Genomic resources for the North American water vole (Microtus richardsoni) and the montane vole (Microtus montanus)

Abstract

Background: Voles of the genus Microtus are important research organisms, yet genomic resources in the genus are lacking. Providing such resources would benefit future studies of immunology, phylogeography, cryptic diversity, and more. Findings: We sequenced and assembled nuclear genomes from two subspecies of water vole (Microtus richardsoni) and from the montane vole (Microtus montanus). The water vole genomes were sequenced with Illumina and 10X Chromium plus Illumina sequencing, resulting in assemblies with ~1,600,000 and ~30,000 scaffolds respectively. The montane vole was assembled into ~13,000 scaffolds using Illumina sequencing also. In addition to the nuclear assemblies, mitochondrial genome assemblies were also performed for both species. We conducted a structural and functional annotation for the best water vole nuclear genome, which resulted in ~24,500 annotated genes, with 83% of these receiving functional annotations. Finally, we find that assembly quality statistics for our nuclear assemblies fall within the range of genomes previously published in the genus Microtus, making the water vole and montane vole genomes useful additions to currently available genomic resources.

The Tien Shan vole (Microtus ilaeus; Rodentia: Cricetidae) as a new species in the Late Pleistocene of Europe

“…The contaminating sequences were likely to be nuclear sequences of mitochondrial origin ( numts ). The presence of numts in mtDNA assemblies was previously reported for various Microtus species (Barbosa et al, 2018 ; Duckett et al, 2021 ; Triant & DeWoody, 2008 ), and their presence are especially expected in the case of the assemblies based on mtDNA‐enriched libraries. Therefore, we called consensus sequences only for mtDNA fragments where numts were not present, and this was either whole mtDNA, ca.…”