title: Species-specific duplications driving the recent expansion of NBS-LRR genes in five Rosaceae species.
abstract: BACKGROUND
  Disease resistance (R) genes from different Rosaceae species have been identified by map-based cloning for resistance breeding. However, there are few reports describing the pattern of R-gene evolution in Rosaceae species because several Rosaceae genome sequences have only recently become available.
  
  
  RESULTS
  Since most disease resistance genes encode NBS-LRR proteins, we performed a systematic genome-wide survey of NBS-LRR genes between five Rosaceae species, namely Fragaria vesca (strawberry), Malus × domestica (apple), Pyrus bretschneideri (pear), Prunus persica (peach) and Prunus mume (mei) which contained 144, 748, 469, 354 and 352 NBS-LRR genes, respectively. A high proportion of multi-genes and similar Ks peaks (Ks = 0.1- 0.2) of gene families in the four woody genomes were detected. A total of 385 species-specific duplicate clades were observed in the phylogenetic tree constructed using all 2067 NBS-LRR genes. High percentages of NBS-LRR genes derived from species-specific duplication were found among the five genomes (61.81% in strawberry, 66.04% in apple, 48.61% in pear, 37.01% in peach and 40.05% in mei). Furthermore, the Ks and Ka/Ks values of TIR-NBS-LRR genes (TNLs) were significantly greater than those of non-TIR-NBS-LRR genes (non-TNLs), and most of the NBS-LRRs had Ka/Ks ratios less than 1, suggesting that they were evolving under a subfunctionalization model driven by purifying selection.
  
  
  CONCLUSIONS
  Our results indicate that recent duplications played an important role in the evolution of NBS-LRR genes in the four woody perennial Rosaceae species. Based on the phylogenetic tree produced, it could be inferred that species-specific duplication has mainly contributed to the expansion of NBS-LRR genes in the five Rosaceae species. In addition, the Ks and Ka/Ks ratios suggest that the rapidly evolved TNLs have different evolutionary patterns to adapt to different pathogens compared with non-TNL resistant genes.
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China. yzhong@njau.edu.cn.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhong
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China. 2011104015@njau.edu.cn.
authors.forename: Huan
authors.initials: H
authors.lastname: Yin
authors.affiliation: Centre for Research and Innovation, Fondazione Edmund Mach, San Michele all'Adige, 38010, Italy. dan.sargent@fmach.it.
authors.forename: Daniel James
authors.initials: DJ
authors.lastname: Sargent
authors.affiliation: Centre for Research and Innovation, Fondazione Edmund Mach, San Michele all'Adige, 38010, Italy. mickael.malnoy@iasma.it.
authors.forename: Mickael
authors.initials: M
authors.lastname: Malnoy
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China. zmc@njau.edu.cn.|Department of Plant Science, University of Tennessee, Knoxville, 37996, USA. zmc@njau.edu.cn.
authors.forename: Zong-Ming Max
authors.initials: ZM
authors.lastname: Cheng
mesh_terms: D060467:Disease Resistance / Q000235:genetics; D019143:Evolution, Molecular; D005638:Fruit / Q000235:genetics / Q000378:metabolism; D020440:Gene Duplication; D018745:Genome, Plant; D010802:Phylogeny; D010940:Plant Proteins / Q000145:classification / Q000235:genetics*; D027824:Rosaceae / Q000235:genetics* / Q000378:metabolism; D013045:Species Specificity
chemical_list: D010940:Plant Proteins