Major Improvements to the Heliconius melpomene Genome Assembly Used to Confirm 10 Chromosome Fusion Events in 6 Million Years of Butterfly Evolution.

The Heliconius butterflies are a widely studied adaptive radiation of 46 species spread across Central and South America, several of which are known to hybridize in the wild. Here, we present a substantially improved assembly of the Heliconius melpomene genome, developed using novel methods that should be applicable to improving other genome assemblies produced using short read sequencing. First, we whole-genome-sequenced a pedigree to produce a linkage map incorporating 99% of the genome. Second, we incorporated haplotype scaffolds extensively to produce a more complete haploid version of the draft genome. Third, we incorporated ∼20x coverage of Pacific Biosciences sequencing, and scaffolded the haploid genome using an assembly of this long-read sequence. These improvements result in a genome of 795 scaffolds, 275 Mb in length, with an N50 length of 2.1 Mb, an N50 number of 34, and with 99% of the genome placed, and 84% anchored on chromosomes. We use the new genome assembly to confirm that the Heliconius genome underwent 10 chromosome fusions since the split with its sister genus Eueides, over a period of about 6 million yr.

JWD is funded by a Herchel Smith Postdoctoral Research Fellowship. PacBio sequencing was carried out by Paul Coupland and Richard Durbin at the Sanger Institute, supported by the ERC grant numbers 339873, the Wellcome Trust grant number 098051 and JWD’s Herchel Smith funding. H. melpomene cross sequencing was carried out at the Harvard FAS Center for Systems Biology core facility and funded by BBSRC grant number G006903/1. E. isabella breeding was supported by ERC grant StG-MimEvol and ANR grant JCJC-HybEvol. E. isabella cross sequencing was carried out by Sylviane Moss at the Gurdon Institute. We thank Jenny Barna for computing support. Alignment and SNP calling was performed using the Darwin Supercomputer of the University of Cambridge High Performance Computing Service (http://www.hpc.cam.ac.uk/), provided by Dell Inc. using Strategic Research Infrastructure Funding from the Higher Education Funding Council for England and funding from the Science and Technology Facilities Council.

This is the final version of the article. It first appeared from the Genetics Society of America via https://doi.org/0.1534/g3.115.023655