- Background: The merging of two divergent genomes during hybridization can result in the remodeling of parental gene expression in hybrids. - 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.. - Cis- and trans-regulatory divergence can be distinguished by measuring the allelic expression between two genotypes and their F 1 hybrid. - In F 1 hybrid, two parental alleles are exposed to a common cellular environment, so trans- regulatory change has same effect on the two alleles, and their imbalanced expression is a readout of the relative cis-regulatory divergence [17]. - Based on this strategy, a substantial effort has been made and revealed variable roles that cis- and trans-regulatory changes would play in reshaping gene expression. - Previous studies on Dros- ophila showed that cis-regulatory change tended to re- sult in the additive inheritance of gene expression [18, 19], but opposite result appeared in plant for that trans- regulatory change contributed more to the additive ex- pression of the Cirsium hybrids [20]. - In addition, the relative frequency of cis- and trans-regulatory divergence among studies was always inconsistent. - Shi et al.’s study on Arabidopsis found that a greater proportion of genes showed significant evidence of cis- than trans-regulatory divergence [21], whereas Combes et al.’s study on Coffea got the opposite result [22]. - found that cis- regulatory divergence seemed to be more common between than within species [16]. - a greater proportion of DEGs between the hybrids and their parents exhibited a non-additively expressed pattern in the inter-sectional cross (98.52%) (Fisher’s exact test, P- value <. - Allelic expression tests reveal cis - and trans -regulatory divergence in different crosses. - Of the 7629 genes detected in the cross of C. - chekiangoleosa showed significant evi- dence of cis-regulatory divergence. - Expression differences between species not attributable to cis-regulatory diver- gence could be caused by trans-regulatory divergence. - amplexicaulis showed significant evidence of both cis- and trans-regulatory divergence. - Genes with significant evidence of both cis- and trans-regulatory divergence were further divided into three clusters, i.e., “cis + trans”, “cis × trans” and “compensatory”. - The proportion of genes belong to the above three clusters in the cross of C.. - The median significant trans-regulatory difference be- tween C. - azalea in the F 1 hybrid. - chekiangoleosa in the F 1 hybrid. - amplexicaulis in the F 1 hybrid. - chekiango- leosa correlated more strongly with trans-regulatory divergence (τ = 0.34, P-value <. - 2.2e − 16 ) than with cis- regulatory divergence (τ = 0.12, P-value <. - amplexicaulis, of which trans-regulatory divergence con- tributed more to the expression divergence (τ = 0.21, P- value <. - 2.2e − 16 ) than cis-regulatory divergence (τ = 0.18, P-value <. - Furthermore, the interaction effect of cis- and trans-regulations functioning in the same direction (cis + trans) could tremendously change the gene expres- sion patterns between two species. - However, when the two regulations worked in the opposite direction (“cis × trans” and “compensatory. - Regulatory divergence underling gene expression patterns in different F 1 hybrids. - 5, in the F 1 hybrid of C. - a Absolute magnitude (fold-change) of parental expression divergence resulting from cis- and trans-regulatory changes. - b Percentage of total regulatory divergence attributable to cis-regulatory changes. - However, different re- sult was detected in the hybrid of C. - cis in the hybrid of C. - amplexi- caulis was significant higher than that in the hybrid of C. - expression patterns, a greater proportion were subjected to “trans only” than any other effects in the F 1 hybrid of C. - chekiangoleosa, while in the hybrid of C.. - 5 Percent of cis-regulatory divergence for genes showing additive and non-additive expression in Camellia F 1 hybrids. - Table 1 Contributions of regulatory divergence to gene expression patterns in F 1 hybrids. - intra-sectional or the inter-sectional hybridization, and most of them were non-additively expressed in the hybrids (Fig. - In our study, although the proportion of DEGs decreased to some extant in the inter-sectional hybrid, a greater proportion of DEGs would be non-additively expressed in the inter-sectional hybrid than that in the intra-sectional hybrid. - Specific- ally, more DEGs were transgressively expressed in the inter-sectional hybrid than that in the intra-sectional hy- brid. - Relative frequency of cis - and trans -regulatory divergence in different hybrids. - According to previous studies, cis- and trans-regulatory divergence have their own ways in affecting gene. - So, the relative frequency of cis- and trans-regulatory divergence has great influence on the inheritance of gene expression patterns in hybrid [18].. - The relative frequency of cis- and trans-regulatory diver- gence revealed by different studies is always variable.. - sechellia found that more genes showed significant evidence of trans- than cis-regulatory divergence [19]. - eugenioides and Bell et al.’s study on the intraspecific hybridization of Cirsium, also found more genes were subjected to trans- regulatory divergence [20, 22]. - arenosa more genes were significantly influenced by cis- rather than trans- regulatory divergence [21]. - That means the relative frequency of cis- and trans-regulatory changes in hybrids may be related to the divergence time between the parental species. - However, the results were completely different for that the propor- tions of genes with significant evidence of cis- and trans- regulatory divergence in the intra-sectional cross (C.. - chekiangoleosa) were 8.09 and 13.34%, respectively, whereas in the inter-sectional cross of C.. - In other words, 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-regula- tory divergence would decrease with genetic divergence between species. - This seems to be inconsistent with a neutral model assuming equal probabilities of fixation for cis- and trans-regulatory polymorphisms. - Cis - and trans -regulatory differences underlying expression divergence between species. - McManus et al.’s study on the hybrid of Drosophila showed that the median significant of trans-regulatory divergence was larger than that of cis-regulatory diver- gence between species, and trans-regulatory divergence correlated more highly with the expression difference between species [19]. - Same profile also appeared in the study of Cirsium [20]. - Similarly, our results showed that trans-regulatory change contributed more to the expres- sion divergence between C. - azalea and the other two species correlated more highly with trans-regulatory changes, too. - That means trans-regulatory change plays a larger role than cis-regulatory change in promoting the differentiation of gene expression between species. - 4b, the relative percent of cis- regulatory divergence decreased with the absolute mag- nitude of total expression divergence between C. - Cis- and trans-regulatory divergence are not mutually exclusive, many genes would be significantly influenced by both cis- and trans-regulatory changes . - Interactions between cis- and trans-regulatory divergences can result. - 4c and d, cis- and trans- regulatory changes promoting expression of the same allele (cis + trans) could greatly stimulate the expression divergence between species. - Specifically, the compensatory effect of cis- and trans-regulatory changes tended to eliminate ex- pression divergence between species. - In our study, the pro- portion of genes with significant evidence of both cis- and trans-regulatory divergence was lower in the cross of C. - Contribution of regulatory divergence to gene expression patterns in hybrid. - Previous studies on Drosophila [19] and yeast [31] showed that cis-regulatory divergence ap- peared to result in additive inheritance of gene expres- sion more often than trans-regulatory divergence.. - In our study, in the F 1 hybrid of C. - How- ever, in the hybrid of C. - amplexicaulis, there was no significant difference in the relative percent of cis- and trans-regulatory divergence for neither addi- tively nor non-additively expressed genes. - We speculate that the relative contribution of cis- and trans-regulatory divergence. - cis-regulatory divergence. - For hybrids whose parents are closely related species, the relative frequency of trans- regulatory divergence is higher than that of cis-regulatory divergence. - however, as genomes between the two parents become more divergent, trans-regulatory mutations are eliminated to some extent and cis-regulatory divergence becomes dominant. - This could be used to explain why a higher proportion of genes would be non-additively (espe- cially transgressively) expressed in the F 1 hybrid of inter- sectional than that of intra-sectional hybridization.. - The interactions between cis- and trans-regulatory divergences can greatly affect gene expression patterns be- tween species. - There were studies showed that “cis × trans” regulatory divergence was more common in trans- gressively expressed genes [19, 29]. - effect in the inter-sectional hybridization for any expres- sion patterns. - So, inheritance of gene expression patterns is more likely to be the result of the comprehensive effects of different regulatory mechanisms, and the change of relative frequency of cis- and trans-regulatory divergence plays an important role in the formation of divergent ex- pression patterns in hybrid.. - Meanwhile, the proportion of genes with significant evidence of cis-regulatory divergence increased, while with trans-regulatory divergence decreased with parental genetic divergence. - Trans-regulatory change con- tributes more to the additively inherited genes in hybrid than cis-. - So, the weakening of trans-regulatory effect and the strengthen of cis-regulatory effect provide a major reason for the phenomenon that the more divergent the parents are, the greater proportion of DEGs would be non-additively expressed in hybrid.. - (iii) the read count of the minor parental allele in the hybrid at each SNP site must be ≥2. - The normalized gene expression for each cross is provided in the supporting information (Additional file 1: Tables S4 and S5). - DEGs whose expression level in the hybrid were significantly higher/lower than both of the parents were classified as transgressivity (overdominance/underdominance).. - Allelic expression patterns and cis - and trans -regulatory divergence assignment. - For each allele, the mean value of the three bio- logical replicates was used for allelic expression as well as the subsequent regulatory divergence analysis. - Expres- sion divergence between the parental species is mainly caused by the combination of cis- and trans-regulatory changes, which could be quantified as log 2 (parent1/par- ent2). - Then trans-regulatory divergence was calculated as the difference between log 2 -transformed ratios of species- specific reads in the parents and the hybrids: trans = log 2 (parent1/parent2. - The relative proportion of total regulatory divergence at- tributable to cis-regulatory divergence. - Regulatory divergence for different genes was then identified based on the. - (i) cis only: the parental alleles were unequally expressed in the same ratio in F 1 hybrid and between the two parents. - (v) Compensatory: the two parental alleles are equally expressed between the two parents but un- equally in the F 1 hybrid. - (vii) ambiguous: other situations not included in the above six categories.. - The main scripts used in this study are available in the supporting information.. - Regulatory divergence in Drosophila revealed by mRNA-seq. - Cis- and trans- regulatory divergence between progenitor species determines gene- expression novelty in Arabidopsis allopolyploids. - Regulatory divergence between parental alleles determines gene expression patterns in hybrids
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