Evidence map›Paper›PMID 41330379›Full record

ArticleCell genomics2026

High-quality mouse reference genomes reveal the structural complexity of the murine protein-coding landscape.

Mohab Helmy, Jin U Li, Xinyu F Yan, Rachel K Meade, Elizabeth Anderson, Patrick B Chen, Anne M Czechanski, Tomás Di Domenico, Jonathan Flint, Erik Garrison and 23 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell genomics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. 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

33 authors.

Mohab HelmyEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Department of Biochemistry, Department of Genetics and Gurdon Institute, University of Cambridge, Cambridge, UK.
Jin U LiOujiang Laboratory, Wenzhou Medical University, Wenzhou, China.
Xinyu F YanOujiang Laboratory, Wenzhou Medical University, Wenzhou, China.
Rachel K MeadeDepartment of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA; University Program in Genetics and Genomics, Duke University, Durham, NC, USA.
Elizabeth AndersonWellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.
Patrick B ChenBrain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA.
Anne M CzechanskiThe Jackson Laboratory, Bar Harbor, ME, USA.
Tomás Di DomenicoDepartment of Biochemistry, Department of Genetics and Gurdon Institute, University of Cambridge, Cambridge, UK; Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
Jonathan FlintBrain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA.
Erik GarrisonUniversity of Tennessee Health Science Center, Memphis, TN, USA.
Marco T P GontijoDepartment of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.
Andrea GuarracinoUniversity of Tennessee Health Science Center, Memphis, TN, USA.
Leanne HaggertyEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Edith HeardEuropean Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
Kerstin HoweWellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.
Narendra MeenaDepartment of Biochemistry, Department of Genetics and Gurdon Institute, University of Cambridge, Cambridge, UK.
Fergal J MartinEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Eric A MiskaDepartment of Biochemistry, Department of Genetics and Gurdon Institute, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.
Isabell RallEuropean Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
Navin B RamakrishnaDepartment of Biochemistry, Department of Genetics and Gurdon Institute, University of Cambridge, Cambridge, UK.
Alexandra SapetschnigDepartment of Biochemistry, Department of Genetics and Gurdon Institute, University of Cambridge, Cambridge, UK.
Swati SinhaEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Diandian SunOujiang Laboratory, Wenzhou Medical University, Wenzhou, China; Central South University, Changsha, Hunan Province, China.
Francesca F TricomiEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Runjia QuOujiang Laboratory, Wenzhou Medical University, Wenzhou, China.
Jonathan M D WoodWellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.
Tianzhen WuOujiang Laboratory, Wenzhou Medical University, Wenzhou, China.
Dian J ZhouOujiang Laboratory, Wenzhou Medical University, Wenzhou, China.
Laura ReinholdtThe Jackson Laboratory, Bar Harbor, ME, USA.
David J AdamsWellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.
Clare M SmithDepartment of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA; University Program in Genetics and Genomics, Duke University, Durham, NC, USA.
Jingtao LilueOujiang Laboratory, Wenzhou Medical University, Wenzhou, China.
Thomas M KeaneEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK; University of Nottingham, Nottingham, UK. Electronic address: tk2@ebi.ac.uk.

Funding

Integrating genetic and circuit variation to identify genes involved in behaviors related to substance use disorderU01DA059695 · NIDA · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI JONATHAN FLINT · 2024 to 2026
$2.1M
Dissecting the genetic basis of protective immunity to tuberculosis in diverse hostsDP2AI183152 · NIAID · DUKE UNIVERSITY · PI SMITH, CLARE MARGARET · 2024 to 2024
$966k
NIAID NIH HHS DP2 AI183152NIDA NIH HHS U01 DA059695
6 · The paper itself

Abstract

We present a collection of 17 high-quality long-read inbred mouse strain genomes with complete annotation (contig N50s of 0.8-33.9 Mbp). This collection includes 12 widely used classical laboratory strains and 5 wild-derived strains. We have resolved previously incomplete genomic regions, including the major histocompatibility complex (MHC), defensin cluster, T cell receptor, and Ly49 complexes. Hundreds of non-reference genes from previous publications not found in GRCm39, such as Defa1, Raet1a, and Klra20 (Ly49T), were localized in the new reference genomes. We conducted a genome-wide scan of variable number tandem repeats (VNTRs) within the coding regions, identifying over 400 genes with VNTR polymorphisms with up to 600 repeat copies and repeat units reaching 990 nucleotides. Our strain-specific annotations enhance RNA sequencing (RNA-seq) analyses, as demonstrated in PWK/PhJ, where we observed a 5.1% improvement in read mapping and expression-level differences in 2.1% of coding genes compared to using GRCm39.

Indexed as

GenomeAnimalsMajor Histocompatibility ComplexMiceMice, Inbred StrainsMolecular Sequence Annotationgenomic variationlaboratory mousemouse genomespangenomesequencing

Identifiers

PMID41330379
PMCPMC12903361

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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.