Ding Mingquan, Chen Jiadong, Jiang Yurong, Lin Lifeng, Cao YueFen, Wang Minhua, Zhang Yuting, Rong Junkang, Ye Wuwei
The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, 311300, Zhejiang, China.
Mol Genet Genomics. 2015 Feb;290(1):151-71. doi: 10.1007/s00438-014-0904-7. Epub 2014 Sep 5.
WRKY transcription factors play important roles in various stress responses in diverse plant species. In cotton, this family has not been well studied, especially in relation to fiber development. Here, the genomes and transcriptomes of Gossypium raimondii and Gossypium arboreum were investigated to identify fiber development related WRKY genes. This represents the first comprehensive comparative study of WRKY transcription factors in both diploid A and D cotton species. In total, 112 G. raimondii and 109 G. arboreum WRKY genes were identified. No significant gene structure or domain alterations were detected between the two species, but many SNPs distributed unequally in exon and intron regions. Physical mapping revealed that the WRKY genes in G. arboreum were not located in the corresponding chromosomes of G. raimondii, suggesting great chromosome rearrangement in the diploid cotton genomes. The cotton WRKY genes, especially subgroups I and II, have expanded through multiple whole genome duplications and tandem duplications compared with other plant species. Sequence comparison showed many functionally divergent sites between WRKY subgroups, while the genes within each group are under strong purifying selection. Transcriptome analysis suggested that many WRKY genes participate in specific fiber development processes such as fiber initiation, elongation and maturation with different expression patterns between species. Complex WRKY gene expression such as differential Dt and At allelic gene expression in G. hirsutum and alternative splicing events were also observed in both diploid and tetraploid cottons during fiber development process. In conclusion, this study provides important information on the evolution and function of WRKY gene family in cotton species.
WRKY转录因子在多种植物物种的各种应激反应中发挥着重要作用。在棉花中，该家族尚未得到充分研究，尤其是与纤维发育相关的方面。在此，对雷蒙德氏棉和亚洲棉的基因组和转录组进行了研究，以鉴定与纤维发育相关的WRKY基因。这是对二倍体A和D棉花物种中WRKY转录因子的首次全面比较研究。总共鉴定出112个雷蒙德氏棉WRKY基因和109个亚洲棉WRKY基因。在这两个物种之间未检测到明显的基因结构或结构域改变，但许多单核苷酸多态性（SNP）在外显子和内含子区域分布不均。物理图谱显示，亚洲棉中的WRKY基因并不位于雷蒙德氏棉的相应染色体上，这表明二倍体棉花基因组中发生了大量的染色体重排。与其他植物物种相比，棉花WRKY基因，尤其是I和II亚组，通过多次全基因组复制和串联复制得到了扩展。序列比较显示WRKY亚组之间存在许多功能上不同的位点，而每组内的基因都受到强烈的纯化选择。转录组分析表明，许多WRKY基因参与特定的纤维发育过程，如纤维起始、伸长和成熟，物种间具有不同的表达模式。在纤维发育过程中，在二倍体和四倍体棉花中还观察到复杂的WRKY基因表达，如陆地棉中Dt和At等位基因的差异表达以及可变剪接事件。总之，本研究为棉花物种中WRKY基因家族的进化和功能提供了重要信息。
