Zhao Na, Ding Xiaoyang, Lian Taotao, Wang Meng, Tong Yan, Liang Di, An Qi, Sun Siwen, Jackson Scott A, Liu Bao, Xu Chunming
Department of Agronomy, Jilin Agricultural University, Changchun, China.
Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China.
Front Genet. 2020 Dec 8;11:601003. doi: 10.3389/fgene.2020.601003. eCollection 2020.
Regulatory changes include divergence in both -elements and -factors, which play roles in organismal evolution. Whole genome duplications (WGD) followed by diploidization are a recurrent feature in the evolutionary history of angiosperms. Prior studies have shown that duplicated genes have different evolutionary fates due to variable selection constraints and results in genomic compositions with hallmarks of paleopolyploidy. The recent sequential WGDs and post-WGD evolution in the common ancestor of cultivated soybean () and wild soybean (), together with other models of gene duplication, have resulted in a highly duplicated genome. In this study, we investigated the transcriptional changes in and . We identified a sizable proportion of interspecific differentially expressed genes (DEGs) and found parental expression level dominance of in their F1 hybrids. By classifying genes into different regulatory divergence types, we found the -regulatory changes played a predominant role in transcriptional divergence between wild and cultivated soybean. The same gene ontology (GO) and protein family (Pfam) terms were found to be over-represented in DEGs and genes of -only between JY47 and GS, suggesting the substantial contribution of -regulatory divergences to the evolution of wild and cultivated soybeans. By further dissecting genes into five different duplication modes, we found genes in different duplication modes tend to accumulate different types of regulatory differences. A relatively higher proportion of -only regulatory divergences was detected in singleton, dispersed, proximal, and tandem duplicates than WGD duplicates and genome-wide level, which is in line with the prediction of gene balance hypothesis for the differential fates of duplicated genes post-WGD. The numbers of -only and -only regulated genes were similar for singletons, whereas there were more genes of -only than -only in the rest duplication types, especially in WGD in which there were two times more -only genes than that in -only type. Tandem duplicates showed the highest proportion of -only genes probably due to some special features of this class. In summary, our results demonstrate that genes in different duplication modes have different fates in transcriptional evolution underpinned by - or -regulatory divergences in soybean and likely in other paleopolyploid higher organisms.
调控变化包括元件和因子的差异，它们在生物进化中发挥作用。全基因组复制（WGD）后紧接着二倍体化是被子植物进化历史中的一个反复出现的特征。先前的研究表明，由于可变的选择限制，复制基因具有不同的进化命运，并导致具有古多倍体特征的基因组组成。栽培大豆（）和野生大豆（）的共同祖先中最近的连续全基因组复制以及全基因组复制后的进化，连同其他基因复制模型，导致了一个高度重复的基因组。在本研究中，我们调查了和中的转录变化。我们鉴定出相当比例的种间差异表达基因（DEGs），并在它们的F1杂种中发现了亲本表达水平优势。通过将基因分类为不同的调控差异类型，我们发现调控变化在野生大豆和栽培大豆之间的转录差异中起主要作用。在JY47和GS之间的差异表达基因以及仅有的基因中，发现相同的基因本体（GO）和蛋白质家族（Pfam）术语过度富集，这表明调控差异对野生大豆和栽培大豆的进化有重大贡献。通过进一步将基因剖析为五种不同的复制模式，我们发现不同复制模式的基因倾向于积累不同类型的调控差异。与全基因组复制重复和全基因组水平相比，在单拷贝、分散、近端和串联重复中检测到相对较高比例的仅调控差异，这与基因平衡假说对全基因组复制后复制基因不同命运的预测一致。单拷贝的仅调控和仅调控基因数量相似，而在其余复制类型中，仅调控的基因比仅调控的基因更多，特别是在全基因组复制中，仅调控的基因是仅调控类型的两倍。串联重复显示仅基因的比例最高，这可能是由于这一类别的一些特殊特征。总之，我们的结果表明，不同复制模式的基因在转录进化中具有不同的命运，其基础是大豆以及可能其他古多倍体高等生物中的或调控差异。
