Rémi's roadkill genomics paper published in eLife!
Rémi's new study about genomics of carnivores based on roadkill samples is finally published in eLife after using their new pre-print review system. In this paper, we generated two reference genomes using hybrid Nanopore/Illumina sequencing to study the genetic differentiation between the allopatric populations of aardwolf (Proteles cristatus) and bat-eared fox (Otocyon megalotis). First, we estimated the genetic diversity among carnivores for the COX1 and CYTB mitochondrial markers to find a gap between intra and inter specific diversity. The results combined with a mitogenomic phylogeny suggested a high divergence between the two allopatric populations of aardwolf. To go further, we generated genomic data for both the aardwolf and the bat-eared fox populations. We developed a protocol to extract good quality DNA from roadkill samples suitable for Nanopore sequencing. Combining short read Illumina and Nanopore long read sequence data using the hybrid MaSuRCA assembler, we generated two assemblies with both high contiguity and high gene completeness. Despite the use of roadkill samples, our genomes rank among the best carnivoran genomes currently assembled. Using additional individuals, we compared the genetic differentiation between our focal populations to that of well-established species. We found that the aardwolf populations present a higher genetic differentiation than the grey wolf and the golden jackal suggesting that the two populations of aardwolf might deserve to be considered as different species: the southern aardwolf (Proteles cristatus) and the eastern aardwolf (Proteles septentrionalis). Finally, we generated a reference phylogenomic tree based on 14,307 single-copy orthologous genes for 52 Carnivora species with genomic data available.
Allio R., Tilak M.-K., Scornavacca C., Avenant N.L., Kitchener A.C., Corre E., Nabholz B. & Delsuc F. (2021). High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox. eLife 10:e63167 doi:10.7554/eLife.63167.