Journal article

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

John W Davey, Mathieu Chouteau, Sarah L Barker, Luana Maroja, Simon W Baxter, Fraser Simpson, Mathieu Joron, James Mallet, Kanchon K Dasmahapatra, Chris D Jiggins

G3-GENES GENOMES GENETICS | GENETICS SOCIETY AMERICA | Published : 2016

Abstract

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 scaffolde..

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University of Melbourne Researchers

Grants

Awarded by European Research Council (ERC)


Awarded by Wellcome Trust


Awarded by Biotechnology and Biological Sciences Research Council


Awarded by Natural Environment Research Council


Funding Acknowledgements

We thank Jenny Barna for computing support. E. isabella cross sequencing was carried out by Sylviane Moss at the Gurdon Institute. PacBio sequencing was carried out by Paul Coupland and Richard Durbin at the Sanger Institute, supported by European Research Council (ERC) grant number 339873, Wellcome Trust grant number 098051, and J.W.D.'s Herchel Smith funding. H. melpomene cross sequencing was carried out at the Harvard FAS Center for Systems Biology core facility, and funded by Biotechnology and Biological Sciences Research Council grant number G006903/1. E. isabella breeding was supported by ERC grant StG-MimEvol, and Agence Nationale de la Recherche grant JCJC-HybEvol. 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. J.W.D. is funded by a Herchel Smith Postdoctoral Research Fellowship.