title: Major Improvements to the Heliconius melpomene Genome Assembly Used to Confirm 10 Chromosome Fusion Events in 6 Million Years of Butterfly Evolution.
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 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.
authors.affiliation: Department of Zoology, University of Cambridge, CB2 3EJ, United Kingdom jd626@cam.ac.uk cj107@cam.ac.uk.
authors.forename: John W
authors.identifier: 0000-0002-1017-9775
authors.initials: JW
authors.lastname: Davey
authors.affiliation: Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 CNRS - EPHE - Université de Montpellier - Université Paul Valéry, 34293 Montpellier 5, France.
authors.forename: Mathieu
authors.initials: M
authors.lastname: Chouteau
authors.affiliation: Department of Zoology, University of Cambridge, CB2 3EJ, United Kingdom.
authors.forename: Sarah L
authors.initials: SL
authors.lastname: Barker
authors.affiliation: Department of Biology, Williams College, Williamstown, Massachusetts, 01267.
authors.forename: Luana
authors.initials: L
authors.lastname: Maroja
authors.affiliation: School of Biological Sciences, University of Adelaide, SA 5005 Australia.
authors.forename: Simon W
authors.initials: SW
authors.lastname: Baxter
authors.affiliation: Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, WC1E 6BT, United Kingdom.
authors.forename: Fraser
authors.initials: F
authors.lastname: Simpson
authors.forename: Richard M
authors.initials: RM
authors.lastname: Merrill
authors.affiliation: Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 CNRS - EPHE - Université de Montpellier - Université Paul Valéry, 34293 Montpellier 5, France.
authors.forename: Mathieu
authors.initials: M
authors.lastname: Joron
authors.affiliation: Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, WC1E 6BT, United Kingdom.
authors.forename: James
authors.initials: J
authors.lastname: Mallet
authors.affiliation: Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, WC1E 6BT, United Kingdom.
authors.forename: Kanchon K
authors.initials: KK
authors.lastname: Dasmahapatra
authors.affiliation: Department of Zoology, University of Cambridge, CB2 3EJ, United Kingdom jd626@cam.ac.uk cj107@cam.ac.uk.
authors.forename: Chris D
authors.initials: CD
authors.lastname: Jiggins
mesh_terms: D000818:Animals; D002080:Butterflies / Q000235:genetics*; D002874:Chromosome Mapping; D059006:Chromosomes, Insect; D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D005260:Female; D008040:Genetic Linkage; D056426:Genetic Loci; D059646:Genome Size; D049750:Genome, Insect; D023281:Genomics / Q000379:methods; D006239:Haplotypes; D059014:High-Throughput Nucleotide Sequencing; D006824:Hybridization, Genetic; D008297:Male; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide
keywords: Eueides; Heliconius; chromosome fusions; genome assembly; linkage mapping