Evidence map›Paper›PMID 42561951›Full record

ArticleCell genomics2026

Telomere-to-telomere genome assembly and a pangenome for the rat.

Kai Li, Julia L Ciosek, Sergey Koren, Adam M Phillippy, Yaming Zhu, William A Lauer, Shelise Y Brooks, Gerard G Bouffard, Brandon D Pickett, Beth L Dumont and 3 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

13 authors.

Kai LiDepartment of Veterinary Science, Martin-Gatton College of Agriculture, Food, and Environment, University of Kentucky, Lexington, KY, USA.
Julia L CiosekDepartment of Veterinary Science, Martin-Gatton College of Agriculture, Food, and Environment, University of Kentucky, Lexington, KY, USA.
Sergey KorenGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Adam M PhillippyGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Yaming ZhuCenter for Human Genetics, Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA.
William A LauerDepartment Biochemistry and Molecular Biology, University of Louisville School of Medicine, Louisville, KY, USA.
Shelise Y BrooksNIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Gerard G BouffardNIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Brandon D PickettGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Beth L DumontThe Jackson Laboratory, 600 Main Street, Bar Harbor, ME, USA.
Melissa L SmithDepartment Biochemistry and Molecular Biology, University of Louisville School of Medicine, Louisville, KY, USA.
Theodore S KalbfleischDepartment of Veterinary Science, Martin-Gatton College of Agriculture, Food, and Environment, University of Kentucky, Lexington, KY, USA.
Peter A DorisCenter for Human Genetics, Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA. Electronic address: peter.a.doris@uth.tmc.edu.

Funding

Long-read assembly and annotation of rat genomes that are important models of complex genetic diseaseR01HG011252 · NHGRI · UNIVERSITY OF TEXAS HLTH SCI CTR HOUSTON · PI DORIS, PETER A, KALBFLEISCH, THEODORE · 2021 to 2025
$2.0M
NHGRI NIH HHS R01 HG011252
6 · The paper itself

Abstract

We report a complete rodent telomere-to-telomere genome assembly from the brown rat, Rattus norvegicus. Annotation was enriched with multi-tissue long-read RNA sequencing and uncovered numerous novel genes. Assembly of both sex chromosomes reveals the absence of gene coding in the presumed pseudo-autosomal regions and the presence of centromeric satellite repeats on distal chromosome Y (chrY). We provide evidence of meiotic conjunction between Xp and Yq. The genome assembly reveals several expanded autosomal regions enriched for testis-expressed genes. Finally, we have generated a pangenome from recent high-quality assemblies of 8 distinct inbred rat strain genomes. This allows the strain-specific distribution of structural variation to be examined. Non-allelic homologous recombination has produced multiple copies of several genes with evidence of transcription from duplicated copies.

Indexed as

GenomeTelomereAnimalsCentromereMaleMeiosisRatsY Chromosomecentromeregenome asemblymeiosispangenomepseudo-autosomal regiontelomere to telomere

Identifiers

PMID42561951
PMCPMC13477028

What OpenQuestion holds

Textmetadata
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.