Genome-wide Analysis Of NBS-encoding Genes In Chinese Chestnut And Kiwifruit

NBS-encoding gene family consists of NBS-only genes and NBS-LRR genes.The class of nucleotide-binding site(NBS)-leucine-rich repeat(LRR)genes is one of the largest R gene families,playing an important role in protecting plants from infection of pathogens.The analysis of this R gene family will help us screen and identify candidate R genes.Chinese chestnut(Castanea mollissima)and kiwifruit(Actinidia chinensis)are commercially valuable and nutritionally important fruits.But they are subject to infection by various pathogens in the natural environment,which reduce yield and quantity of fruit.In this study,we used the bioinformatics methods to identify NBS-encoding genes,classify gene families,calculate duplication time and selection pressure,and analyze cis-acting elements.1.We identified 519 NBS-encoding genes in Chinese chestnut,including 374 NBS-LRR genes.Ks peaked at a range of 0.4 to 0.5,indicating that ancient duplications arose during the evolution.Species-specific duplications were detected in NBS-encoding genes.The majority of Ka/Ks were less than 1,suggesting that the purifying selection operated during the evolutionary history of NBS-encoding genes.A minority(4/34)of Ka/Ks in non-TIR gene families were greater than 1,showing that some genes were under positive selection.The relationship between Ka/Ks and Ks indicated greater selective pressure on the newer and older genes with the critical value of Ks = 0.4-0.5.RPW8-NBS-encoding genes clustered together as an independent clade located at a relatively basal position in the phylogenetic tree.Many cis-acting elements related to plant defense responses were detected in promoters of NBS-encoding genes in Chinese chestnut.2.In kiwifruiti we identified 96 NBS-encoding genes,including 74 NBS-LRR genes.The curve of Ks peaked in a range from 0.1 to 0.2,demonstrating that the recent duplication of NBS-encoding genes occurred in kiwifruit genome.Ka/Ks increased gradually with the Ks increasing from 0 to 1,indicating that the more recent genes were under the less selection pressure in the evolutionary process.The majority(11/13)of Ka/Ks in gene families were smaller than 1,indicating that the purifying selection played the major role in evolution in kiwifruit NBS-encoding genes.Meanwhile,125 amino acid sites identified in six multi-gene families underwent positive selection.