Rapid evolutionary diversification of theflamencolocus across simulans cladeDrosophilaspecies

Abstract

AbstractEffective suppression of transposable elements (TEs) is paramount to maintain genomic integrity and organismal fitness. InD. melanogaster,flamencois a master suppressor of TEs, preventing their movement from somatic ovarian support cells to the germline. It is transcribed by Pol II as a long (100s of kb), single-stranded, primary transcript, that is metabolized into Piwi-interacting RNAs (piRNAs) that target active TEs via antisense complementarity.flamencois thought to operate as a trap, owing to its high content of recent horizontally transferred TEs that are enriched in antisense orientation. Using newly-generated long read genome data, which is critical for accurate assembly of repetitive sequences, we find thatflamencohas undergone radical transformations in sequence content and even copy number acrosssimulansclade Drosophilid species.D. simulans flamencohas duplicated and diverged, and neither copy exhibits synteny withD. melanogasterbeyond the core promoter. Moreover,flamencoorganization is highly variable acrossD. simulansindividuals. Next, we find thatD. simulansandD. mauritiana flamencodisplay signatures of a dual-stranded cluster, with ping-pong signals in the testis and/or embryo. This is accompanied by increased copy numbers of germline TEs, consistent with these regions operating as functional dual stranded clusters. Overall, the physical and functional diversity offlamencoorthologs is testament to the extremely dynamic consequences of TE arms races on genome organization, not only amongst highly related species, but even amongst individuals.