RT Journal Article
SR Electronic
T1 Movement of transposable elements contributes to cichlid diversity
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.02.26.961987
DO 10.1101/2020.02.26.961987
A1 Karen L. Carleton
A1 Matt Conte
A1 Milan Malinsky
A1 Sri Pratima Nandamuri
A1 Ben Sandkam
A1 Joana I Meier
A1 Salome Mwaiko
A1 Ole Seehausen
A1 Thomas D Kocher
YR 2020
UL http://biorxiv.org/content/early/2020/02/26/2020.02.26.961987.abstract
AB African cichlid fishes are a prime model for studying the mechanisms of speciation. Despite the development of extensive genomic resources, it has been difficult to determine which sources of genetic variation are responsible for variation in cichlid phenotypes. Cichlids have some of the largest known shifts in vertebrate visual sensitivity. These shifts arise mainly from the differential expression of seven cone opsin genes. By mapping expression quantitative trait loci (eQTL) in intergeneric crosses of Lake Malawi (LM) cichlids, we have thus far identified four causative genetic variants that correspond to indels in the promoters of either key transcription factors or of the opsin gene itself. Here we show that these indels are caused by the movement of transposable elements (TEs). These precise indels are not found outside of LM, suggesting that these TEs are recently active and are segregating within the Malawi cichlid lineage. A similar indel has arisen independently outside of LM at one locus, suggesting that some locations are primed for TE insertion and the resulting indels. Increased TE mobility may be associated with interspecific hybridization, which disrupt mechanisms of TE suppression. Overall, our study suggests that TEs may contribute to key regulatory changes, and may facilitate rapid phenotypic change and possibly speciation in African cichlids.