State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of CAAS, Wuhan, 430062, China.
BMC Genomics. 2019 Apr 25;20(1):317. doi: 10.1186/s12864-019-5684-3.
WUSCHEL-related homeobox (WOX) genes encoding plant-specific homeobox (HB) transcription factors play important roles in the growth and development of plants. To date, WOX genes has been identified and analyzed in many polyploids (such as cotton and tobacco), but the evolutionary analysis of them during polyploidization is rare. With the completion of genome sequencing, allotetraploid Brassica napus and its diploid progenitors (B. rapa and B. oleracea) are a good system for studying this question.
In this study, 52, 25 and 29 WOX genes were identified in allotetraploid B. napus (2n = 4x = 38, AC), the A genome donor B. rapa (2n = 2x = 20, A) and the C genome donor B. oleracea (2n = 2x = 18, C), respectively. All identified WOX genes in B. napus and its diploid progenitors were divided into three clades, and these genes were selected to perform gene structure and chromosome location analysis. The results showed that at least 70 and 67% of WOX genes maintained the same gene structure and relative position on chromosomes, respectively, indicating that WOX genes in B. napus were highly conserved at the DNA level during polyploidization. In addition, the analysis of duplicated genes and transposable elements (TEs) near WOX genes showed that whole-genome triplication (WGT) events, segmental duplication and abundant TEs played important roles in the expansion of the WOX gene family in B. napus. Moreover, the analysis of the expression profiles of WOX gene pairs with evolutionary relationships suggested that the WOX gene family may have changed at the transcriptional regulation level during polyploidization.
The results of this study increased our understanding of the WOX genes in B. napus and its diploid progenitors, providing a rich resource for further study of WOX genes in these species. In addition, the changes in WOX genes during the process of polyploidization were discussed from the aspects of gene number, gene structure, gene relative location and gene expression, which provides a reference for future polyploidization analysis.
WUSCHEL 相关同源盒（WOX）基因编码植物特异性同源盒（HB）转录因子，在植物的生长和发育中发挥重要作用。迄今为止，WOX 基因已在许多多倍体（如棉花和烟草）中被鉴定和分析，但在多倍体化过程中对它们的进化分析却很少。随着基因组测序的完成，异源四倍体甘蓝型油菜及其二倍体祖先（甘蓝和白菜）是研究这一问题的良好系统。
本研究在异源四倍体甘蓝型油菜（2n=4x=38，AC）、A 基因组供体白菜（2n=2x=20，A）和 C 基因组供体甘蓝（2n=2x=18，C）中分别鉴定出 52、25 和 29 个 WOX 基因。甘蓝型油菜及其二倍体祖先中鉴定出的所有 WOX 基因分为三个分支，选择这些基因进行基因结构和染色体定位分析。结果表明，至少有 70%和 67%的 WOX 基因在多倍体化过程中保持了相同的基因结构和染色体相对位置，表明 WOX 基因在甘蓝型油菜中在 DNA 水平上高度保守。此外，对 WOX 基因附近的重复基因和转座元件（TEs）的分析表明，全基因组三倍化（WGT）事件、片段重复和丰富的 TEs 在甘蓝型油菜 WOX 基因家族的扩张中发挥了重要作用。此外，对具有进化关系的 WOX 基因对表达谱的分析表明，WOX 基因家族在多倍体化过程中可能在转录调控水平上发生了变化。
本研究结果增加了我们对甘蓝型油菜及其二倍体祖先中 WOX 基因的认识，为进一步研究这些物种中的 WOX 基因提供了丰富的资源。此外，从基因数量、基因结构、基因相对位置和基因表达等方面讨论了 WOX 基因在多倍体化过程中的变化，为未来的多倍体化分析提供了参考。
