Xiang Liuxin, Liu Jinggao, Wu Chaofeng, Deng Yushan, Cai Chaowei, Zhang Xiao, Cai Yingfan
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.
BMC Genomics. 2017 Apr 12;18(1):292. doi: 10.1186/s12864-017-3682-x.
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.
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.
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.
核苷酸结合位点（NBS）基因在植物中编码一大类抗病（R）蛋白。二倍体棉花物种亚洲棉（Gossypium arboreum）和雷蒙德氏棉（Gossypium raimondii）以及两个异源四倍体棉花物种陆地棉（Gossypium hirsutum，TM-1）和海岛棉（Gossypium barbadense）的基因组数据，使得对NBS编码基因进行更全面、系统的比较研究成为可能，从而阐明棉花抗病机制。
基于基因组组装数据，分别在亚洲棉、雷蒙德氏棉、陆地棉和海岛棉中鉴定出246、365、588和682个NBS编码基因。NBS编码基因在染色体间的分布是非随机且不均匀的，并且倾向于形成簇。基因结构分析表明，与雷蒙德氏棉和海岛棉相比，亚洲棉和陆地棉中CN、CNL和N基因的比例更高，而NL、TN和TNL基因的比例更低，而RN和RNL基因的百分比相对保持不变。其中TNL基因的百分比变化最大，约为7倍。外显子统计表明，雷蒙德氏棉和海岛棉中每个NBS基因的平均外显子数均多于亚洲棉和陆地棉。系统发育分析表明，海岛棉的TIR-NBS基因与雷蒙德氏棉的密切相关。序列相似性分析表明，二倍体棉花亚洲棉拥有与异源四倍体棉花陆地棉相似的较大比例的NBS编码基因，而二倍体雷蒙德氏棉拥有与异源四倍体棉花海岛棉相似的较大比例的NBS编码基因。共线性分析表明，雷蒙德氏棉和亚洲棉中分别有更多的NBS基因与海岛棉和陆地棉中的NBS基因共线性。
亚洲棉与陆地棉之间以及雷蒙德氏棉与海岛棉之间NBS编码基因的结构架构、氨基酸序列相似性和共线性在二倍体和异源四倍体基因组之间的比较中是最高的，这表明陆地棉从亚洲棉继承了更多的NBS编码基因，而海岛棉从雷蒙德氏棉继承了更多的NBS编码基因。NBS编码基因的这种不对称进化可能有助于解释为什么雷蒙德氏棉和海岛棉对黄萎病更具抗性，而亚洲棉和陆地棉对黄萎病更敏感。异源四倍体棉花的抗病性与其NBS编码基因有关，特别是与其衍生的二倍体祖先有关，并且TNL基因可能在雷蒙德氏棉和海岛棉对黄萎病的抗病性中起重要作用。
