Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution

Abstract

Detecting the genomic changes underlying phenotypic changes between species is a main goal of evolutionary biology and genomics. Evolutionary theory predicts that changes in cis-regulatory elements are important for morphological changes. We combined genome sequencing, functional genomics and genome-wide comparative analyses to investigate regulatory elements in lineages that lost morphological traits. We first show that limb loss in snakes is associated with widespread divergence of limb regulatory elements. We next show that eye degeneration in subterranean mammals is associated with widespread divergence of eye regulatory elements. In both cases, sequence divergence results in an extensive loss of transcription factor binding sites. Importantly, diverged regulatory elements are associated with genes required for normal limb patterning or normal eye development and function, suggesting that regulatory divergence contributed to the loss of these phenotypes. Together, our results show that genome-wide decay of the phenotype-specific cis-regulatory landscape is a hallmark of lost morphological traits.

Recapitulating evolutionary divergence in a singlecis-regulatory element is sufficient to cause expression changes of the lens geneTdrd7

“…Similarly, our study showed that perturbing a single lens repressor element in a model organism, where the entire genetic machinery required for functional eyes is intact, did not result in a detectable organismal phenotype. However, we have previously shown that numerous components of the genetic "eye-making" machinery are highly diverged in the BMR and other subterranean mammals, as these species lost several eye-related genes and exhibit divergence in hundreds of eye regulatory elements (21)(22)(23). This suggests that eye degeneration in subterranean mammals most likely has a polygenic basis and that perturbations of several regulatory elements are necessary to obtain a detectable phenotype.…”

“…In previous studies, we used two comparative genomics approaches to identify and associate sequence and transcription factor (TF) binding site divergence in CNEs to the vision-impaired phenotype of the subterranean blind mole rat, naked mole rat, cape golden mole, and star-nosed mole (21,22). Both screens detected significantly higher sequence and binding site divergence in subterranean mammals in a locus that comprises two CNEs located 97 bp from each other ( Figures 1A,B).…”

“…Two CNEs upstream of Tdrd7 were identified in two previous genome-wide screens for CNEs that are diverged in subterranean mammals (21,22). In the first screen, we generated a multiple wholegenome alignment with mouse (mm10 assembly) as the reference and 24 other mammals, used PhastCons (66) to obtain conserved regions, and extracted CNEs by excluding protein-coding regions.…”

“…In addition to the widespread loss of genes, recent studies discovered divergence in many eye regulatory elements (20)(21)(22)(23). In particular, genome-wide analysis of conserved non-coding elements (CNEs) revealed that CNEs with preferential sequence divergence in subterranean mammals are significantly associated with eye-related genes and significantly overlap regulatory elements that are active in developing and adult eyes of mice or humans (21). Sequence divergence in these CNEs also resulted in a large-scale divergence of binding sites of eye-related transcription factors (21)(22)(23).…”

“…In particular, genome-wide analysis of conserved non-coding elements (CNEs) revealed that CNEs with preferential sequence divergence in subterranean mammals are significantly associated with eye-related genes and significantly overlap regulatory elements that are active in developing and adult eyes of mice or humans (21). Sequence divergence in these CNEs also resulted in a large-scale divergence of binding sites of eye-related transcription factors (21)(22)(23). Together, this suggests that widespread divergence in both genes and in cis-regulatory elements may have contributed to the degeneration of eye structures in subterranean mammals, leading to a greatly impaired visual system.…”