Cis- and trans-regulatory divergence betweenprogenitor species determines gene-expressionnovelty in Arabidopsis allopolyploids

摘要

Gene-expression divergence between species shapes morphological evolution, but themolecular basis is largely unknown. Here we show cis- and trans-regulatory elements andchromatin modifications on gene-expression diversity in genetically tractable Arabidopsisallotetraploids. In Arabidopsis thaliana and Arabidopsis arenosa, both cis and trans withpredominant cis-regulatory effects mediate gene-expression divergence. The majority of geneswith both cis- and trans-effects are subjected to compensating interactions and stabilizingselection. Interestingly, cis- and trans-regulation is associated with chromatin modifications.In F1 allotetraploids, Arabidopsis arenosa trans factors predominately affect allelic expressiondivergence. Arabidopsis arenosa trans factors tend to upregulate Arabidopsis thaliana alleles,whereas Arabidopsis thaliana trans factors up- or down-regulate Arabidopsis arenosa alleles. Inresynthesized and natural allotetraploids, trans effects drive expression of both homoeologousloci into the same direction. We provide evidence for natural selection and chromatin regulationin shaping gene-expression diversity during plant evolution and speciation.