Dynamic co-evolution of transposable elements and the piRNA pathway in East African cichlid fishes [smallRNA-seq]
East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of the phenotypic diversity of these fishes remains largely unknown. Although transposable elements (TEs) have been associated with phenotypic variation in cichlids, little is known about their transcriptional activity and epigenetic silencing. Here, we describe dynamic patterns of TE expression in African cichlid gonads and during early development. Orthology inference revealed an expansion of piwil1 genes in Lake Malawi cichlids, likely driven by PiggyBac TEs. The expanded piwil1 copies have signatures of positive selection and retain amino acid residues essential for catalytic activity. Furthermore, the gonads of African cichlids express a Piwi-interacting RNA (piRNA) pathway that target TEs. We define the genomic sites of piRNA production in African cichlids and find divergence in closely related species, in line with fast evolution of piRNA-producing loci. Our findings suggest dynamic co-evolution of TEs and host silencing pathways in the African cichlid radiations. We propose that this co-evolution has contributed to cichlid genomic diversity. Overall design: To profile small RNAs and identify Piwi-interacting RNAs (piRNAs) in the East African cichlid radiations, we have sequenced small RNAs from ovaries and testes of cichlid species representative of the three East African Great Lakes, as well as of Nile Tilapia (Orechromis niloticus) an outgroup to radiating cichlids. We also sequenced muscle, a somatic tissue which is not expected to have prominent piRNA populations.