Evidence map›Paper›PMID 37793045›Full record

ArticleThe Journal of heredity2024

A highly contiguous genome assembly for the pocket mouse Perognathus longimembris longimembris.

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

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in The Journal of heredity, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. Article
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, Santa Cruz, CA 95064, United States.ORCID 0000-0003-0213-4777
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, 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
Ruta SahasrabudheDNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, United States.ORCID 0000-0002-3285-6845
William SeligmannDepartment of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, United States.ORCID 0000-0002-5762-3095
Chris 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 OD010786
6 · The paper itself

Abstract

The little pocket mouse, Perognathus longimembris, and its nine congeners are small heteromyid rodents found in arid and seasonally arid regions of Western North America. The genus is characterized by behavioral and physiological adaptations to dry and often harsh environments, including nocturnality, seasonal torpor, food caching, enhanced osmoregulation, and a well-developed sense of hearing. Here we present a genome assembly of Perognathus longimembris longimembris generated from PacBio HiFi long read and Omni-C chromatin-proximity sequencing as part of the California Conservation Genomics Project. The assembly has a length of 2.35 Gb, contig N50 of 11.6 Mb, scaffold N50 of 73.2 Mb, and includes 93.8% of the BUSCO Glires genes. Interspersed repetitive elements constitute 41.2% of the genome. A comparison with the highly endangered Pacific pocket mouse, P. l. pacificus, reveals broad synteny. These new resources will enable studies of local adaptation, genetic diversity, and conservation of threatened taxa.

Indexed as

ChromosomesGenomeAnimalsGenomicsMiceNorth AmericaCalifornia Conservation Genomics Projectcomparative genomicsconservation geneticsHeteromyidaePerognathusrepetitive elements

Identifiers

PMID37793045
PMCPMC10838119

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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.