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The Effects of Gene Duplication Modes on the Evolution of Regulatory Divergence in Wild and Cultivated Soybean

Authors :
Na Zhao
Xiaoyang Ding
Taotao Lian
Meng Wang
Yan Tong
Di Liang
Qi An
Siwen Sun
Scott A. Jackson
Bao Liu
Chunming Xu
Source :
Frontiers in Genetics, Frontiers in Genetics, Vol 11 (2020)
Publication Year :
2020
Publisher :
Frontiers Media SA, 2020.

Abstract

Regulatory changes include divergence in bothcis-elements andtrans-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 (Glycine max) and wild soybean (Glycine soja), together with other models of gene duplication, have resulted in a highly duplicated genome. In this study, we investigated the transcriptional changes inG. sojaandG. max. We identified a sizable proportion of interspecific differentially expressed genes (DEGs) and found parental expression level dominance ofG. maxin their F1 hybrids. By classifying genes into different regulatory divergence types, we found thetrans-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 ofcis-only between JY47 and GS, suggesting the substantial contribution ofcis-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 ofcis-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 ofcis-only andtrans-only regulated genes were similar for singletons, whereas there were more genes oftrans-only thancis-only in the rest duplication types, especially in WGD in which there were two times moretrans-only genes than that incis-only type. Tandem duplicates showed the highest proportion oftrans-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 bycis- ortrans-regulatory divergences in soybean and likely in other paleopolyploid higher organisms.

Details

ISSN :
16648021
Volume :
11
Database :
OpenAIRE
Journal :
Frontiers in Genetics
Accession number :
edsair.doi.dedup.....81f1a8f9670be833fb504e97c0a7c5b1