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The Effects of Gene Duplication Modes on the Evolution of Regulatory Divergence in Wild and Cultivated Soybean
- 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.
- Subjects :
- 0106 biological sciences
0301 basic medicine
duplicate gene
lcsh:QH426-470
Glycine max
Protein family
01 natural sciences
Genome
03 medical and health sciences
regulatory divergence
Gene duplication
Genetics
soybean
Gene
Genetics (clinical)
Original Research
Hybrid
Dominance (genetics)
hybrid
biology
biology.organism_classification
Glycine soja
lcsh:Genetics
030104 developmental biology
Paleopolyploidy
Molecular Medicine
010606 plant biology & botany
Subjects
Details
- ISSN :
- 16648021
- Volume :
- 11
- Database :
- OpenAIRE
- Journal :
- Frontiers in Genetics
- Accession number :
- edsair.doi.dedup.....81f1a8f9670be833fb504e97c0a7c5b1