Synteny-based genome assembly for 16 species of Heliconius butterflies , and an assessment of 1 structural variation across the genus 2 3 Running Title : 4 Synteny and structural genomics in Heliconius 5 6

12 Heliconius butterflies (Lepidoptera: Nymphalidae) are a group of 48 neotropical species widely studied in 13 evolutionary research. Despite the wealth of genomic data generated in past years, chromosomal level 14 genome assemblies currently exist for only two species, Heliconius melpomene and H. erato, each a 15 representative of one of the two major clades of the genus. Here, we use these reference genomes to 16 improve the contiguity of previously published draft genome assemblies of 16 Heliconius species. Using 17 a reference-assisted scaffolding approach, we place and order the scaffolds of these genomes onto 18 chromosomes, resulting in 95.7-99.9% of their genomes anchored to chromosomes. Genome sizes are 19 somewhat variable among species (270-422 Mb) and in one small group of species (H. hecale, H. 20 elevatus and H. pardalinus) differences in genome size are mainly driven by a few restricted repetitive 21 regions. Genes within these repeat regions show an increase in exon copy number, an absence of internal 22 stop codons, evidence of constraint on non-synonymous changes, and increased expression, all of which 23 . CC-BY-NC-ND 4.0 International license available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint this version posted October 29, 2020. ; https://doi.org/10.1101/2020.10.29.359505 doi: bioRxiv preprint