title: Genome-wide analysis of the gene families of resistance gene analogues in cotton and their response to Verticillium wilt.
abstract: BACKGROUND
  Gossypium raimondii is a Verticillium wilt-resistant cotton species whose genome encodes numerous disease resistance genes that play important roles in the defence against pathogens. However, the characteristics of resistance gene analogues (RGAs) and Verticillium dahliae response loci (VdRLs) have not been investigated on a global scale. In this study, the characteristics of RGA genes were systematically analysed using bioinformatics-driven methods. Moreover, the potential VdRLs involved in the defence response to Verticillium wilt were identified by RNA-seq and correlations with known resistance QTLs.
  
  
  RESULTS
  The G. raimondii genome encodes 1004 RGA genes, and most of these genes cluster in homology groups based on high levels of similarity. Interestingly, nearly half of the RGA genes occurred in 26 RGA-gene-rich clusters (Rgrcs). The homology analysis showed that sequence exchanges and tandem duplications frequently occurred within Rgrcs, and segmental duplications took place among the different Rgrcs. An RNA-seq analysis showed that the RGA genes play roles in cotton defence responses, forming 26 VdRLs inside in the Rgrcs after being inoculated with V. dahliae. A correlation analysis found that 12 VdRLs were adjacent to the known Verticillium wilt resistance QTLs, and that 5 were rich in NB-ARC domain-containing disease resistance genes.
  
  
  CONCLUSIONS
  The cotton genome contains numerous RGA genes, and nearly half of them are located in clusters, which evolved by sequence exchanges, tandem duplications and segmental duplications. In the Rgrcs, 26 loci were induced by the V. dahliae inoculation, and 12 are in the vicinity of known Verticillium wilt resistance QTLs.
authors.affiliation: Laboratory of Cotton Disease, Institute of Agro-Products Processing Science & Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. chenjieyin@caas.cn.
authors.forename: Jie-Yin
authors.initials: JY
authors.lastname: Chen
authors.affiliation: BGI-Shenzhen, Shenzhen, Guangdong, 518083, China. huangjinqun@bgitechsolutions.com.
authors.forename: Jin-Qun
authors.initials: JQ
authors.lastname: Huang
authors.affiliation: Laboratory of Cotton Disease, Institute of Agro-Products Processing Science & Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. linanyang130430@126.com.
authors.forename: Nan-Yang
authors.initials: NY
authors.lastname: Li
authors.affiliation: Laboratory of Cotton Disease, Institute of Agro-Products Processing Science & Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. maxuefeng@caas.cn.
authors.forename: Xue-Feng
authors.initials: XF
authors.lastname: Ma
authors.affiliation: Laboratory of Cotton Disease, Institute of Agro-Products Processing Science & Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. jlwang201@163.com.
authors.forename: Jin-Long
authors.initials: JL
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen, Guangdong, 518083, China. liuchuan2@genomics.cn.
authors.forename: Chuan
authors.initials: C
authors.lastname: Liu
authors.affiliation: BGI-Shenzhen, Shenzhen, Guangdong, 518083, China. liuyongfeng@bgitechsolutions.com.
authors.forename: Yong-Feng
authors.initials: YF
authors.lastname: Liu
authors.affiliation: BGI-Shenzhen, Shenzhen, Guangdong, 518083, China. liangyong@genomics.org.cn.
authors.forename: Yong
authors.initials: Y
authors.lastname: Liang
authors.affiliation: Laboratory of Cotton Disease, Institute of Agro-Products Processing Science & Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. baoyuming@caas.cn.
authors.forename: Yu-Ming
authors.initials: YM
authors.lastname: Bao
authors.affiliation: Laboratory of Cotton Disease, Institute of Agro-Products Processing Science & Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. daixiaofeng@caas.cn.
authors.forename: Xiao-Feng
authors.initials: XF
authors.lastname: Dai
mesh_terms: D060467:Disease Resistance / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D055106:Genome-Wide Association Study; D003368:Gossypium / Q000235:genetics* / Q000382:microbiology*; D054884:Host-Pathogen Interactions / Q000235:genetics; D005810:Multigene Family; D010802:Phylogeny; D010935:Plant Diseases / Q000235:genetics* / Q000276:immunology / Q000382:microbiology; D040641:Quantitative Trait Loci / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid; D020172:Verticillium / Q000502:physiology*