Comparative Genomics Of Plant NBS-LRR Disease Resistance Genes And Small RNAs

Crop disease is a global problem, posing a serious threat to food security. Utilizing resistant cultivars is an efficient, economical and environmentally friendly method to control crop disease. The proper use of resistance resources for breeding requires a comprehensive understanding of the evolution of the genescontrolling disease resistance and related regulatory element. In this study, the evolution of plant resistance gene(R gene) and related small RNAs were examined systematically.We first identified R genes in four Poaceae genomes. R gene loci identified from different genomes were mapped onto the chromosomes of rice using comparative genomics. We found that frequent deletions and translocations of R genes generated prevalent presence/absence polymorphism between different species. R genes significantly reduced the synteny of their flanking regions. We extended analyze with 70 available land plant genomes, clustering all their R genes to R gene families. The Poaceae stood out for their composition of R genes, as the total number of R gene families encoded per genome was significantly higher than other plant families. Brassicaceae and Poaceae both stood out for more heterogeneous R gene pairs. In these two usuall species,the highly duplicated N gene and Form-2 families in other species were either absent or found in very low numbers; coupled with the relatively high level of heterogeneity in the R genes in Brassicaceae and Poaceae.Next, we examined the connection between R genes and the miRNAs that target them. For R genes highly amplified in a genome, there is a high probability that those genes are targeted by miRNAs. Duplicated gene families widely targeted by miR482/2118 are poorly amplified in Brassicaceae and Poaceae. The high level of conservation in the miRNAs matching with the first two positions of each codon, and the diversity in the third position, is consistent with selection acting more strongly at the amino acid level, with miRNAs diversifying to target the broadest range of proteinencoding targets. The results suggest a genomic model of a dynamic relationship between R genes and miRNAs, characterized by expansion in R gene copy number, leading to the periodic emergence of miRNAs which then act to contain potential fitness costs of their R progenitors.Finally, GC content of small RNA-generating sites and their flanking sequences inArabidopsis thaliana and rice was systematically analyzed in silico. High GC content fluctuation(GCF) exhibits at the borders of sRNA sites, while the GCF within sRNA sites is low. Furthermore, The GC content along sequences of some miniature invertedrepeat transposable elements(MITEs) families coincides with the abundance of MITEderived small RNAs. The GCF within phasiRNA clusters is negatively correlated with its phasing score. We conclude that high GC content and low GCF could increase the expression of small RNA. Our results provide further insights on small RNA expression,which might be applied to improve the silencing efficiency of RNAi and virus induced gene silencing.