Genomic data for the North American water vole (Microtus richardsoni)

Dataset type: Genomic, Bioinformatics
Data released on April 14, 2021

Duckett DJ; Sullivan J; Pirro S; Carstens BC (2021): Genomic data for the North American water vole (Microtus richardsoni) GigaScience Database. http://dx.doi.org/10.5524/100886

DOI10.5524/100886

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. We sequenced and assembled nuclear genomes from two subspecies of water vole (Microtus richardsoni) and from the montane vole (Microtus montanus).
The North American water vole (M. richardsoni) is adapted to a semi-aquatic lifestyle, relying on alpine and sub-alpine streams for creating burrows and escaping predators. The present study provides two nuclear and one mitochondrial genome assembly for M. richardsoni. The nuclear genomes were sequenced with Illumina and 10X Chromium plus Illumina sequencing. Sequencing of M. r. arvicoloides produced over 800 million reads and 47x coverage. The final genome assembly consisted of ~32,000 scaffolds with an N50 of 2.3 Mb, 1.3% missing data (N's), and a BUSCO score of 85.8%. Sequencing of M. r. macropus produced over 600 million reads and 35x coverage. The final genome assembly consisted of ~1,600,000 scaffolds with an N50 of 16Kb, 0.06% missing data, and a BUSCO score of 54.5%. In addition to the nuclear assemblies, a mitochondrial genome assembly was also performed for M. r. arvicoloides.

Additional details

Github links:

https://github.com/djlduckett/Genome_Resources/

Accessions (data generated as part of this study):

BioProject: PRJNA673719
BioProject: PRJNA509068

Accessions (data referenced by this study):

Assembly: GCA_902806755.1
Assembly: GCA_007455615.1
Assembly: GCA_000317375.1
Assembly: GCA_007455595.1





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
DD142821547  Microtus richardsoni arvicoloides Description:Genomic DNA extracted from heart of a ...
Alternative accession-BioSample:SAMN16621608
Analyte type:DNA
...
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DD2111840 water voleMicrotus richardsoni Description:Genomic DNA extracted from muscle of a...
Alternative accession-BioSample:SAMN10536510
Analyte type:DNA
...
+
Displaying 1-2 of 2 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
DD14Genome sequenceGZIP677.2 MB2021-04-07
DD2Genome sequenceGZIP710.16 MB2021-04-07
GitHub archivearchive13.06 KB2021-04-14
Genome sequenceGZIP706.16 MB2021-04-07
BUSCOTSV1.28 MB2021-04-07
DD2Genome sequenceGZIP876.03 MB2021-04-07
DD2BUSCOTSV843.68 KB2021-04-07
DD2Genome sequenceGZIP794.37 MB2021-04-07
DD2BUSCOTSV1022.71 KB2021-04-07
DD2Genome sequenceGZIP822.59 MB2021-04-07
Displaying 1-10 of 30 File(s).
Funding body Awardee Award ID Comments
National Science Foundation B Carstens DEB-1457519
The Ohio State University D Duckett NA Salary support
National Science Foundation R Ramnath DBI-1945347
Date Action
April 14, 2021 Dataset publish
February 9, 2023 Link updated : Assembly:GCA_902806755.1
February 9, 2023 Link updated : Assembly:GCA_007455615.1
February 9, 2023 Link updated : Assembly:GCA_000317375.1
February 9, 2023 Link updated : Assembly:GCA_007455595.1