Major Improvements to theHeliconius melpomeneGenome 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.

No evidence for maintenance of a sympatricHeliconiusspecies barrier by chromosomal inversions

“…2007; Davey et al. 2016), and we could find no evidence to the contrary in any of our crosses (Fig. S2), so we focus on paternal crossovers throughout (see Supporting Information note for a discussion and defense of this point).…”

“…2016). This resulted in an updated genome assembly with 13 complete chromosomes, the remaining eight chromosomes having one long central scaffold with short unconnected scaffolds at either end (272.6 Mb placed on 21 chromosomes in 38 scaffolds, including 17 minor scaffolds at chromosome ends totaling 1.3 Mb; 294 additional scaffolds [2.6 Mb] were not placed on chromosomes and unused in further analyses).…”

“…2014, Davey et al. 2016; we have transferred the H. melpomene loci to positions in the ordered Hmel2 genome in Table S8 and also included a table of all candidate inversion positions for comparison in Table S7; the BD region has been narrowed based on the results of Wallbank et al. 2016).…”

“…2013) and Illumina RAD and whole genome reads were aligned to version 2 of the H. melpomene genome (Hmel2; Davey et al . 2016) with Stampy (Lunter and Goodson 2011), Picard (http://broadinstitute.github.io/picard/), and GATK (dePristo et al. 2011) and genotype posteriors called with SAMtools mpileup (Li 2011).…”

“…H. melpomene melpomene has a high‐quality genome assembly with 99% of the genome placed on chromosomes and 84% ordered and oriented (Heliconius Genome Consortium 2012; Davey et al. 2016). Whole genome resequencing has shown that F ST between H. melpomene melpomene and H. melpomene rosina is consistently low across the genome, with only a few small, narrow peaks of divergence, but F ST between H. melpomene rosina and H. cydno chioneus is substantially higher and heterogeneous (Martin et al.…”