Evidence map›Paper›PMID 40130537›Full record

ArticleG3 (Bethesda, Md.)2025

Chromosome-level genome assembly of a doubled haploid brook trout (Salvelinus fontinalis).

Laurie Lecomte, Anne-Laure Ferchaud, Eric Normandeau, Claire Mérot, Isabelle Langlois-Parisé, Jean-Christophe Therrien, Pierre Bérubé, Haig Djambazian, Pubudu Manoj Nawarathna, Jiannis Ragoussis and 1 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 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Article
  2. Article
  3. 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

11 authors.

Laurie LecomteInstitut de Biologie Intégrative et des Systèmes (IBIS), Université Laval 1030, Avenue de la Médecine, Québec, Canada, QC G1V 0A6.ORCID 0009-0001-7083-5770
Anne-Laure FerchaudParks Canada, Office of the Chief Ecosystem Scientist, Protected Areas Establishment, 30 Rue Victoria, Gatineau, Canada, QC J8X 0B3.ORCID 0000-0002-9577-5508
Eric NormandeauPlateforme de bio-informatique de l'IBIS (Institut de Biologie Intégrative et des Systèmes), Université Laval, 1030, Avenue de la Médecine, Québec, Canada, QC G1V 0A6.ORCID 0000-0003-2841-9391
Claire MérotUMR 6553 Ecobio, OSUR, CNRS, Université de Rennes, 263 Avenue du Général Leclerc, Rennes 35004, France.ORCID 0000-0003-2607-7818
Isabelle Langlois-PariséLaboratoire de Recherche en Sciences Environnementales et Médicales (LARSEM), Université Laval, 1030, Avenue de la Médecine, Québec, Canada, QC G1V 0A6.
Jean-Christophe TherrienLaboratoire de Recherche en Sciences Environnementales et Médicales (LARSEM), Université Laval, 1030, Avenue de la Médecine, Québec, Canada, QC G1V 0A6.
Pierre BérubéMcGill Genome Centre, Department of Human Genetics, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, 740 Dr Penfield Ave, Montréal, Canada, QC H3A0G1.
Haig DjambazianMcGill Genome Centre, Department of Human Genetics, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, 740 Dr Penfield Ave, Montréal, Canada, QC H3A0G1.ORCID 0000-0003-0222-4182
Pubudu Manoj NawarathnaCellCarta, 201 President Kennedy Ave, Suite 3900, Montréal, Canada, QC H2X 3Y7.ORCID 0000-0002-9507-6205
Jiannis RagoussisMcGill Genome Centre, Department of Human Genetics, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, 740 Dr Penfield Ave, Montréal, Canada, QC H3A0G1.ORCID 0000-0002-8515-0934
Dylan FraserDepartment of Biology, Concordia University, 3475 West Broadway Street, Montréal, Canada, QC H4B 2A7.

Funding

Canada Foundation for Innovation CFI 33406 and 40104Canada Foundation for Innovation CFI MSI 35444CanSeq150 initiative of the Canadian Genome EnterpriseGenome Québec and Genome Canada
6 · The paper itself

Abstract

Brook trout (Salvelinus fontinalis) is a socioeconomically important fish species for fisheries, aquaculture, and aquatic conservation. We produced a 2.5-Gb reference assembly by combining Hi-C chromosome conformation capture with high-coverage short- and long-read sequencing of a fully homozygous mitotic gynogenic doubled-haploid fish, which facilitates the assembly of highly complex salmonid genomes. The assembly has an N50 of 50.98 Mb and 88.9% of the total assembled sequence length is anchored into 42 main chromosomes, of which 63.44% represents repeated contents, including 1,461,010 DNA transposons. 56,058 genes were found, with 98.6% of the 3,640 expected conserved orthologs BUSCO genes (actinopterygii_odb10 lineage database). Additionally, we found significant homology within the 42 chromosomes, as expected for this pseudo-tetraploid species, as well as with the sister species lake trout (Salvelinus namaycush) and Atlantic salmon (Salmo salar). This assembly will serve as a reliable genomic resource for brook trout, thus enabling a wider range of reference-based applications to support ongoing research and management decision-making for the species.

Indexed as

ChromosomesGenomeGenomicsHaploidyTroutAnimalsMolecular Sequence AnnotationBrook troutgenome assemblyHi-Clong-read sequencingsalmonidSalvelinus fontinalisshort-read sequencing

Identifiers

PMID40130537
PMCPMC12134987

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.