# Prairie Vole Genome Resource > Near telomere-to-telomere, haplotype-resolved prairie vole and meadow vole reference genomes, with annotation, tracks, and contact maps. Free to download. Chromosome-scale, haplotype-resolved reference genomes for the prairie vole (Microtus ochrogaster) and the meadow vole (M. pennsylvanicus), each assembled from a single HiFi and CiFi library. Includes gene annotation, repeat and segmental duplication maps, copy number across seven Microtus species, CpG methylation, and chromatin contact maps. Free to download and reuse. ## Genome browser - [Prairie vole tracks, mMicOch_UCD_v1 (hap1)](https://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=mabuelanin&hgS_otherUserSessionName=prairie_vole_cifi_hifi_hap1): Microtus ochrogaster, UCSC Genome Browser session with every track loaded. - [Meadow vole tracks, mMicPen_UCD_v1 (hap1)](https://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=mabuelanin&hgS_otherUserSessionName=meadow_vole_cifi_hifi_hap1): Microtus pennsylvanicus, UCSC Genome Browser session with every track loaded. ## Genome assemblies - [Prairie vole haplotype 1](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/assemblies/mMicOch_UCD_v1_hap1.fasta.gz): Prairie vole (Microtus ochrogaster), 26 autosomes plus X and Y. - [Prairie vole haplotype 2](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/assemblies/mMicOch_UCD_v1_hap2.fasta.gz): Prairie vole, second haplotype. - [Meadow vole haplotype 1](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/assemblies/mMicPen_UCD_v1_hap1.fasta.gz): Meadow vole (Microtus pennsylvanicus), 22 autosomes plus X and Y. - [Meadow vole haplotype 2](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/assemblies/mMicPen_UCD_v1_hap2.fasta.gz): Meadow vole, second haplotype. ## Gene annotation - [Prairie vole gene models (v1, short reads only)](https://raw.githubusercontent.com/mydennislab/2026-voles-assembly/main/annotation/prairie_hap1_egapx.gff.gz): First EGAPx round, short-read RNA-seq evidence only. Superseded by v2; use it only to reproduce earlier results. - [Prairie vole gene models (v2)](https://raw.githubusercontent.com/mydennislab/2026-voles-assembly/main/annotation/v2/prairie/complete.genomic.gff.gz): EGAPx v2 on prairie vole hap1. NCBI convention, with mRNA, exon, and CDS features. - [Prairie vole gene models, with UTRs (v2)](https://raw.githubusercontent.com/mydennislab/2026-voles-assembly/main/annotation/v2/prairie/complete.genomic.with_utrs.gff.gz): The same models with UTR features added by AGAT, for tools that expect them. - [Meadow vole gene models (v1, short reads only)](https://raw.githubusercontent.com/mydennislab/2026-voles-assembly/main/annotation/meadow_hap1_egapx.gff.gz): First EGAPx round, short-read RNA-seq evidence only. Superseded by v2. - [Meadow vole gene models (v2)](https://raw.githubusercontent.com/mydennislab/2026-voles-assembly/main/annotation/v2/meadow/complete.genomic.gff.gz): EGAPx v2 on meadow vole hap1. NCBI convention, with mRNA, exon, and CDS features. - [Meadow vole gene models, with UTRs (v2)](https://raw.githubusercontent.com/mydennislab/2026-voles-assembly/main/annotation/v2/meadow/complete.genomic.with_utrs.gff.gz): The same models with UTR features added by AGAT. ## Sequencing reads - [RNA-seq](https://www.ncbi.nlm.nih.gov/bioproject/PRJEB89367): Prairie vole brain, liver, testes, and embryo RNA-seq. - [All sequencing data](https://www.ncbi.nlm.nih.gov/bioproject/PRJEB108798): HiFi, CiFi, Hi-C, and Illumina WGS for both species and the woodland vole. ## Liftover chains - [Prairie vole to MicOch1.0](https://raw.githubusercontent.com/mydennislab/2026-voles-assembly/main/prairie_vole_chain_files/prairie_vole_mMicOch_UCD_ERZ29502723_vs_Broad_MicOch1.0_GCF_000317375.1.liftover_chains.tar.gz): Convert to the previous prairie reference GCF000317375.1. - [Meadow vole to VGP mMicPen1](https://raw.githubusercontent.com/mydennislab/2026-voles-assembly/main/meadow_vole_chain_files/meadow_vole_mMicPen_UCD_ERZ29502725_vs_VGP_GCF_037038515.1.liftover_chains.tar.gz): Convert to the VGP meadow reference GCF037038515.1. ## Chromatin contact maps - [Prairie vole CiFi contact map](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/prairie/hap1/bigfiles/hic/prairie_hap1.hic): CiFi proximity-ligation contacts on prairie hap1. - [Prairie vole Hi-C contact map](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/prairie/hap1/bigfiles/hic/prairie_hap1.shortread_hic.hic): Proximo Hi-C contacts on prairie hap1. - [Meadow vole Hi-C contact map](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/meadow/hap1/bigfiles/hic/meadow_hap1.shortread_hic.hic): Proximo Hi-C contacts on meadow hap1. ## Browser tracks - [Repeat annotation (prairie)](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/prairie/hap1/bigfiles/repeats/repeatmasker_detailed.bb): RepeatMasker annotations, colored by repeat class. - [Segmental duplications (prairie)](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/prairie/hap1/bigfiles/segdups/sedef_sd_bed.bb): SDs >1 kb at >90% identity, with mate coordinates. - [Orthologs (prairie)](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/prairie/hap1/bigfiles/orthologs/prairie_orthologs.bb): Prairie and meadow ortholog groups, colored by copy-number relationship. - [Repeat annotation (meadow)](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/meadow/hap1/bigfiles/repeats/repeatmasker_detailed.bb): RepeatMasker annotations, colored by repeat class. - [Segmental duplications (meadow)](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/meadow/hap1/bigfiles/segdups/sedef_sd_bed.bb): SDs >1 kb at >90% identity, with mate coordinates. - [Orthologs (meadow)](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/meadow/hap1/bigfiles/orthologs/meadow_orthologs.bb): Prairie and meadow ortholog groups, colored by copy-number relationship. - [CpG methylation (prairie)](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/prairie/hap1/bigfiles/methylation/prairie_hap1.cpg_methylation.bw): 5mC fraction from HiFi reads. - [HiFi read depth (prairie)](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/prairie/hap1/bigfiles/coverage/prairie_hap1.hifi_coverage.bw): PacBio HiFi read depth. - [Hi-C read depth (prairie)](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/prairie/hap1/bigfiles/coverage/prairie_hap1.hic_coverage.bw): Proximo Hi-C read depth. - [CpG methylation (meadow)](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/meadow/hap1/bigfiles/methylation/meadow_hap1.cpg_methylation.bw): 5mC fraction from HiFi reads. - [HiFi read depth (meadow)](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/meadow/hap1/bigfiles/coverage/meadow_hap1.hifi_coverage.bw): PacBio HiFi read depth. - [Hi-C read depth (meadow)](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/meadow/hap1/bigfiles/coverage/meadow_hap1.hic_coverage.bw): Proximo Hi-C read depth. - [Copy number, prairie vole](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/prairie/hap1/bigfiles/copynumber/prairie.CN.bw): Prairie vole (M. ochrogaster) read depth on the prairie assembly. - [Copy number, meadow vole](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/prairie/hap1/bigfiles/copynumber/meadow.CN.bw): Meadow vole (M. pennsylvanicus) read depth on the prairie assembly. - [Copy number, montane vole](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/prairie/hap1/bigfiles/copynumber/montane.CN.bw): Montane vole (M. montanus) read depth on the prairie assembly. - [Copy number, common vole](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/prairie/hap1/bigfiles/copynumber/common.CN.bw): Common vole (M. arvalis) read depth on the prairie assembly. - [Copy number, field vole](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/prairie/hap1/bigfiles/copynumber/field.CN.bw): Field vole (M. agrestis) read depth on the prairie assembly. - [Copy number, pine vole](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/prairie/hap1/bigfiles/copynumber/pine.CN.bw): Pine vole (M. pinetorum) read depth on the prairie assembly. - [Copy number, water vole](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/prairie/hap1/bigfiles/copynumber/water.CN.bw): Water vole (Arvicola amphibius) read depth on the prairie assembly. - [Copy number, prairie vole](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/meadow/hap1/bigfiles/copynumber/prairie.CN.bw): Prairie vole (M. ochrogaster) read depth on the meadow assembly. - [Copy number, meadow vole](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/meadow/hap1/bigfiles/copynumber/meadow.CN.bw): Meadow vole (M. pennsylvanicus) read depth on the meadow assembly. - [Copy number, montane vole](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/meadow/hap1/bigfiles/copynumber/montane.CN.bw): Montane vole (M. montanus) read depth on the meadow assembly. - [Copy number, common vole](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/meadow/hap1/bigfiles/copynumber/common.CN.bw): Common vole (M. arvalis) read depth on the meadow assembly. - [Copy number, field vole](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/meadow/hap1/bigfiles/copynumber/field.CN.bw): Field vole (M. agrestis) read depth on the meadow assembly. - [Copy number, pine vole](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/meadow/hap1/bigfiles/copynumber/pine.CN.bw): Pine vole (M. pinetorum) read depth on the meadow assembly. - [Copy number, water vole](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/meadow/hap1/bigfiles/copynumber/water.CN.bw): Water vole (Arvicola amphibius) read depth on the meadow assembly. - [Assembly gaps (prairie)](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/prairie/hap1/bigfiles/gaps/gaps.bb): Assembly gaps on the prairie assembly. - [Telomere positions (prairie)](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/prairie/hap1/bigfiles/gaps/telomeres.bb): Telomere positions on the prairie assembly. - [Centromere regions (prairie)](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/prairie/hap1/bigfiles/centromeres/centromere_regions.bb): Centromere regions on the prairie assembly. - [Assembly gaps (meadow)](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/meadow/hap1/bigfiles/gaps/gaps.bb): Assembly gaps on the meadow assembly. - [Telomere positions (meadow)](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/meadow/hap1/bigfiles/gaps/telomeres.bb): Telomere positions on the meadow assembly. - [Centromere regions (meadow)](https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/voles_2026/meadow/hap1/bigfiles/centromeres/centromere_regions.bb): Centromere regions on the meadow assembly. ## Paper - [Single-library chromosome-scale diploid assemblies of vole genomes resolve a species-specific duplication implicated in pair bonding](https://www.cell.com/cell-genomics/fulltext/S2666-979X(26)00198-9): Abuelanin et al., Cell Genomics 2026. ## Optional - [Full catalog](https://voles.dennislab.org/data/): every file with its size and format. - [How to cite](https://voles.dennislab.org/cite/): formatted citation, BibTeX and RIS. - [Source and workflows](https://github.com/mydennislab/2026-voles-assembly): code behind the assemblies.