Major Improvements to the Heliconius melpomene Genome Assembly Used to Confirm 10 Chromosome Fusion Events in 6 Million Years of Butterfly Evolution.
Major Improvements to the Heliconius melpomene Genome Assembly Used to Confirm 10 Chromosome Fusion Events in 6 Million Years of Butterfly Evolution.
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DOI：
10.1534/g3.115.023655
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发表时间：
2016-01-15
期刊：
影响因子：
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通讯作者：
Jiggins CD
中科院分区：
文献类型：
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作者：
Davey JW;Chouteau M;Barker SL;Maroja L;Baxter SW;Simpson F;Merrill RM;Joron M;Mallet J;Dasmahapatra KK;Jiggins CD
Heliconius蝴蝶是一种广泛研究的适应性辐射，分布在中美洲和南美洲的46种，其中几种已知在野外杂交。在这里，我们提出了一个大大改善的组装Heliconius melpomene基因组，开发使用新的方法，应适用于改善其他基因组组装使用短读测序。首先，我们对一个家系进行全基因组测序，以产生一个包含99%基因组的连锁图。其次，我们广泛地整合了单倍型支架，以产生更完整的基因组草图的单倍体版本。第三，我们整合了Pacific Biosciences测序的20倍覆盖率，并使用该长读段序列的组装构建了单倍体基因组。这些改进导致795个支架的基因组，长度为275 Mb，N50长度为2.1 Mb，N50数量为34，并且99%的基因组放置在染色体上，84%锚定在染色体上。我们使用新的基因组组装，以确认Heliconius基因组经历了10个染色体融合，因为分裂与它的姐妹属Eueides，在一段时间内约600万年。
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.