Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations DOI Creative Commons
Laurie Lecomte, Mariann Árnyasi, Anne‐Laure Ferchaud

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Sept. 15, 2023

Abstract Genomic structural variants (SVs) are now recognized as an integral component of intraspecific polymorphism and known to contribute evolutionary processes in various organisms. However, they inherently difficult detect genotype from readily available short-read sequencing data, therefore remain poorly documented wild populations. Salmonid species displaying strong interpopulation variability both life history traits habitat characteristics, such Atlantic salmon ( Salmo salar ), offer a prime context for studying adaptive polymorphism, but the contribution SVs fine-scale local adaptation has yet be explored. Here, we performed comparative analysis SVs, single nucleotide polymorphisms (SNPs) small indels (< 50 bp) segregating Romaine Puyjalon salmon, two putatively locally adapted populations inhabiting neighboring rivers (Québec, Canada) showing pronounced variation traits, namely growth, fecundity, age at maturity smoltification. We first catalogued using hybrid SV characterization approach pairing short (16X) long-read (20X) variant discovery with graph-based genotyping across 60 genomes, along SNPs reads. thus identified 115,907 8,777,832 1,089,321 indels, covering 4.8 times more base pairs than SNPs. All three types revealed highly congruent population structure similar patterns F ST density genome. Finally, outlier detection redundancy (RDA) identify interest putative salmon. Genes located near these were enriched biological related nervous system function, suggesting that observed smoltification could arise differences neural development. This study demonstrates feasibility large-scale highlights its relevance salmonid genomics.

Language: Английский

Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations DOI Creative Commons
Laurie Lecomte, Mariann Árnyasi, Anne‐Laure Ferchaud

et al.

Evolutionary Applications, Journal Year: 2024, Volume and Issue: 17(3)

Published: March 1, 2024

Genomic structural variants (SVs) are now recognized as an integral component of intraspecific polymorphism and known to contribute evolutionary processes in various organisms. However, they inherently difficult detect genotype from readily available short-read sequencing data, therefore remain poorly documented wild populations. Salmonid species displaying strong interpopulation variability both life history traits habitat characteristics, such Atlantic salmon (

Language: Английский

Citations

7
Population Genetic Structure of Three‐Spined Sticklebacks in the St. Lawrence: A Gradient of Change DOI Creative Commons

Sann Delaive,

Florent Sylvestre, Amanda Xuereb

et al.

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(4)

Published: April 1, 2025

ABSTRACT Understanding how environmental gradients shape population genetic structure is critical for elucidating evolutionary dynamics in heterogeneous landscapes. The St. Lawrence Estuary, spanning fluvial, middle, and marine zones, presents a steep salinity gradient that serves as an ideal setting to study such question. Three‐spined sticklebacks ( Gasterosteus aculeatus ) thrive across these offering model system investigate the interplay of gene flow natural selection shaping structure. Using whole‐genome resequencing from 12 sites, this aimed resolve fine‐scale diversity differentiation are influenced by flow. By integrating single nucleotide polymorphisms (SNPs) structural variants (SVs), we assessed patterns, examined clinal variation, evaluated relative roles dynamics. Our findings reveal clear between fluvial saltwater populations, with Baie‐Saint‐Paul forming potential third group. Salinity emerged key driver structure, variation allele frequencies suggesting ongoing adaptation along gradient. Demographic modeling indicated history secondary contact recent weak Structural variants, particularly indels, complemented SNP‐based analyses, underscoring their importance detecting These results highlight complex forces biodiversity transitional environments, providing basis exploring local connected populations contributing broader efforts conservation genomics.

Language: Английский

Citations

0
Development of SNP Panels from Low‐Coverage Whole Genome Sequencing (lcWGS) to Support Indigenous Fisheries for Three Salmonid Species in Northern Canada DOI Creative Commons
Anne Beemelmanns, Raphaël Bouchard, Sozos Michaelides

et al.

Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 18, 2024

Single nucleotide polymorphism (SNP) panels are powerful tools for assessing the genetic population structure and dispersal of fishes can enhance management practices commercial, recreational subsistence mixed-stock fisheries. Arctic Char (Salvelinus alpinus), Brook Trout fontinalis) Lake Whitefish (Coregonus clupeaformis) among most harvested consumed fish species in Northern Indigenous communities Canada, contributing significantly to food security, culture, tradition economy. However, resources supporting fisheries have not been widely accessible northern (e.g. Inuit, Cree, Dene). Here, we developed Genotyping-in-Thousands by sequencing (GT-seq) assignment analyses three salmonids, support stewardship or co-management Canada. Using low-coverage Whole Genome Sequencing data from 418 individuals across source populations Cambridge Bay (Nunavut), Great Slave (Northwest Territories), James (Québec) Mistassini (Québec), a bioinformatic SNP filtering workflow select informative markers genotype likelihoods. These were then used design GT-seq panels, thus enabling high-throughput genotyping these species. The yielded an average 413 autosomal loci validated using 525 with accuracy 83%. Thus, quantifying relative contributions populations/stocks multiple regions. Interweaving genomic derived Traditional Ecological Knowledge will ensure sustainable harvest culturally important salmonids communities, security programmes economy

Language: Английский

Citations

3
Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations DOI Creative Commons
Laurie Lecomte, Mariann Árnyasi, Anne‐Laure Ferchaud

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Sept. 15, 2023

Abstract Genomic structural variants (SVs) are now recognized as an integral component of intraspecific polymorphism and known to contribute evolutionary processes in various organisms. However, they inherently difficult detect genotype from readily available short-read sequencing data, therefore remain poorly documented wild populations. Salmonid species displaying strong interpopulation variability both life history traits habitat characteristics, such Atlantic salmon ( Salmo salar ), offer a prime context for studying adaptive polymorphism, but the contribution SVs fine-scale local adaptation has yet be explored. Here, we performed comparative analysis SVs, single nucleotide polymorphisms (SNPs) small indels (< 50 bp) segregating Romaine Puyjalon salmon, two putatively locally adapted populations inhabiting neighboring rivers (Québec, Canada) showing pronounced variation traits, namely growth, fecundity, age at maturity smoltification. We first catalogued using hybrid SV characterization approach pairing short (16X) long-read (20X) variant discovery with graph-based genotyping across 60 genomes, along SNPs reads. thus identified 115,907 8,777,832 1,089,321 indels, covering 4.8 times more base pairs than SNPs. All three types revealed highly congruent population structure similar patterns F ST density genome. Finally, outlier detection redundancy (RDA) identify interest putative salmon. Genes located near these were enriched biological related nervous system function, suggesting that observed smoltification could arise differences neural development. This study demonstrates feasibility large-scale highlights its relevance salmonid genomics.

Language: Английский

Citations

0