Supporting data for "Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes"

African cichlid fishes are well known for their rapid radiations and are a model system for studying evolutionary processes. Here we compare multiple, high-quality, chromosome scale genome assemblies to understand the genetic mechanisms underlying cichlid diversification and study how genome structure evolves in rapidly radiating lineages.<br> We re-anchored our recent assembly of the Nile tilapia (<i>Oreochromis niloticus</i>) genome using a new high-density genetic map. We developed a new de novo genome assembly of the Lake Malawi cichlid, <i>Metriaclima zebra</i>, using high-coverage PacBio sequencing, and anchored contigs to linkage groups (LGs) using four different genetic maps. These new anchored assemblies allow the first chromosome-scale comparisons of African cichlid genomes. Large intra-chromosomal structural differences (~2-28Mbp) among species are common, while inter-chromosomal differences are rare (&lt; 10Mbp total). Placement of the centromeres within chromosome-scale assemblies identifies large structural differences that explain many of the karyotype differences among species. Structural differences are also associated with unique patterns of recombination on sex chromosomes. Structural differences on LG9, LG11 and LG20 are associated with reductions in recombination, indicative of inversions between the rock- and sanddwelling clades of Lake Malawi cichlids. <i>M. zebra</i> has a larger number of recent transposable element (TE) insertions compared to <i>O. niloticus</i>, suggesting that several TE families have a higher rate of insertion in the haplochromine cichlid lineage.<br>This study identifies novel structural variation among East African cichlid genomes and provides a new set of genomic resources to support research on the mechanisms driving cichlid adaptation and speciation.