Genome assembly of three AmazonianMorphobutterfly species reveals Z-chromosome rearrangements between closely-related species living in sympatry

Abstract

The genomic processes enabling speciation and the coexistence of species in sympatry are still largely unknown. Here we describe the whole genome sequence of three closely-related species from the butterfly genus Morpho : Morpho achilles (Linnaeus, 1758), M. helenor (Cramer, 1776) and M. deidamia (H ̈ubner, 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 M. deidamia to 2n = 56 for M. achilles and M. helenor. 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 (L-opsin). 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 Morpho butterflies as a new eco-evolutionary model.

Increased evolutionary rate in the Z-chromosome ofMorphobutterflies and implications for speciation

“…achilles and M . deidamia), we found significantly more genes predicted and better proteome BUSCO scores using BRAKER2 than with the previous methodology using Maker v2.31.10 [3]. Overall, for most M orpho species, we annotated between 18,159 and 21,017 protein coding genes in their genomes (see table S2).…”

“…For every species, we chose the final assembly among the different assemblies produced with or without the use of Purge_dups, based in the basic statistics and the BUSCO score. The mitochondrial genome for all M orpho species was assembled directly from the PacBio Hifi reads with Rebaler (https://github.com/rrwick/Rebaler) as described in [3] and using the mitochondrial genome from M . helenor as a reference.…”

“…achilles and M . deidamia, were already identified [3]. We then used D-genies to pair-map the genome of M.…”

“…Subsequently, we employed SyRI for targeted paired comparisons, specifically concentrating on the Z chromosome between the same closely-related species pairs used for whole-genome comparisons. Paired comparisons followed the methodology described in [3]. Briefly, paired alignments of the Z contig were generated using Minimap2, and the resulting SAM files were analyzed with SyRI to detect inversions [27].…”

“…We report the sequencing, assembly and annotation of the genomes of 8 species from the genus Morpho. We then used these new genome assemblies, as well as the previously published genomes of 3 other Morpho species [3] to perform comparative genomic…”