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References from A Mid-Atlantic Brook Trout ( Salvelinus fontinalis ) genome to advance conservation and comparative genomics. Local targets link to admitted publications; unresolved targets remain external evidence.
Reference genome choice compromises population genetic analyses
10.1016/j.cell.2025.08.034 · 2025 · External reference
De novo genome assemblies of four rainbow trout genetic lines reveal structural variants in pursuit of a pangenome reference
10.1111/1755-0998.70167 · 2026 · External reference
RAD capture (Rapture): flexible and efficient sequence-based genotyping
10.1534/genetics.115.183665 · 2016 · External reference
Effects of crossovers between homeologs on inheritance and population genomics in polyploid-derived salmonid fishes
10.1093/jhered/esv015 · 2015 · External reference
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
10.1093/nar/25.17.3389 · 1997 · External reference
Rapid and sensitive detection of genome contamination at scale with FCS-GX
10.1186/s13059-024-03198-7 · 2024 · External reference
Autosomal sdY pseudogenes explain discordances between phenotypic sex and DNA marker for sex identification in Atlantic Salmon
10.3389/fgene.2020.544207 · 2020 · External reference
Development of SNP panels from low-coverage whole genome sequencing (lcWGS) to support Indigenous fisheries for three salmonid species in northern Canada
10.1111/1755-0998.14040 · 2025 · External reference
A nonfunctional copy of the salmonid sex-determining gene (sdY) is responsible for the “apparent” XY females in Chinook Salmon, Oncorhynchus tshawytscha
10.1093/g3journal/jkab451 · 2022 · External reference
The structural variation landscape in 492 Atlantic Salmon genomes
10.1038/s41467-020-18972-x · 2020 · External reference
Evaluating the effect of reference genome divergence on the analysis of empirical RADseq datasets
10.1002/ece3.6483 · 2020 · External reference
The value of reference genomes in the conservation of threatened species
10.3390/genes10110846 · 2019 · External reference
Neutral and adaptive drivers of genomic change in introduced brook trout (Salvelinus fontinalis) populations revealed by pooled sequencing
10.1002/ece3.8584 · 2022 · External reference
Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph
10.1038/s41592-024-02269-8 · 2024 · External reference
Masu salmon species complex relationships and sex chromosomes revealed from analyses of the masu salmon (Oncorhynchus masou masou) genome assembly
10.1093/g3journal/jkae278 · 2025 · External reference
Evolutionary causes and consequences of gene duplication
10.1038/s41576-026-00935-5 · 2026 · External reference
ntSynt: multi-genome synteny detection using minimizer graph mappings
10.1186/s12915-025-02455-w · 2025 · External reference
10.1101/2025.01.15.633221
10.1101/2025.01.15.633221 · 2025 · External reference
Twelve years of SAMtools and BCFtools
10.1093/gigascience/giab008 · 2021 · External reference
A major sextet of mitochondrial DNA phylogenetic assemblages extant in eastern north American brook trout (Salvelinus fontinalis): distribution and postglacial dispersal patterns
10.1139/z98-056 · 1998 · External reference
Conserving genetic and genomic diversity in accordance with the global biodiversity framework
10.1146/annurev-animal-030424-070756 · 2025 · External reference
NanoPack: visualizing and processing long-read sequencing data
10.1093/bioinformatics/bty149 · 2018 · External reference
Complications of estimating hatchery introgression in the face of rapid divergence: a case study in Brook Trout (Salvelinus fontinalis)
10.1111/eva.70026 · 2024 · External reference
Comparative analysis of the shared sex-determination region (SDR) among salmonid fishes
10.1093/gbe/evv123 · 2015 · External reference
The genome assembly of the westslope cutthroat Trout, Oncorhynchus lewisi, reveals interspecific chromosomal rearrangements with the rainbow Trout, Oncorhynchus mykiss
10.1093/g3journal/jkaf064 · 2025 · External reference
RepeatModeler2 for automated genomic discovery of transposable element families
10.1073/pnas.1921046117 · 2020 · External reference
Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs
10.1093/bioinformatics/btac460 · 2022 · External reference
The era of reference genomes in conservation genomics
10.1016/j.tree.2021.11.008 · 2022 · External reference
Harnessing genomics for delineating conservation units
10.1016/j.tree.2012.05.012 · 2012 · External reference
Integrating Hi-C links with assembly graphs for chromosome-scale assembly
10.1371/journal.pcbi.1007273 · 2019 · External reference
Using linkage maps as a tool to determine patterns of chromosome synteny in the genus Salvelinus
10.1534/g3.117.300317 · 2017 · External reference
Significantly improving the quality of genome assemblies through curation
10.1093/gigascience/giaa153 · 2021 · External reference
10.1186/s12864-026-12917-2
10.1186/s12864-026-12917-2 · 2025 · External reference
Distribution, status, and land use characteristics of subwatersheds within the native range of Brook Trout in the eastern United States
10.1577/m07-017.1 · 2008 · External reference
Adaptive phenotypic plasticity in Brook Trout, Salvelinus fontinalis, life histories
10.1080/11956860.1996.11682311 · 1996 · External reference
Life's a ditch: demographic history and environmental factors shape fine-scale local adaptation within small populations of Brook Trout
10.1139/cjfas-2024-0075 · 2024 · External reference
Conservation genetics of Brook Trout (Salvelinus fontinalis): population structuring in Fundy National Park, New Brunswick, and eastern Canada
10.1139/f96-237 · 1996 · External reference
The crucial role of genome-wide genetic variation in conservation
10.1073/pnas.2104642118 · 2021 · External reference
Population genetics of Brook Trout in the southern Appalachian mountains
10.1002/tafs.10337 · 2022 · External reference
Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations
10.1111/eva.13653 · 2024 · External reference
Chromosome-level genome assembly of a doubled haploid Brook Trout (Salvelinus fontinalis)
10.1093/g3journal/jkaf066 · 2025 · External reference
Mitotic and meiotic analyses of Brook Trout, Salvelinus fontinalis
10.1093/oxfordjournals.jhered.a109515 · 1981 · External reference
The sequence alignment/map format and SAMtools
10.1093/bioinformatics/btp352 · 2009 · External reference
10.48550/arxiv.1303.3997
10.48550/arxiv.1303.3997 · 2013 · External reference
Genome assembly in the telomere-to-telomere era
10.1038/s41576-024-00718-w · 2024 · External reference
Identification of high-confidence structural variants in domesticated rainbow trout using whole-genome sequencing
10.3389/fgene.2021.639355 · 2021 · External reference
Genomic instability of the sex-determining locus in Atlantic salmon (Salmo salar)
10.1534/g3.115.020115 · 2015 · External reference
Dams and introduced Species drive patterns of environmental adaptation in an iconic but imperiled coldwater fish (Brook Trout, Salvelinus fontinalis)
10.1111/eva.70239 · 2026 · External reference
A new genomic resource to enable standardized surveys of SNPs across the native range of Brook Trout (Salvelinus fontinalis)
10.1111/1755-0998.13853 · 2023 · External reference
BUSCO: assessing genomic data quality and beyond
10.1002/cpz1.323 · 2021 · External reference
MUMmer4: a fast and versatile genome alignment system
10.1371/journal.pcbi.1005944 · 2018 · External reference
Reference genome bias in light of species-specific chromosomal reorganization and translocations
10.1186/s13059-025-03761-w · 2025 · External reference
The genomics revolution in nonmodel Species: predictions vs. Reality for salmonids
10.1111/mec.17758 · 2025 · External reference
BLAST: at the core of a powerful and diverse set of sequence analysis tools
10.1093/nar/gkh435 · 2004 · External reference
The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data
10.1101/gr.107524.110 · 2010 · External reference
A mobile sex-determining region, male-specific haplotypes and rearing environment influence age at maturity in Chinook salmon
10.1111/mec.15712 · 2021 · External reference
Redlisting genetics: towards inclusion of genetic data in IUCN red list assessments
10.1007/s10592-024-01671-1 · 2025 · External reference
Range-wide climate risk and adaptive potential in a cold-water fish species
10.1038/s41467-025-62811-w · 2025 · External reference
Genome assembly, structural variants, and genetic differentiation between lake whitefish young species pairs (Coregonus sp.) with long and short reads
10.1111/mec.16468 · 2023 · External reference
Conservation planning at the intersection of landscape and climate change: brook trout in the Chesapeake Bay watershed
10.1002/ecs2.2585 · 2019 · External reference
A fast, reproducible, high-throughput variant calling workflow for population genomics
10.1093/molbev/msad270 · 2024 · External reference
Variant calling in the goldilocks zone: how reference genome choice and read mapping stringency impact heterozygosity estimates and phylogenetic analyses
10.1111/1755-0998.70079 · 2025 · External reference
The potential role of haploblocks in the persistence of small, isolated populations of Brook Trout (Salvelinus fontinalis)
10.1002/ece3.72075 · 2025 · External reference
Pairtools: from sequencing data to chromosome contacts
10.1371/journal.pcbi.1012164 · 2024 · External reference
Reference genomes for conservation
10.1126/science.abm8127 · 2022 · External reference
Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database
10.1186/s12864-016-2709-z · 2016 · External reference
A genome assembly for Lahontan Cutthroat Trout, Oncorhynchus clarkii henshawi
10.1093/jhered/esaf050 · 2025 · External reference
Measuring genome sizes using read-depth, k-mers, and flow cytometry: methodological comparisons in beetles (Coleoptera)
10.1534/g3.120.401028 · 2020 · External reference
Intraspecific genome size variation is attributed to adaptive silencing of transposable elements in Hordeum species
10.1093/molbev/msag051 · 2026 · External reference
Evaluating the role of reference-genome phylogenetic distance on evolutionary inference
10.1111/1755-0998.13457 · 2022 · External reference
Mapping 3D genome architecture through in situ DNase Hi-C
10.1038/nprot.2016.126 · 2016 · External reference
GenomeScope 2.0 and smudgeplot for reference-free profiling of polyploid genomes
10.1038/s41467-020-14998-3 · 2020 · External reference
Towards complete and error-free genome assemblies of all vertebrate species
10.1038/s41586-021-03451-0 · 2021 · External reference
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies
10.1186/s13059-020-02134-9 · 2020 · External reference
Reference genome choice and filtering thresholds jointly influence phylogenomic analyses
10.1093/sysbio/syad065 · 2024 · External reference
Experimental test of genetic rescue in isolated populations of Brook Trout
10.1111/mec.14225 · 2017 · External reference
Estimates of effective number of breeders identify drivers of decline in mid-Atlantic Brook Trout populations
10.1111/eva.13769 · 2024 · External reference
Insights from a chum salmon (Oncorhynchus keta) genome assembly regarding whole-genome duplication and nucleotide variation influencing gene function
10.1093/g3journal/jkad127 · 2023 · External reference
Genetic predictors of population resilience: a case study of native Brook Trout in headwater streams
10.1002/nafm.11003 · 2024 · External reference
HiFiAdapterFilt, a memory efficient read processing pipeline, prevents occurrence of adapter sequence in PacBio HiFi reads and their negative impacts on genome assembly
10.1186/s12864-022-08375-1 · 2022 · External reference
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
10.1093/bioinformatics/btv351 · 2015 · External reference
Chromosomal characteristics and distribution of rDNA sequences in the Brook Trout Salvelinus fontinalis (Mitchill, 1814)
10.1007/s10709-015-9841-6 · 2015 · External reference
Unresolved reference
2015 · External reference
A beginner's guide to structural variants in eco-evolutionary population genomics
10.1111/mec.70216 · 2026 · External reference
Origin matters: using a local reference genome improves measures in population genomics
10.1111/1755-0998.13838 · 2023 · External reference
Genomic vulnerability of a freshwater salmonid under climate change
10.1111/eva.13602 · 2023 · External reference
The genomic basis of reproductive and migratory behaviour in a polymorphic salmonid
10.1111/mec.16724 · 2022 · External reference
Mitohifi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads
10.1186/s12859-023-05385-y · 2023 · External reference
Genomic erosion in the assessment of species’ extinction risk and recovery potential
10.1093/jhered/esag011 · 2026 · External reference
Pacific salmon, Oncorhynchus spp., and the definition of” species” under the endangered Species act
1991 · External reference
A nonlethal genetic assay for discriminating sex in Brook Trout
10.1002/nafm.10615 · 2021 · External reference
Is now the time? Review of genetic rescue as a conservation tool for Brook Trout
10.1002/ece3.10142 · 2023 · External reference
Unresolved reference
2019 · External reference
Improved metagenomic analysis with Kraken 2
10.1186/s13059-019-1891-0 · 2019 · External reference
The sexually dimorphic on the Y-chromosome gene (sdY) is a conserved male-specific Y-chromosome sequence in many salmonids
10.1111/eva.12032 · 2013 · External reference
YaHS: yet another Hi-C scaffolding tool
10.1093/bioinformatics/btac808 · 2023 · External reference