title: Dramatic Number Variation of R Genes in Solanaceae Species Accounted for by a Few R Gene Subfamilies.
abstract: Most disease resistance genes encode nucleotide-binding-site (NBS) and leucine-rich-repeat (LRR) domains, and the NBS-LRR encoding genes are often referred to as R genes. Using newly developed approach, 478, 485, 1,194, 1,665, 2,042 and 374 R genes were identified from the genomes of tomato Heinz1706, wild tomato LA716, potato DM1-3, pepper Zunla-1 and wild pepper Chiltepin and tobacco TN90, respectively. The majority of R genes from Solanaceae were grouped into 87 subfamilies, including 16 TIR-NBS-LRR (TNL) and 71 non-TNL subfamilies. Each subfamily was annotated manually, including identification of intron/exon structure and intron phase. Interestingly, TNL subfamilies have similar intron phase patterns, while the non-TNL subfamilies have diverse intron phase due to frequent gain of introns. Prevalent presence/absence polymorphic R gene loci were found among Solanaceae species, and an integrated map with 427 R loci was constructed. The pepper genome (2,042 in Chiltepin) has at least four times of R genes as in tomato (478 in Heinz1706). The high number of R genes in pepper genome is due to the amplification of R genes in a few subfamilies, such as the Rpi-blb2 and BS2 subfamilies. The mechanism underlying the variation of R gene number among different plant genomes is discussed.
authors: Key Laboratory of Horticultural Plant Biology, Ministry of Education, and Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, P.R. China, 430070.|College of Horticulture, Northwest A&F University, Yangling, Shanxi, China, 712100.
authors: Chunhua
authors: C
authors: Wei
authors: Key Laboratory of Horticultural Plant Biology, Ministry of Education, and Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, P.R. China, 430070.
authors: Jiongjiong
authors: J
authors: Chen
authors: Key Laboratory of Horticultural Plant Biology, Ministry of Education, and Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, P.R. China, 430070.
authors: Hanhui
authors: H
authors: Kuang
mesh_terms: D056915:DNA Copy Number Variations; D060467:Disease Resistance / Q000235:genetics*; D019143:Evolution, Molecular; D018628:Gene Dosage; D017343:Genes, Plant; D018745:Genome, Plant; D005810:Multigene Family; D011110:Polymorphism, Genetic; D019657:Solanaceae / Q000235:genetics*