Effects of parental genetic divergence on gene expression patterns in interspecific hybrids of Camellia

Min Zhang,Zhi-Ping Song,Dan-Feng Yan,Yi-Wei Tang,Nai-Sheng Zhong,Ji Yang,Yu-Guo Wang,Ji Qi,Ji-Yin Gao,Nai-Qi Tao,Xin-Kai Liu,Wen-Ju Zhang

doi:10.1186/s12864-019-6222-z

Min Zhang, Zhi-Ping Song + Show 10 more

Open Access

https://doi.org/10.1186/s12864-019-6222-z

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Abstract

BackgroundThe merging of two divergent genomes during hybridization can result in the remodeling of parental gene expression in hybrids. A molecular basis underling expression change in hybrid is regulatory divergence, which may change with the parental genetic divergence. However, there still no unanimous conclusion for this hypothesis.ResultsThree species of Camellia with a range of genetic divergence and their F1 hybrids were used to study the effect of parental genetic divergence on gene expression and regulatory patterns in hybrids by RNA-sequencing and allelic expression analysis. We found that though the proportion of differentially expressed genes (DEGs) between the hybrids and their parents did not increase, a greater proportion of DEGs would be non-additively (especially transgressively) expressed in the hybrids as genomes between the parents become more divergent. In addition, the proportion of genes with significant evidence of cis-regulatory divergence increased, whereas with trans-regulatory divergence decreased with parental genetic divergence.ConclusionsThe discordance within hybrid would intensify as the parents become more divergent, manifesting as more DEGs would be non-additively expressed. Trans-regulatory divergence contributed more to the additively inherited genes than cis, however, its contribution to expression difference would be weakened as cis mutations accumulated over time; and this might be an important reason for that the more divergent the parents are, the greater proportion of DEGs would be non-additively expressed in hybrid.

Highlights

Hybridization is an important power facilitating adaptive evolution [1]
Sequencing and mapping As described above, two crosses representing intra- and inter-sectional hybridization of Camellia were used in this study (Fig. 1). cDNA libraries were constructed using RNA extracted from flower buds of the F1 hybrids and their parental species, and sequenced using the Illumina HiSeq X-ten platform
Trans-regulatory divergence was more prevailing than cis- in the intra-sectional cross, while in the inter-sectional cross was just the opposite. These results indicate that the proportion of genes with significant evidence of cis-regulatory divergence would increase, while with significant evidence of trans-regulatory divergence would decrease with genetic divergence between species

Summary

Introduction

Hybridization is an important power facilitating adaptive evolution [1]. In nature, hybridization is ubiquitous. Most hybrids are infertile, some can possess novel phenotypic traits, like stronger stress tolerance and improved growth rate, which are better for their adaptation to hostile environments or expansion into new habitats; under natural selection, they have the opportunity to evolve into new species [4,5,6]. Novel phenotypes can arise from changes of protein sequences. There is growing evidence that merging of two divergent genomes during hybridization can result in the remodeling of parental gene expression patterns in hybrids, a phenomenon called “transcriptome shock” [9,10,11,12]. The merging of two divergent genomes during hybridization can result in the remodeling of parental gene expression in hybrids.

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