Genomic signatures of adaptation to novel environments: hatchery and life history-associated loci in landlocked and anadromous Atlantic salmon (<i>Salmo salar</i>)

Harder, Avril M.; Christie, Mark R.

doi:10.1139/cjfas-2021-0066

Cited by 3 publications

(4 citation statements)

References 65 publications

(85 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Such transcriptomes enable in-depth analyses of molecular physiology, such as in population-specific thermal stress responses (34)(35)(36). While RNA-seq and transcriptome-based approaches are less commonly used for population genetics than DNA-based approaches, single nucleotide polymorphisms in RNA can be used to investigate population structure and signatures of selection (37)(38)(39)(40)(41). Transcriptomes would also enable investigations into evolution, both through descriptions of gene expression evolution (42,43) and by phylogenetic analyses of mutations (44,45).…”

Section: Introductionmentioning

confidence: 99%

Tissue-specific transcriptomes reveal mechanisms of microbiome regulation in an ancient fish

Thorstensen

Weinrauch

Bugg

et al. 2022

Preprint

View full text Add to dashboard Cite

The lake sturgeon (Acipenser fulvescens) is an ancient, octoploid fish faced with conservation challenges across its range in North America but a lack of genomic resources has hindered molecular research in the species. To support such research we aimed to provide a transcriptomic database from 13 tissues: brain, esophagus, gill, head kidney, heart, white muscle, liver, glandular stomach, muscular stomach, anterior intestine, pyloric cecum, spiral valve, and rectum. The transcriptomes for each tissue were sequenced and assembled individually from a mean of 98.3 million (38.9 million std. dev.) reads each. In addition, an overall transcriptome was assembled and annotated with all data used for each tissue-specific transcriptome. All assembled transcriptomes and their annotations were made publicly available as a scientific resource. The non-gut transcriptomes provide important resources for many research avenues, however, the gut represents a compartmentalized organ system with compartmentalized functions and the sequenced gut tissues were from each of these portions. Therefore, we focused our analysis on mRNA transcribed in different tissues of the gut and explored evidence of microbiome regulation. Gene set enrichment analyses were used to reveal the presence of photoperiod and circadian-related transcripts in the pyloric caecum, which may support periodicity in lake sturgeon digestion. Similar analyses were used to identify different types of innate immune regulation across the gut, while analyses of unique transcripts annotated to microbes revealed heterogeneous genera and genes among different gut tissues. The present results provide a scientific resource and information about the mechanisms of compartmentalized function across gut tissues in a phylogenetically ancient vertebrate.

show abstract

Section: Introductionmentioning

confidence: 99%

Tissue-specific transcriptomes reveal mechanisms of microbiome regulation in an ancient fish

Thorstensen

Weinrauch

Bugg

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…Initially, hatchery rearing was thought to induce genetic changes, though genetic changes are often minimal and transcriptional changes are more pronounced. A single generation of hatchery rearing is generally insufficient to cause genetic differentiation between captive and wild salmon (Gavery, Nichols, Goetz, Middleton, & Swanson, 2018; Le Luyer et al, 2017), though SNPs associated with domestication have been detected after several generations of hatchery rearing in Atlantic salmon (Harder & Christie, 2022). However, the hatchery environment has been shown to induce transcriptional changes in steelhead ( Oncorhynchus mykiss ; Christie, Marine, Fox, French, & Blouin, 2016), Atlantic salmon (Frisk et al, 2020), and Coho salmon ( O. kisutch ; Leitwein et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

Captive rearing effects on the methylome of Atlantic salmon after oceanic migration: sex-specificity and intergenerational stability

Venney

Bouchard

April

et al. 2022

Preprint

View full text Add to dashboard Cite

In the absence of genetic evolution, captive rearing in salmon hatcheries can have considerable impacts on both fish phenotype and fitness in a single generation. Evidence for hatchery-induced changes in DNA methylation is becoming abundant, though questions remain on the sex-specificity of these effects, their persistence until spawning, and potential for transmission to future generations. Here we performed whole genome bisulfite sequencing for 16 hatchery and 16 wild Atlantic salmon (Salmo salar) returning to spawn in the Rimouski River, Québec. We identified two cohorts of hatchery-reared salmon through methylation analysis, one of which was epigenetically similar to wild fish, suggesting that supplementation efforts may be able to minimize the epigenetic effects of hatchery rearing. We found considerable sex-specific effects of hatchery rearing, with few genomic regions being affected in both males and females. We also analysed the methylome of 32 F1 offspring from four groups (pure wild, pure hatchery origin, and reciprocal hybrids). We found that few epigenetic changes due to parental hatchery rearing persisted in the F1 offspring though the patterns of inheritance appear to be complex, involving nonadditive effects. Our results suggest that the epigenetic effects of hatchery rearing could be minimizable in F0. There may also be minimal epigenetic inheritance and rapid loss of epigenetic changes associated with hatchery rearing. However, due to sex-specificity and nonadditive patterns of inheritance, methylation changes due to captive rearing are more complex than initially thought and may be difficult to account for in management decisions.

show abstract

“…Freshwater adaptation among marine fish species opens them new ecological niches and evolutionary opportunities. In contrast, this environmental shift requires substantial changes in immunity, physiological and metabolic processes, osmoregulation, and behavior [ 1 ]. The genetic basis of adaptation to different salinity environments has been studied for the different teleost species—prickly sculpin ( Cottus asper ) [ 2 ], mummichog ( Fundulus heteroclitus ) [ 3 ], Atlantic cod ( Gadus morhua ) [ 4 ], rainwater killifish ( Lucania parva ) [ 5 ].…”

Section: Introductionmentioning

confidence: 99%

“…The genetic basis of adaptation to different salinity environments has been studied for the different teleost species—prickly sculpin ( Cottus asper ) [ 2 ], mummichog ( Fundulus heteroclitus ) [ 3 ], Atlantic cod ( Gadus morhua ) [ 4 ], rainwater killifish ( Lucania parva ) [ 5 ]. Genetic comparisons between anadromous and nonmigratory ecotypes of rainbow trout ( Oncorhynchus mykiss ) and Atlantic salmon ( Salmo salar ) were also carried out [ 1 , 6 , 7 ].…”

Section: Introductionmentioning

confidence: 99%

Genomic Signatures of Freshwater Adaptation in Pacific Herring (Clupea pallasii)

Nedoluzhko

Orlova

Курносов³

et al. 2022

Genes

View full text Add to dashboard Cite

Pacific herring (Clupea pallasii) is an essential target of commercial fishing in the North Pacific Ocean. Previous studies have suggested the existence of marine and lake ecological forms of this species within its range. The lake ecological form of herring has a shortened life cycle, spending the winter and spawning in brackish waters near the shoreline without long migrations for feeding; it also has a relatively smaller body size than the marine form. Genetic-based studies have shown that brackish water Pacific herring not only can be distinguished as a separate lake ecological form but possibly has its genetic legacy. Here, as part of an ongoing study, using ddRAD-sequencing data for marine and lake ecological forms from a total of 54 individuals and methods of comparative bioinformatics, we describe genomic signatures of freshwater adaptivity in Pacific herring. In total, 253 genes containing discriminating SNPs were found, and part of those genes was organized into genome clusters, also known as “genomic islands of divergence”. Moreover, the Tajima’s D test showed that these loci are under directional selection in the lake populations of the Pacific herring. Yet, most discriminating loci between the lake and marine ecological forms of Pacific herring do not intersect (by gene name) with those in other known marine fish species with known freshwater/brackish populations. However, some are associated with the same physiological trait—osmoregulation.

show abstract

Genomic signatures of adaptation to novel environments: hatchery and life history-associated loci in landlocked and anadromous Atlantic salmon (Salmo salar)

Cited by 3 publications

References 65 publications

Tissue-specific transcriptomes reveal mechanisms of microbiome regulation in an ancient fish

Tissue-specific transcriptomes reveal mechanisms of microbiome regulation in an ancient fish

Captive rearing effects on the methylome of Atlantic salmon after oceanic migration: sex-specificity and intergenerational stability

Genomic Signatures of Freshwater Adaptation in Pacific Herring (Clupea pallasii)

Contact Info

Product

Resources

About