de novo assembly of 5 highly contiguous Heliconius butterfly genomes with long-read sequencing alone.

Authors

Ava Mackay-Smith, Graham C Alexander, W Owen McMillan, Arnaud Martin, Gregory A Wray

Published in

Genome biology and evolution. Jul 11, 2026. Epub Jul 11, 2026.

Abstract

Rapidly decreasing costs of sequencing whole genomes has caused a boom in genomic resources for many species. However, many key nonmodel systems that were sequenced early in the genomic revolution lack assemblies that reflect the quality and contiguity that are routine with current technology. Some of these "early for assembly, late for contiguity" genomes belong to the butterfly genus Heliconius, a remarkably fruitful clade for exploring questions of phenotypic mimicry, speciation dynamics, and population genetics. We de novo assembled five new reference genomes of Heliconius butterflies based on PacBio HiFi sequencing: two subspecies of H. erato, two subspecies of H. melpomene, and a closely related species, H. numata. While independent assemblies of multiple subspecies are already a valuable resource, these specific genomes are important for exploration of the genomic basis of mimicry, because the four H. erato and H. melpomene genomes represent two pairs of H. erato/H. melpomene local comimics. These genomes prove to be high quality (merqury quality score 51-58) and approach completeness (>98% BUSCO complete genes) over a lower number of longer contigs than earlier Heliconius genomes, illustrating how PacBio long-read technology alone can unlock untapped genomic resources. This set of high-quality, uniformly processed genomes represents an important resource for exploring the genomics of adaptation, hybridization, and speciation.
Although a Heliconius butterfly was among the first animal genomes to be sequenced, the genus lacks high-quality, publicly accessible, de novo reference genomes for most of its species. This is particularly important for Heliconius because independent and complete genomes are necessary to unambiguously determine the history of introgression and phenotypic innovation that makes this system so relevant for evolutionary research. We address this gap by generating deep-coverage PacBio long-read data from 5 Heliconius subspecies, assembling genomes de novo with a uniform and reproducible Snakemake processing pipeline. We recover excellent genome contiguity, quality, and completeness scores using only long-read data. We further annotate these genomes with subspecies-specific RNA-seq data to produce annotations with >97% BUSCO completeness. This group of Heliconius genomes represent an important contribution of identically processed, high-quality genomes for comparative genomic investigation into the evolution and innovation of ecologically relevant phenotypes.

PMID:
42433034
Bibliographic data and abstract were imported from PubMed on 11 Jul 2026.

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