Evidence map›Paper›PMID 40682131›Full record

ArticleBMC biology2025

A chromosome-level genome assembly of the Hispid cotton rat (Sigmodon hispidus), a model for human pathogenic virus infections.

Jingtao Lilue, André Corvelo, Jèssica Gómez-Garrido, Keiko Akagi, Fengtang Yang, Gia Green, Bee Ling Ng, Beiyuan Fu, Uciel Pablo Chorostecki, Sarah C Warner and 8 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC biology, 2025. 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

18 authors.

Jingtao Lilue *European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
André Corvelo *New York Genome Center, New York, NY, USA.
Jèssica Gómez-Garrido *Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain.
Keiko Akagi *Department of Cancer Biology and Genetics, Ohio State University, Columbus, OH, USA.
Fengtang Yang *European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
Gia GreenDepartment of Veterinary Biosciences, College of Veterinary Medicine, Ohio State University, Columbus, OH, USA.
Bee Ling NgWellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
Beiyuan FuWellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
Uciel Pablo ChorosteckiMechanisms of Disease Program, Institute for Research in Biomedicine, Barcelona, Spain.
Sarah C WarnerGenomics Shared Resource, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
Marina Marcet-HoubenMechanisms of Disease Program, Institute for Research in Biomedicine, Barcelona, Spain.
Thomas M KeaneEuropean Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
James C MullikinNational Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Tyler AliotoCentro Nacional de Análisis Genómico (CNAG), Barcelona, Spain.
Toni GabaldónMechanisms of Disease Program, Institute for Research in Biomedicine, Barcelona, Spain.
Benjamin HubertNew York Genome Center, New York, NY, USA.
David E Symer *Department of Cancer Biology and Genetics, Ohio State University, Columbus, OH, USA. desymer@gmail.com.
Stefan Niewiesk *Department of Veterinary Biosciences, College of Veterinary Medicine, Ohio State University, Columbus, OH, USA. niewiesk.1@osu.edu.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundThe cotton rat (Sigmodon hispidus), a rodent species native to the Americas, has emerged as a valuable laboratory model of infections by numerous human pathogens including poliovirus and respiratory syncytial virus (RSV).

resultsHere we report the first reference assembly of the cotton rat genome organized at a chromosomal level, providing annotation of 24,878 protein-coding genes. Data from PCR-free whole genome sequencing, linked-read sequencing, and RNA sequencing from pooled cotton rat tissues were analyzed to assemble and annotate this novel genome sequence. Spectral karyotyping data using fluorescent probes derived from mouse chromosomes facilitated the assignment of cotton rat orthologs to syntenic chromosomes, comprising 25 autosomes and a sex chromosome in the haploid genome. Comparative phylome analysis revealed both gains and losses of numerous genes including immune defense genes against pathogens. We identified thousands of recently retrotransposed L1, SINE B2, and ERV elements, revealing widespread genomic insertions unique to this species.

conclusionsWe anticipate that annotation and characterization of the first chromosome-level cotton rat genome assembly as described here will enable and accelerate ongoing investigations into its host defenses against viral and other pathogens, genome biology, and mammalian evolution.

Indexed as

Disease Models, AnimalGenomeSigmodontinaeVirus DiseasesAnimalsHumansComparative genomicsCotton ratGene annotationsLinked-read sequencingPhylome analysisReference genome assemblyRNA-seqRodentTransposable elementsWhole genome sequencing

Identifiers

PMID40682131
PMCPMC12275374

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.