Draft genome from facultatively parthenogenetic Opiliones indicates frequent mitonuclear sequence transfer and novel full-length insertions

Abstract

Background: Facultative parthenogenesis and intra-population mixed ploidy are rare in animals. These unique characteristics allow opportunities to investigate the relationship between sexual modality and ploidy. We have completed a draft genome of the Japanese harvester ("daddy-longlegs") Leiobunum manubriatum, a species which reproduces sexually and asexually, and with mixed diploid and tetraploid populations in some areas.

Results: We combined Oxford Nanopore’s MinION long-read sequencing platform with Dovetail Hi-C scaffolding to assemble the haploid genome for the diploid race, which is approximately 336 MBp after collapsing heterozygous sequence. The assembly’s completeness was measured using BUSCOs from Eukaryota (complete: 92.6%), Arthropoda (complete: 96.9%), and Arachnida (complete: 95.3%). We searched raw sequence reads and the draft genome for nuclear mitochondrial DNA (numt) sequences. While only one complete mitochondrial genomic transfer was found in the draft genome, there are at least 12 complete numts across 9 reads within the raw sequencing data that were lost during the assembly process.

Conclusions: The genome of the L. manubriatum diploid race is an invaluable resource not only for opilionid research, but also for facilitating studies investigating the evolution of their unique reproductive mode and mixed ploidy. To our knowledge, this is the first published genome of a wild-derived facultative parthenogen. Future work will leverage this resource in comparative genomics and transcriptomics of L. manubriatum to understand the connection between ploidy and sexual strategy.