Genomics from roadkill - high quality mammalian genomes using hybrid assembly with MinION long reads
About Frédéric Delsuc
Frédéric Delsuc is Research Director at the French National Centre for Scientific Research (CNRS), working in the Institute of Evolutionary Sciences at the University of Montpellier. He received his PhD in molecular phylogeny from the University of Montpellier, then worked on mammalian and tunicate phylogenomics during post-doctoral positions in New Zealand and Canada before coming back to Montpellier as a permanent CNRS researcher. He is currently directing the ERC ConvergeAnt project aimed at understanding convergent evolution in ant-eating mammals through an integrative approach combining morphology, genomes, and microbiomes. The project team has adopted nanopore sequencing technology using the MinION to produce long-reads combined with Illumina short-reads to assemble mammalian genomes mostly from roadkill animals.
With thousands of fatalities due to car collisions with wildlife reported each year, roadkill are an underexploited resource in genomics. Here we show that mammalian roadkill samples could be used as a suitable source of DNA for long-read sequencing using the MiniON device for two carnivoran species frequently encountered along South African roads: the bat-eared fox (Otocyon megalotis) and the aardwolf (Proteles cristatus). For both species, hybrid assembly of 150PE Illumina reads at ~85X coverage (~215 Gb) and MiniON long reads at ~12X coverage (~30 Gb) using the MaSuRCA assembler provided genomes with high contiguity (~10,000 contigs with N50 of ~700 Kb) and completeness (>90% of complete BUSCOs). We further demonstrate that about 90% of the 14,509 single-copy orthologous genes of the OrthoMaM database could be successfully retrieved from these assemblies. These figures compare favourably with current mammalian genome assemblies and set our genomes among the best carnivore genomes currently available. This cost-effective strategy to obtain high quality reference mammalian genomes opens the way for large-scale population genomic studies of mammalian wildlife using resequencing of samples collected from roadkill. We illustrate the potential of the approach for genome scale species delimitation in both species for which subspecies have been defined based on disjunct distributions and morphological differences.