of all the BLAST hits were performed using InterProScan version 5RC2 [33] with standard options and the InterPro database release 7.2; in the third step, the genes with NBS domain were filtered out according to the NBS domain annotation (PF00931) given by the Pfam (Protein family) database [34]
Identification and classification of NBS-encoding genes Using the most recent diploid cotton (G. raimondii) genome sequence data provided by Cotton Research Institute, Chinese Academy of Agricultural Sciences, a total of 355 NBS disease resistance genes were identified within the assembled sequence of G. raimondii
Summary
Plant diseases can dramatically reduce crop yield and quality. Pathogens and pests are the two major factors causing plant diseases. Disease resistance genes (R-genes) play a critical role in plant disease-resistance detection and they response to several pathogens and pests, including viruses, bacteria, fungi, nematodes, and insects. Evolution, and molecular basis of the NBS genes, Genome-wide identification and analysis of NBS genes have been performed on many plants [3,4,5,6,7,8,9,10,11,12,13,14,15,16,17]. In order to increase crop yield and quality, it is important to conduct genomic studies of NBS genes to better understand the mechanism of plant susceptibility and resistance
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