title: Genome-wide comparative analysis of NBS-encoding genes in four Gossypium species.
abstract: BACKGROUND
  Nucleotide binding site (NBS) genes encode a large family of disease resistance (R) proteins in plants. The availability of genomic data of the two diploid cotton species, Gossypium arboreum and Gossypium raimondii, and the two allotetraploid cotton species, Gossypium hirsutum (TM-1) and Gossypium barbadense allow for a more comprehensive and systematic comparative study of NBS-encoding genes to elucidate the mechanisms of cotton disease resistance.
  
  
  RESULTS
  Based on the genome assembly data, 246, 365, 588 and 682 NBS-encoding genes were identified in G. arboreum, G. raimondii, G. hirsutum and G. barbadense, respectively. The distribution of NBS-encoding genes among the chromosomes was nonrandom and uneven, and was tended to form clusters. Gene structure analysis showed that G. arboreum and G. hirsutum possessed a greater proportion of CN, CNL, and N genes and a lower proportion of NL, TN and TNL genes compared to that of G. raimondii and G. barbadense, while the percentages of RN and RNL genes remained relatively unchanged. The percentage changes among them were largest for TNL genes, about 7 times. Exon statistics showed that the average exon numbers per NBS gene in G. raimondii and G. barbadense were all greater than that in G. arboretum and G. hirsutum. Phylogenetic analysis revealed that the TIR-NBS genes of G. barbadense were closely related with that of G. raimondii. Sequence similarity analysis showed that diploid cotton G. arboreum possessed a larger proportion of NBS-encoding genes similar to that of allotetraploid cotton G. hirsutum, while diploid G. raimondii possessed a larger proportion of NBS-encoding genes similar to that of allotetraploid cotton G. barbadense. The synteny analysis showed that more NBS genes in G. raimondii and G. arboreum were syntenic with that in G. barbadense and G. hirsutum, respectively.
  
  
  CONCLUSIONS
  The structural architectures, amino acid sequence similarities and synteny of NBS-encoding genes between G. arboreum and G. hirsutum, and between G. raimondii and G. barbadense were the highest among comparisons between the diploid and allotetraploid genomes, indicating that G. hirsutum inherited more NBS-encoding genes from G. arboreum, while G. barbadense inherited more NBS-encoding genes from G. raimondii. This asymmetric evolution of NBS-encoding genes may help to explain why G. raimondii and G. barbadense are more resistant to Verticillium wilt, whereas G. arboreum and G. hirsutum are more susceptible to Verticillium wilt. The disease resistances of the allotetraploid cotton were related to their NBS-encoding genes especially in regard from which diploid progenitor they were derived, and the TNL genes may have a significant role in disease resistance to Verticillium wilt in G. raimondii and G. barbadense.
authors.affiliation: State Key Laboratory of Cotton Biology, College of Life Science, Henan Key Laboratory of Plant Stress Biology, Henan University, Kaifeng, Henan, 475004, China.|College of Bioinformation, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China.
authors.forename: Liuxin
authors.initials: L
authors.lastname: Xiang
authors.affiliation: United States Department of Agriculture, Southern Plains Agricultural Research Center, Agricultural Research Service, 2765 F & B Rd, College Station, TX, 77845, USA.
authors.forename: Jinggao
authors.initials: J
authors.lastname: Liu
authors.affiliation: College of Bioinformation, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China.
authors.forename: Chaofeng
authors.initials: C
authors.lastname: Wu
authors.affiliation: College of Bioinformation, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China.
authors.forename: Yushan
authors.initials: Y
authors.lastname: Deng
authors.affiliation: State Key Laboratory of Cotton Biology, College of Life Science, Henan Key Laboratory of Plant Stress Biology, Henan University, Kaifeng, Henan, 475004, China.
authors.forename: Chaowei
authors.initials: C
authors.lastname: Cai
authors.affiliation: State Key Laboratory of Cotton Biology, College of Life Science, Henan Key Laboratory of Plant Stress Biology, Henan University, Kaifeng, Henan, 475004, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Cotton Biology, College of Life Science, Henan Key Laboratory of Plant Stress Biology, Henan University, Kaifeng, Henan, 475004, China. yingfancai@outlook.com.
authors.forename: Yingfan
authors.initials: Y
authors.lastname: Cai
mesh_terms: D001665:Binding Sites; D002874:Chromosome Mapping / Q000379:methods; D060467:Disease Resistance; D019143:Evolution, Molecular; D018506:Gene Expression Regulation, Plant; D003368:Gossypium / Q000145:classification* / Q000235:genetics*; D005810:Multigene Family; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D017422:Sequence Analysis, DNA; D026801:Synteny
chemical_list: D010940:Plant Proteins
keywords: Amino acid sequence similarity; Disease resistance; Gene structure; Gossypium species; NBS-encoding gene