DNA was extracted using a Qiagen DNeasy Blood and Tissue Kit, and the DNA was sent for library preparation and sequencing by Iridian Genomes, Inc (Bethesda, MD, USA). macropus individual collected from the northern Rocky Mountains (JMG_88 46.333333N, −114.633333E ). Īdditional tissue was obtained from a single M. Despite being listed in the International Union for Conservation of Nature (IUCN) Red List as being of ‘ Least Concern’, the species is listed as ‘critically imperiled’ in the Wyoming Natural Diversity Database owing to its specific habitat requirements, which can be substantially degraded by livestock grazing. richardsoni does not appear to experience regular population boom and bust cycles, although population size in the species may correlate with levels of precipitation. Water voles are among the largest species of Microtus, and their frequent movement makes runways of trampled vegetation along streams. Like other semiaquatic mammals (e.g., otters), adaptations to this lifestyle have probably been driven by natural selection. richardsoni is adapted to a semiaquatic lifestyle, relying on alpine and subalpine streams for creating burrows and escaping predators. macropus in the central Rocky Mountains and Wyoming, and M. richardsoni in the Canadian Rocky Mountains, M. arvicoloides in the Cascades Mountains, M. Four subspecies are currently recognized: M. richardsoni) occupies a large, disjunct distribution in the Pacific Northwest of North America, with habitat in the Cascades Mountains and the Rocky Mountains, spanning from southern Canada into central Utah. 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. Structural and functional annotation for the best water vole nuclear genome resulted in ∼24,500 annotated genes, with 83% of these having functional annotations. Mitochondrial genome assemblies were also performed for both species. The montane vole was also assembled into ∼13,000 scaffolds using Illumina sequencing. The water vole genomes were sequenced with Illumina and 10× Chromium plus Illumina sequencing, resulting in assemblies with ∼1600,000 and ∼30,000 scaffolds, respectively. We sequenced and assembled nuclear genomes from two subspecies of water vole ( Microtus richardsoni) and from the montane vole ( Microtus montanus). Such resources would benefit future studies of immunology, phylogeography, cryptic diversity, and more. Users should refer to the original published version of the material for the full abstract.Voles of the genus Microtus are important research organisms, yet genomic resources are lacking. No warranty is given about the accuracy of the copy. However, users may print, download, or email articles for individual use. Copyright of Bioinformatics is the property of Oxford University Press / USA and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission.Supplementary information Supplementary data are available at Bioinformatics online. Availability and implementation Transcript ranking code can be found on GitHub at. Based on the set of expression data provided, TRaCE can identify the most common isoforms from a broad expression atlas or prioritize alternative transcripts expressed in specific contexts. The winner is selected as the canonical transcript, but the election proceeds through multiple rounds of voting to order all the transcripts by relevance. These sample-specific votes are tallied along with other criteria such as protein length and InterPro domain coverage. To choose canonical transcripts, Transcript Ranking and Canonical Election (TRaCE) holds an 'election' in which a set of RNA-seq samples rank transcripts by annotation edit distance. However, downstream analyses often operate on only one representative transcript per gene locus, sometimes known as the canonical transcript.
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