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.

袖蝶属（Heliconius）蝴蝶是一类被广泛研究的适应性辐射类群，包含46个物种，广泛分布于中美洲与南美洲，其中多个物种已知可在野外发生自然杂交。本研究完成了红带袖蝶（Heliconius melpomene）基因组的显著优化组装，所采用的创新方法可推广应用于优化其他基于短读长测序技术构建的基因组组装结果。具体而言，我们首先对一个家系开展全基因组测序，构建了覆盖99%基因组的连锁图谱；其次，广泛整合单倍型支架，以获得更完整的单倍体草稿基因组；第三，纳入约20倍覆盖度的太平洋生物科学（Pacific Biosciences）长读长测序数据，并利用该长读长序列的组装结果对单倍体基因组进行支架挂载。经上述优化，最终得到的基因组包含795个支架，总长275 Mb，其N50长度为2.1 Mb，N50数量为34；99%的基因组序列已完成定位，其中84%锚定至染色体上。我们借助新的基因组组装结果证实，自与其姊妹属优蝶属（Eueides）分化以来，袖蝶属基因组在约600万年的演化历程中共计发生了10次染色体融合事件。