Supplementary files for: A T2T genome of the lobed-lip Iguazu joana (Crenicichla tuca) reveals widespread intrachromosomal rearrangements in cichlid fishes

Genomic architecture is a key factor shaping the landscape of linkage disequilibrium between divergently selected traits. Despite the link between rearrangements and speciation, cichlid fishes, one of the most emblematic examples of adaptive radiation, exhibit stable karyotypes.Here, we used a field-based extraction protocol to a) generate a complete assembly of Crenicichla tuca (iguassuensis group) collected in close vicinity to the type locality and b) investigate structural variation in South American cichlids. This repository contains the supplementary files resulting from genome assembly and annotation, in addition to intermediate files required for the different analysis perform in the article. https://www.henninglab.com/