Supporting data for "Genome assembly of three Amazonian Morpho butterfly species reveals Z-chromosome rearrangements between closely-related species living in sympatry"

The genomic processes enabling speciation and species coexistence in sympatry are still largely unknown. Here we describe the whole genome sequence of three closely-related species from the butterfly genus <i>Morpho : Morpho achilles</i> (Linnaeus, 1758), <i>M. helenor</i> (Cramer, 1776) and <i>M. deidamia</i> (Hübner, 1819). These large blue butterflies are emblematic species of the Amazonian rainforest. They live in sympatry in a wide range of their geographical distribution and display parallel diversification of dorsal wing colour pattern, suggesting local mimicry. By sequencing, assembling and annotating their genomes, we aim at uncovering pre-zygotic barriers preventing gene flow between these sympatric species. We found a genome size of 480 Mb for the three species and a chromosomal number ranging from 2n = 54 for <i>M. deidamia</i> to 2n = 56 for <i>M. achilles</i> and <i>M. helenor</i>. We also detected inversions on the sex chromosome Z that were differentially fixed between species, suggesting that chromosomal rearrangements may contribute to their reproductive isolation. The annotation of their genomes allowed us to recover in each species at least 12,000 protein-coding genes and to discover duplications of genes potentially involved in pre-zygotic isolation like genes controlling colour discrimination (<i>L-opsin</i>). Altogether, the assembly and the annotation of these three new reference genomes open new research avenues into the genomic architecture of speciation and reinforcement in sympatry, establishing <i>Morpho</i> butterflies as a new eco-evolutionary model.