State Key Laboratory of Cotton Biology/ Institute of Cotton Research, Chinese Academy of Agricultural Sciences / Key Laboratory for Cotton Genetic Improvement, Anyang, 455000, Henan, China.
Hanzhong Agricultural Science Institute, Hanzhong, 723000, Shanxi, China.
BMC Genomics. 2020 Mar 6;21(1):213. doi: 10.1186/s12864-020-6638-5.
The U-box gene encodes a ubiquitin ligase that contain U-box domain. The plant U-box gene (PUB) plays an important role in the response to stresses, but few reports about PUBs in cotton were available. Therefore research on PUBs is of great importance and a necessity when studying the mechanisms of stress- tolerance in cotton.
In this study, we identified 93, 96, 185 and 208 PUBs from four sequenced cotton species G. raimondii (D), G. arboreum (A), G. hirsutum (AD) and G. barbadense (AD2), respectively. Prediction analysis of subcellular localization showed that the PUBs in cotton were widely localized in cells, but primarily in the nucleus. The PUBs in cotton were classified into six subfamilies (A-F) on the basis of phylogenetic analysis, which was testified by the analysis of conserved motifs and exon-intron structures. Chromosomal localization analysis showed that cotton PUBs were unevenly anchored on all chromosomes, varying from 1 to 14 per chromosome. Through multiple sequence alignment analysis, 3 tandem duplications and 28 segmental duplications in cotton genome D, 2 tandem duplications and 25 segmental duplications in A, and 143 homologous gene pairs in A and D were found; however no tandem duplications in A or D were found. Additionally, 105, 14 and 17 homologous gene pairs were found in the intra-subgenome of At and Dt, At sub-genome and Dt sub-genome of G. hirsutum, respectively. Functional analysis of GhPUB85A and GhPUB45D showed that these genes positively responded to abiotic stresses, but the expression patterns were different. In addition, although the expression levels of these two homologous genes were similar, their contributions were different when responding to stresses, specifically showing different responses to abiotic stresses and functional differences between the two subgenomes of G. hirsutum.
This study reported the genome-wide identification, structure, evolution and expression analysis of PUBs in cotton, and the results showed that the PUBs were highly conserved throughout the evolutionary history of cotton. All PUB genes were involved in the response to abiotic stresses (including salt, drought, hot and cold) to varying degrees.
U 盒基因编码一种含有 U 盒结构域的泛素连接酶。植物 U 盒基因（PUB）在应对胁迫反应中发挥着重要作用，但有关棉花 PUB 的报道很少。因此，研究 PUB 对于研究棉花的耐胁迫机制具有重要意义。
本研究从四个已测序的棉花物种中分别鉴定出雷蒙德氏棉（D）、亚洲棉（A）、陆地棉（AD）和海岛棉（AD2）中的 93、96、185 和 208 个 PUB。亚细胞定位预测分析表明，棉花 PUB 广泛定位于细胞中，但主要位于细胞核中。基于系统进化分析，将棉花 PUB 分为六个亚家族（A-F），这一点通过保守基序和外显子-内含子结构分析得到了验证。染色体定位分析表明，棉花 PUB 不均匀地定位于所有染色体上，每个染色体上有 1 到 14 个 PUB。通过多序列比对分析，在棉花基因组 D 中发现了 3 个串联重复和 28 个片段重复，在 A 中发现了 2 个串联重复和 25 个片段重复，在 A 和 D 中发现了 143 对同源基因对；但在 A 或 D 中未发现串联重复。此外，在 G. hirsutum 的 At 和 Dt 亚基因组、At 亚基因组和 Dt 亚基因组之间分别发现了 105、14 和 17 对同源基因对。GhPUB85A 和 GhPUB45D 的功能分析表明，这些基因对非生物胁迫呈正响应，但表达模式不同。此外，尽管这两个同源基因的表达水平相似，但它们在应对胁迫时的贡献不同，具体表现为对非生物胁迫的不同响应以及 G. hirsutum 两个亚基因组之间的功能差异。
本研究报道了棉花 PUB 的全基因组鉴定、结构、进化和表达分析，结果表明 PUB 在棉花的进化历史中高度保守。所有 PUB 基因都不同程度地参与了对非生物胁迫（包括盐、干旱、热和冷）的响应。
