First chromosome scale genomes of ithomiine butterflies (Nymphalidae: Ithomiini): Comparative models for mimicry genetic studies

Abstract

The ithomiine butterflies (Nymphalidae: Danainae) represent the largest known radiation of Müllerian mimetic butterflies. They dominate by number the mimetic butterfly communities, which include species such as the iconic neotropical Heliconius genus. Recent studies on the ecology and genetics of speciation in Ithomiini have suggested that sexual pheromones, colour pattern and perhaps hostplant could drive reproductive isolation. However, no reference genome was available for Ithomiini, which has hindered further exploration on the genetic architecture of these candidate traits, and more generally on the genomic patterns of divergence. Here, we generated high-quality, chromosome-scale genome assemblies for two Melinaea species, M. marsaeus and M. menophilus, and a draft genome of the species Ithomia salapia. We obtained genomes with a size ranging from 396 to 503 Mb across the three species and scaffold N50 of 40.5 and 23.2 Mb for the two chromosome-scale assemblies. Using collinearity analyses we identified massive rearrangements between the two closely related Melinaea species. An annotation of transposable elements and gene content was performed, as well as a specialist annotation to target chemosensory genes, which is crucial for host plant detection and mate recognition in mimetic species. A comparative genomic approach revealed independent gene expansions in ithomiines and particularly in gustatory receptor genes. These first three genomes of ithomiine mimetic butterflies constitute a valuable addition and a welcome comparison to existing biological models such as Heliconius, and will enable further understanding of the mechanisms of adaptation in butterflies.

Keywords: Hi-C; chromosome-level genome; ithomiine butterflies; mimicry; olfaction.

Figure 1

Melinaea marsaeus, Melinaea menophilus, Ithomia salapia and wing pattern variation between subspecies of each of these species (source Joron et al., 2006 and photograph credits Céline Houssin)

Figure 2

Low synteny between M. marsaeus and M. menophilus despite very recent splitting time. The positions of BUSCO genes mapping uniquely to both genomes are shown in the order of the M. marsaeus chromosomes. The colours reflect the different M. marsaeus chromosomes. A fully conserved chromosome would be reflected as a single diagonal line as in M. marsaeus chromosome 7, which corresponds to M. menophilus chromosome 1. Grey lines indicate chromosome ends

Figure 3

Phylogeny and orthologous gene numbers across 10 butterfly genomes. “Shared by some” represents orthologues shared by eight out of the 10 species and without phylogenetic signal

Figure 4

Maximum-likelihood phylogeny of lepidopteran GRs, built from amino acid sequences from B. mori, H. melpomene, D. plexippus, I. salapia, M. marsaeus and M. menophilus. Deep nodes highly supported by the likelihood-ratio test (aLRT >0.95) are indicated by black dots. Those that correspond to Ithomiini-specific large expansions (more than 10 genes) are shown with stars. The scale bar represents the expected number of amino acid substitutions per site

Figure 5

Maximum-likelihood phylogeny of lepidopteran CSPs, built from amino acid sequences from B. mori (Bmor), S. frugiperda (Sfru), H. melpomene (Hmel), D. plexippus (Dple), I. salapia (Isal), M. marsaeus (Mmar) and M. menophilus (Mmen). Deep nodes highly supported by the likelihood-ratio test (aLRT >0.95) are indicated by black dots. The scale bar represents the expected number of amino acid substitutions per site