Evidence map›Paper›PMID 40105693›Full record

ArticleG3 (Bethesda, Md.)2025

The genome assembly of the westslope cutthroat trout, Oncorhynchus lewisi, reveals interspecific chromosomal rearrangements with the rainbow trout, Oncorhynchus mykiss.

Anne-Marie Flores, Kris A Christensen, Theresa Godin, Yniv Palti, Matthew R Campbell, Geoffrey C Waldbieser, Sheron A Simpson, Brian E Scheffler, Seth R Smith, Andrew R Whiteley and 7 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in G3 (Bethesda, Md.), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Article
  2. Article
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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

17 authors.

Anne-Marie FloresDepartment of Biology, University of Victoria, Victoria, Canada, V8W 2Y2 BC.
Kris A ChristensenDepartment of Biology, University of Victoria, Victoria, Canada, V8W 2Y2 BC.ORCID 0000-0003-0021-0326
Theresa GodinScience Division, Freshwater Fisheries Society of BC, 80 Regatta Landing, Suite 101, Victoria, BC, Canada, V9A 7S2.
Yniv PaltiUSDA-ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, WV 25430, USA.ORCID 0000-0002-4953-8878
Matthew R CampbellEagle Fish Genetics Lab, Idaho Department of Fish and Game, 1800 Trout Road, Eagle, ID 83616, USA.
Geoffrey C WaldbieserUSDA-ARS Warmwater Aquaculture Research Unit, 141 Experimental Station Road, Stoneville, MS 38776, USA.
Sheron A SimpsonUSDA-ARS Genomics and Bioinformatics Research Unit, 141 Experimental Station Road, Stoneville, MS 38776, USA.
Brian E SchefflerUSDA-ARS Genomics and Bioinformatics Research Unit, 141 Experimental Station Road, Stoneville, MS 38776, USA.
Seth R SmithWashington Department of Fish and Wildlife, Molecular Genetics Laboratory, 1111 Washington St. SE, Olympia, WA 98501, USA.
Andrew R WhiteleyWildlife Biology Program, W.A. Franke College of Forestry and Conservation, University of Montana, Missoula, MT 59812, USA.
Ryan P KovachMontana Fish, Wildlife and Parks, University of Montana Conservation Genetics Laboratory, University of Montana, Missoula, MT 59812, USA.
Gordon LuikartWildlife Biology Program, W.A. Franke College of Forestry and Conservation, University of Montana, Missoula, MT 59812, USA.
Matthew C BoyerMontana Fish, Wildlife and Parks, Kalispell, MT 59901, USA.
Marty KardosWildlife Biology Program, W.A. Franke College of Forestry and Conservation, University of Montana, Missoula, MT 59812, USA.
Scott RelyeaSekokini Springs Hatchery, Montana Fish, Wildlife and Parks, Kalispell, MT 59901, USA.
Craig WellsBioinformatics and Computational Biology, University of Idaho, Moscow, ID 83844, USA.ORCID 0000-0002-5851-3250
Ben F KoopDepartment of Biology, University of Victoria, Victoria, Canada, V8W 2Y2 BC.ORCID 0000-0003-0045-5200

Funding

Natural Sciences and Engineering Research Council of CanadaUSDA Agricultural Research Service
6 · The paper itself

Abstract

Cutthroat trout (Oncorhynchus clarkii) are popular among anglers throughout their native range along the West Coast and interior of North America. As they colonized the interior of North America, cutthroat trout diverged into several genetically distinct groups. Many of these groups are now threatened by habitat destruction, hybridization with rainbow trout (Oncorhynchus mykiss), and competition from introduced species. These groups were previously classified as subspecies, but recent research suggests that they may represent distinct species. In this study, we produced a chromosomal-level genome assembly and a genetic map for one of the species in the cutthroat trout species complex, the westslope cutthroat trout (Oncorhynchus lewisi-formerly Oncorhynchus clarkii lewisi). We also constructed haplotype-resolved assemblies from a westslope cutthroat-rainbow trout F1 hybrid. We used the new genome assemblies to identify major interspecific chromosomal rearrangements between the 2 sister species, including fusions, fissions, and inversions. These genome assemblies and chromosome data provide valuable insights regarding genetic variation within cutthroat trout and in hybrids between rainbow and cutthroat trout.

Indexed as

Chromosome AberrationsGene RearrangementGenomeOncorhynchusOncorhynchus mykissAnimalsChromosome MappingChromosomesGenomicsHaplotypesHybridization, Geneticchromosomal rearrangementscutthroat troutkaryotyperainbow troutspecies complexstockingsubspecies

Identifiers

PMID40105693
PMCPMC12117426

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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.