Evidence map›Paper›PMID 40972894›Full record

ArticleThe Journal of heredity2026

A highly contiguous genome assembly for the California vole, Microtus californicus, provides insight into phylogenetic relationships and patterns of synteny among voles.

Krzysztof M Kozak, Merly Escalona, Isaac J Linn, Noravit Chumchim, Colin Fairbairn, Mohan P A Marimuthu, Oanh Nguyen, William Seligmann, Chris J Conroy, James L Patton and 2 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in The Journal of heredity, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

12 authors.

Krzysztof M KozakMuseum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, United States.ORCID 0000-0001-8980-3173
Merly EscalonaDepartment of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, United States.ORCID 0000-0003-0213-4777
Isaac J LinnMuseum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, United States.ORCID 0000-0003-4143-0296
Noravit ChumchimDNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, United States.ORCID 0000-0003-1139-9427
Colin FairbairnDepartment of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, United States.ORCID 0009-0007-8129-0095
Mohan P A MarimuthuDNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, United States.ORCID 0000-0001-6121-3286
Oanh NguyenDNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, United States.ORCID 0000-0003-1492-2084
William SeligmannDepartment of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, United States.ORCID 0000-0002-5762-3095
Chris J ConroyMuseum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, United States.ORCID 0000-0001-7198-9651
James L PattonMuseum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, United States.ORCID 0000-0002-8709-7196
Rauri C K BowieMuseum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, United States.ORCID 0000-0001-8328-6021
Michael W NachmanMuseum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, United States.ORCID 0000-0003-4321-5135

Funding

Acquisition of Covaris E220 and Sciclone G3 systems for high throughput sequencinS10OD010786 · OD · UNIVERSITY OF CALIFORNIA AT DAVIS · PI COMAI, LUCA · 2012 to 2012
$311k
NIH HHS 1S10OD010786-01NIH HHS S10 OD010786State of California, State Budget Act of 2019 RSI-19-690224
6 · The paper itself

Abstract

The California vole (Microtus californicus) is a small cricetid rodent and one of the 20 species of Microtus in North America and 60 worldwide. Several subspecies are listed as being of conservation concern in California, and one is federally protected. Here we present the first de novo genome assembly for the California vole, generated as a part of the California Conservation Genomics Project. The M. californicus genome was generated using a combination of PacBio HiFi long reads and Omni-C chromatin-proximity sequencing technology. Our high-quality genome is one of the most complete vole assemblies available, with a contig N50 of 49.8 Mb, scaffold N50 of 83.7 Mb, and BUSCO completeness score of 96.4%. Analysis of this genome together with genomes of closely related species revealed phylogenetic relationships and high levels of synteny among voles. The California vole genome provides an important new resource for comparative work across cricetid and muroid genomes. It will also serve as a reference for the analysis of within-species genetic diversity across widespread subspecies as well as more restricted populations of conservation concern.

Indexed as

ArvicolinaeGenomePhylogenySyntenyAnimalsCaliforniaGenomicsCalifornia Conservation Genomics ProjectCCGPgenomicslong-read assemblyreference genomerodents

Identifiers

PMID40972894
PMCPMC13016638

What OpenQuestion holds

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LicenceCC BY-NC
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.