title: Species-specific duplications of NBS-encoding genes in Chinese chestnut (Castanea mollissima).
abstract: The disease resistance (R) genes play an important role in protecting plants from infection by diverse pathogens in the environment. The nucleotide-binding site (NBS)-leucine-rich repeat (LRR) class of genes is one of the largest R gene families. Chinese chestnut (Castanea mollissima) is resistant to Chestnut Blight Disease, but relatively little is known about the resistance mechanism. We identified 519 NBS-encoding genes, including 374 NBS-LRR genes and 145 NBS-only genes. The majority of Ka/Ks were less than 1, suggesting 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 pressure. Furthermore, Ks peaked at a range of 0.4 to 0.5, indicating that ancient duplications arose during the evolution. 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. Notably, species-specific duplications were detected in NBS-encoding genes. In addition, the group of 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.
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhong
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
authors.forename: Yingjun
authors.initials: Y
authors.lastname: Li
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
authors.forename: Kaihui
authors.initials: K
authors.lastname: Huang
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
authors.forename: Zong-Ming
authors.initials: ZM
authors.lastname: Cheng
mesh_terms: D029962:Fagaceae / Q000145:classification / Q000235:genetics*; D018628:Gene Dosage; D020440:Gene Duplication; D017343:Genes, Plant; D018745:Genome, Plant; D010802:Phylogeny; D011401:Promoter Regions, Genetic; D012641:Selection, Genetic; D013045:Species Specificity