Evidence map›Paper›PMID 41272845›Full record

ArticleGenome biology2025

Long-read structural variant discovery and targeted short read genotyping enables population scale characterization of structural variation in rhesus macaques.

Karina Ray, Christina Mulch, Samuel M Peterson, Sebastian Benjamin, Nathan Gullicksrud, Adam J Ericsen, Eric J Vallender, Betsy M Ferguson, Jeffrey D Wall, Benjamin N Bimber

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In one paragraph

Article in Genome 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

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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

10 authors.

Karina RayOregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA.
Christina MulchOregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA.
Samuel M PetersonOregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA.
Sebastian BenjaminOregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA.
Nathan GullicksrudDivision of Microbiology and Immunology, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA, 30322, USA.
Adam J EricsenDivision of Microbiology and Immunology, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA, 30322, USA.
Eric J VallenderUniversity of Mississippi Medical Center, Jackson, MS, 39216, USA.
Betsy M FergusonOregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA.
Jeffrey D WallOregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA.
Benjamin N BimberOregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA. bimber@ohsu.edu.

Funding

Upgrade of confocal microscopy at the Oregon National Primate Research CenterP51OD011092 · OD · OREGON HEALTH & SCIENCE UNIVERSITY · PI Bonnie J. Nagel · 2012 to 2026
$203.9M
Tulane NPRC SPF Sheltered Outdoor Enclosure ExpansionP51OD011104 · OD · TULANE UNIVERSITY OF LOUISIANA · PI L Lee HAMM · 2012 to 2026
$142.4M
Genomic Sequencing to Establish a Macaque Genotype and Phenotype Research ResourceR24OD021324 · OD · OREGON HEALTH & SCIENCE UNIVERSITY · PI FERGUSON, BETSY M · 2016 to 2023
$7.7M
NIH HHS P51 OD011092NIH HHS P51 OD011104NIH HHS R24OD021324
6 · The paper itself

Abstract

backgroundDue to their close evolutionary relationship with humans, rhesus macaques are an important pre-clinical model. While genetic diversity driven by short nucleotide variation has long been studied in rhesus macaques, there is comparatively little known about structural variation, with most published studies focused on cross-species comparative analyses. Understanding the degree and implications of intraspecies structural variation is essential to all biomedical research using rhesus macaques as a model.

resultsHere we present long-read sequencing of 59 rhesus macaques, identifying a catalog of 339,334 structural variants (SVs), which we subsequently genotype in a cohort of 2,645 individuals with short read whole genome sequencing data to create the largest public dataset of rhesus macaque SVs. These data reveal population structure within rhesus macaque SVs based on both geographic ancestry and to a lesser degree, breeding center. While there is evidence of strong purifying selection against SVs within exons, 0.7% of SVs overlap exons, with an average of 16.9 rare SVs per subject predicted to have a high impact on protein coding sequences. Notably, rhesus macaque SVs are dominated by Alu retrotransposition events, which comprise 55.7% of SVs and suggest significantly different modes of SV formation relative to humans and great apes.

conclusionsThis dataset represents the largest study of structural variation in rhesus macaques to date and demonstrates use of both long and short-read datasets to generate SV genotype data. These data enable the consideration of structural variation impact in rhesus macaque-based research and will also aid the development of primate pangenomes.

Indexed as

Genomic Structural VariationGenotyping TechniquesMacaca mulattaAnimalsGenetic VariationGenotypeWhole Genome Sequencing

Identifiers

PMID41272845
PMCPMC12636206

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LicenceCC BY-NC-ND
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Registered trials

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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.