A haplotype-resolved,de novogenome assembly for the wood tiger moth (Arctia plantaginis) through trio binning

  1. Eugenie C. Yen
  2. Shane A. McCarthy
  3. Juan A. Galarza
  4. Tomas N. Generalovic
  5. Sarah Pelan
  6. Petr Nguyen
  7. Joana I. Meier
  8. Ian A. Warren
  9. Johanna Mappes
  10. Richard Durbin
  11. Chris D. Jiggins
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Abstract

Background

Diploid genome assembly is typically impeded by heterozygosity, as it introduces errors when haplotypes are collapsed into a consensus sequence. Trio binning offers an innovative solution which exploits heterozygosity for assembly. Short, parental reads are used to assign parental origin to long reads from their F1 offspring before assembly, enabling complete haplotype resolution. Trio binning could therefore provide an effective strategy for assembling highly heterozygous genomes which are traditionally problematic, such as insect genomes. This includes the wood tiger moth (Arctia plantaginis), which is an evolutionary study system for warning colour polymorphism.

Findings

We produced a high-quality, haplotype-resolved assembly forArctia plantaginisthrough trio binning. We sequenced a same-species family (F1 heterozygosity ∼1.9%) and used parental Illumina reads to bin 99.98% of offspring Pacific Biosciences reads by parental origin, before assembling each haplotype separately and scaffolding with 10X linked-reads. Both assemblies are highly contiguous (mean scaffold N50: 8.2Mb) and complete (mean BUSCO completeness: 97.3%), with complete annotations and 31 chromosomes identified through karyotyping. We employed the assembly to analyse genome-wide population structure and relationships between 40 wild resequenced individuals from five populations across Europe, revealing the Georgian population as the most genetically differentiated with the lowest genetic diversity.

Conclusions

We present the first invertebrate genome to be assembled via trio binning. This assembly is one of the highest quality genomes available for Lepidoptera, supporting trio binning as a potent strategy for assembling highly heterozygous genomes. Using this assembly, we provide genomic insights into geographic population structure ofArctia plantaginis.

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