Biology subjects

Sutherland, B. J. G.

Publications and source records attributed to Sutherland, B. J. G..

At least 19 recordsLinked to original sources

bioRxiv2025

An amplicon panel for high-throughput and low-cost genotyping of Yesso scallop Mizuhopecten yessoensis

The Yesso scallop Mizuhopecten yessoensis was imported from Japan to western Canada in the late 1980s to establish an economically viable scallop aquaculture industry. Since this time, the industry in Canada has operated with existing genetic diversity within the broodstock, which is considerably limited relative to wild populations. The sector has not been able to realise its full potential in part due to idiopathic hatchery failures and farm stock collapses due to disease outbreaks associated with the intracellular bacterial pathogen Francisella halioticida. To support Yesso scallop production and breeding, here we generate a low-density, genotyping-by-sequencing amplicon panel using single nucleotide polymorphism (SNP) markers that are evenly spaced across the M. yessoensis genome and that show high heterozygosity in Canada and Japan. The panel can also exploit the high genetic polymorphism of the M. yessoensis genome, with de novo SNP calling identifying over 2,500 high quality SNPs within the 579 sequenced amplicons. We demonstrate the utility and versatility of this new genotyping tool for breeding applications including parentage assignment, low density family-based genome-wide association study, trait heritability evaluation to determine potential for genomic selection, and species differentiation (against the weathervane scallop Patinopecten caurinus). We did not find any genomic regions significantly associated with F. halioticida resistance but did identify potential for genomic selection. We could separate the two species based on genotypes, and we did not see evidence of a past M. yessoensis x P. caurinus hybridization event within the M. yessoensis breeding population at Vancouver Island University. This low-cost genotyping panel is expected to accelerate selective breeding improvements for M. yessoensis in Canada and elsewhere.

genomics↗

bioRxiv2025

Genome-wide characterization of upper Fraser River sockeye salmon identifies a region of major differentiation between run timing groups in the Stuart River Watershed

Effective wildlife conservation and management depends on a thorough understanding of both neutral and adaptive intraspecific genomic variation. Although population structure is often well understood for many ecologically or economically important species, the extensive population genomic resources required to characterize putatively adaptive variation, for example in punctuated genomic regions, is typically only recently available in many species, if at all. Here we explore recently published whole-genome resequencing data in the upper Fraser River and identify a large island of divergence separating populations with different run timings in the Nechako Watershed. The island of divergence at approximately 56.3-58.0 Mbp of Chr18 has extended homozygosity and reduced Tajimas D in specific populations of the upper Fraser River. These include the Nadina and Stellako River sockeye, as well as the Stuart-Summer run timing group, but not the geographically proximal Early Stuart sockeye. In the populations without the Stuart-Summer haploblock, genetic variation looks more similar to elsewhere throughout the chromosome. When investigating the gene content of this region, importantly it was determined to contain the leucine rich-repeat containing 9-like (lrrc9-like) gene and surrounding homeologous region to the lrrc9 region of Chr12, known to contain a conserved and selected island of divergence that has been associated with life history traits and run timing throughout the species range. By also inspecting the samples in the present work at the Chr12 haploblock, three genotypic states were observed throughout the region, although the Stuart River run timing groups contained mainly the reference haplotype. Using similar methods, no other regions of major differentiation were observed in the available samples for the Chilcotin or Quesnel River systems. These results provide additional evidence for the importance of both homeologous regions holding lrrc9 and lrrc9-like in different geographic regions and underscore the uniqueness of upper Fraser River sockeye in this potentially adaptive island of divergence.

genomics↗

bioRxiv2025

Pedigree-based genome-wide imputation using a low-density amplicon panel for the highly polymorphic Pacific oyster Crassostrea (Magallana) gigas

High-density genomic data are instrumental for selective breeding, but the costs associated with these approaches can hinder progress, as is the case for most aquaculture species. A strategy to reduce genotyping costs is to genotype a few select individuals at high-density (e.g., parents, grandparents), and many others at low density (e.g., offspring), then impute genotypes. This has been demonstrated in silico for Pacific oyster Crassostrea (Magallana) gigas but was particularly challenging relative to other species and has never been empirically tested. Here, four families of Pacific oysters, bred via marker-assisted selection for variation at a locus for field survival in an ostreid herpesvirus 1 (OsHV-1)-positive estuary, were exposed to OsHV-1 then genotyped using a low-density amplicon panel (n = 240 individuals). Parents were genotyped with the amplicon panel and by whole-genome resequencing. Offspring genotypes were imputed, and accuracy was determined by comparing against held-out whole-genome data for offspring. Imputation resulted in reduced minor allele frequencies and enriched homozygosity relative to empirical data. An in silico three-generation analysis was used to investigate the effect of deepening the pedigree, resulting in superior concordance in genotypes (GC = 84.5%) and allelic dosage (r = 0.73) compared to two-generation imputation (GC = 75.3%; r = 0.63). Genome-wide associations to OsHV-1 survivorship with imputed data identified significantly associated regions on the expected chromosome 8, but not at the expected position based on previous work, pointing to a potentially more complex genetic architecture for the trait. Our results empirically demonstrate the utility of amplicon panel-based genome-wide imputation in shellfish, and thus enable low-cost selective breeding techniques.

genomics↗

bioRxiv2024

The presence of the Pacific Oyster OSHV-1 resistance marker on chromosome 8 does not impact susceptibility to infection by Vibrio aestuarianus

The Pacific oyster, Crassostrea (Magallana) gigas, is an important species in aquaculture globally, but its production is threatened by pathogens including ostreid herpesvirus 1 (OsHV-1) and Vibrio aestuarianus. A genetic marker associated with resistance to OsHV-1 infection has been identified on chromosome 8 (Chr8) of the Pacific oyster genome. Marker-assisted selective breeding has used the Chr8 marker to produce oyster families with increased survivorship and resistance to OsHV-1 infection. The potential effect of the Chr8 marker on susceptibility to other pathogens remains largely unknown, but was recently associated with increased resistance of spat to Vibrio coralliilyticus. Here we assess the effect of the presence and allelic dosage of the Chr8 marker on the susceptibility of selectively bred juvenile Pacific oysters to V. aestuarianus infection. Sixteen families were produced with various Chr8 marker genotypes, and a V. aestuarianus disease challenge was conducted. Challenged oysters were individually genotyped at the Chr8 marker, and Vibrio susceptibility was evaluated among genotypes within and between families. Prior to the challenge trial, the Chr8 marker did not occur at the expected Mendelian ratios in families with heterozygous parents; in multiple families the homozygous alternate genotype occurred at a lower frequency than was expected. Mortality rates in the Vibrio challenge differed between families, ranging from 47.9% to 85.4%, but no association was observed between the Chr8 marker and survival to V. aestuarianus exposure. Therefore, we observed no pleiotropic effect (positive or negative) of the Chr8 marker on survivorship to V. aestuarianus at the evaluated life stage. Reduced-representation sequencing was used to genotype the challenged oysters and a genome-wide association study for V. aestuarianus survivorship was performed, but no significant associations were found, suggesting polygenic architecture for the trait.

genomics↗

bioRxiv2024

Revealing the evolutionary history and contemporary population structure of Pacific salmon in the Fraser River through genome resequencing

The Fraser River once supported massive salmon returns, but now years with half of the recorded historical maximum are considered good. There is substantial interest from surrounding communities, governments, and other groups to increase salmon returns for both human use and for functional ecosystems. To help generate resources for this endeavour, we resequenced hundreds of genomes at moderate coverage ([~]16x) of Chinook (Oncorhynchus tshawytscha), coho (O. kisutch), and sockeye salmon (O. nerka) from the Fraser River. The resequenced genomes are an important resource that can give us new insights. In this study, we found evidence that Chinook salmon have 1.5-2x more polymorphic loci than coho or sockeye salmon. Using principal component analysis (PCA) and admixture analysis, we also identified genetic groups similar to those previously identified with only a few microsatellite markers. As the higher density data supports these previous genetic groups, it suggests that the identity of these groups is not overly sensitive to the number of genetic markers or when the groups were sampled. With the increased resolution from resequenced genomes, we were able to further identify factors influencing these genetic groups, including isolation-by-distance, migration barriers, recolonization from different glacial refugia, and environmental factors like precipitation. We were also able to identify 20 potentially adaptive loci among the genetic groups by analyzing runs of homozygosity. All of the resequenced genomes have been submitted to a public database where they can be used as a reference for the contemporary genomics of Fraser River salmon. Article SummaryConcerns over Fraser River salmon declines led us to generate resources to better understand the genetics of these salmon. Our findings were similar to previous studies that examined a very small fraction of the genetic markers examined here. We expanded upon previous studies by identifying possible influences on the genetics of Fraser River salmon. These included environmental factors, historical differences, and a lack of connectivity in the river caused by the Fraser Canyon.

evolutionary biology↗

bioRxiv2023

An amplicon panel for high-throughput and low-cost genotyping of Pacific oyster

Maintaining genetic diversity in cultured shellfish can be challenging due to high variance in individual reproductive success, founder effects, and rapid genetic drift, but is important to retain adaptive potential and avoid inbreeding depression. To support broodstock management and selective breeding in cultured Pacific oysters (Crassostrea (Magallana) gigas), we developed an amplicon panel targeting 592 genomic regions and SNP variants with an average of 50 amplicons per chromosome. Target SNPs were selected based on elevated observed heterozygosity or differentiation in Pacific oyster populations in British Columbia (BC), Canada. The use of the panel for parentage applications was evaluated by genotyping three generations of oysters from a breeding program in BC (n = 181) and a set of families that were selected for Ostreid herpesvirus-1 (OSHV-1) resistance from the Molluscan Broodstock Program, a Pacific oyster breeding program in Oregon, USA (n = 136). Population characterization was evaluated using collections of wild, naturalized, farmed, or hatchery oysters sampled throughout the Northern Hemisphere (n = 190). Technical replicate samples showed high genotype concordance (97.5%; n = 68 replicates). Initial parentage analysis found instances of suspected pedigree and sample handling errors, demonstrating the panels value for quality control in breeding programs. Suspected null alleles were identified in parentage datasets and were found to reduce assignment success. Null alleles were largely population dependent, suggesting population-specific variation impacts target amplification. By taking an iterative approach, null alleles were identified using existing data without the need for pedigree information, and once null alleles were removed, assignments increased to 93.0% and 86.0% of possible assignments in the two breeding program datasets. A pipeline for analyzing the amplicon sequence data from sequencer output, amplitools, is also provided.

genetics↗

bioRxiv2023

The Prokaryotic and Eukaryotic Microbiome of Pacific Oyster Spat is Shaped by Ocean Warming but not Acidification

Pacific oysters (Magallana gigas, also known as Crassostrea gigas), the most widely farmed oysters, are under threat from climate change and emerging pathogens. In part, their resilience may be affected by their microbiome, which, in turn, may be influenced by ocean warming and acidification. Consequently, for three weeks, we exposed early-development Pacific oyster spat to different temperatures (18 and 24 {degrees}C) and pCO2 levels (800, 1600 and 2800 {micro}atm) in a fully crossed design. Under all conditions, the microbiome developed over time, with potentially pathogenic ciliates (Uronema marinum) greatly reduced in all treatments, suggesting that the spats microbiome undergoes adaptive shifts as the oysters age. The microbiome composition also differed significantly with temperature, but not acidification, indicating that M. gigas spat microbiomes can be altered by ocean warming but resilient to ocean acidification in our experiments. These findings highlight the spat microbiomes flexibility to environmental changes as well as its "protective" capability against potentially pathogenic microbes.

microbiology↗

bioRxiv2023

Genomic diversity of wild and cultured Yesso scallop Mizuhopecten yessoensis from Japan and Canada

The Yesso scallop Mizuhopecten yessoensis is an important aquaculture species that was introduced to Western Canada from Japan to establish an economically viable scallop farming industry. This highly fecund species has been propagated in Canadian aquaculture hatcheries for the past 40 years, raising questions about genetic diversity and genetic differences among hatchery stocks. In this study, we compare cultured Canadian and wild Japanese populations of Yesso scallop using double-digest restriction site-associated DNA (ddRAD)-sequencing to genotype 21,048 variants in 71 wild-caught scallops from Japan, 65 scallops from the Vancouver Island University breeding population, and 37 scallops obtained from a commercial farm off Vancouver Island, British Columbia. The wild scallops are largely comprised of equally unrelated individuals, whereas cultured scallops are comprised of multiple families of related individuals. The polymorphism rate estimated in wild scallops was 1.7%, whereas in the cultured strains it ranged between 1.35% and 1.07%. Interestingly, heterozygosity rates were highest in the cultured populations, which is likely due to shellfish hatchery practices of crossing divergent strains to gain benefits of heterosis and to avoid inbreeding. Evidence of founder effects and drift were observed in the cultured strains, including high genetic differentiation between cultured populations and between cultured populations and the wild population. Cultured populations had effective population sizes ranging from 9-26 individuals whereas the wild population was estimated at 25-50K individuals. Further, a depletion of low frequency variants was observed in the cultured populations. These results indicate significant genetic diversity losses in cultured scallops in Canadian breeding programs. Article SummaryYesso scallop was introduced to breeding programs in Canada around 40 years ago and has become a valuable aquaculture species in the country with little information regarding its genetic diversity. This work genotypes over 20K genetic variants in wild Yesso scallops from Japan and compares to a major broodstock collection in British Columbia, Canada, as well as a commercial farm in the same region. Reduced polymorphism but elevated heterozygosity indicates value of using genetic information to guide breeding programs.

genomics↗

bioRxiv2023

Population genomics of harbour seal Phoca vitulina from northern British Columbia through California and comparison to the western Atlantic sub-species

The harbour seal Phoca vitulina is a ubiquitous pinniped species found throughout coastal waters of the Northern Hemisphere. Harbour seal impacts on ecosystem dynamics may be significant due to their high abundance and food web position. Two subspecies exist in North America, P. v. richardii in the Pacific Ocean, and P. v. vitulina in the Atlantic. Strong natal philopatry of harbour seals can result in fine-scale genetic structure and isolation-by-distance. Management of harbour seals is expected to benefit from improved resolution of seal population structure and dynamics. Here we use genotyping-by-sequencing to genotype 146 harbour seals from the eastern Pacific Ocean (i.e., British Columbia (BC), Oregon, and California) and the western Atlantic Ocean (i.e., Quebec, Newfoundland, and Labrador). Using 12,742 identified variants, we confirm the recently identified elevated genetic diversity in the eastern Pacific relative to the western Atlantic and greatest differentiation between the subspecies. Further, we demonstrate that this is independent of reference genome bias or other potential technical artefacts. Coast-specific analyses with 8,933 and 3,828 variants in Pacific and Atlantic subspecies, respectively, identify divergence between BC and Oregon-California, and between Quebec and Newfoundland-Labrador. Unexpected PCA outlier clusters were observed in two populations due to cryptic relatedness of individuals; subsequently, closely related samples were removed. Admixture analysis indicates an isolation-by-distance signature where Oregon seals contained some of the BC signature, whereas California did not. Additional sampling is needed in the central and north coast of BC to determine whether a discrete separation of populations exists within the region.

genomics↗

bioRxiv2022

Effects of ancient anthropogenic clam gardens on the growth, survival, and transcriptome of Pacific littleneck clams (Leukoma staminea)

Clam gardens traditionally established and maintained by coastal Indigenous Peoples of northwest North America are habitat modifications to enhance intertidal clam productivity for reliable local food production. In this study, phenotypic and transcriptomic responses of Pacific littleneck clams (Leukoma staminea) were evaluated 16 weeks after transplantation to either unmaintained clam gardens or reference (unmodified) clam beaches. Beach sediment characteristics including grain size and organic content were examined across all beaches. Large differences in abiotic characteristics and phenotypic responses were observed among beaches; however, differences were not related to the clam garden/reference beach effect. Clam survival and growth were negatively associated with small rocks, very fine sand, and silt, along with carbonate and organic content, and positively associated with coarse sand, sand, and fine sand. To investigate molecular responses to unmaintained clam gardens, a de novo transcriptome containing 52,000 putative transcripts was assembled for L. staminea and was used to test for differential expression between transplanted clams in unmaintained clam gardens or on reference beaches. As expected, given the lack of significant phenotypic differences between treatments, transcriptomic responses to unmaintained clam gardens were minor, although several weakly-associated transcripts were identified. By contrast, the strong survival gradient across beaches was used to identify genes associated with survival and, combined with characterization of tissue-specific expression in the gill and digestive gland, contributes to our understanding of molecular processes in this non-model species.

ecology↗

bioRxiv2022

Metatranscriptomics reveals a shift in microbial community composition and function during summer months in a coastal marine environment

Temperate coastal marine waters are often thermally stratified from spring through fall but can be dynamic and disrupted by tidal currents and wind-driven upwelling. These mixing events introduce deeper, cooler water with a higher partial pressure of CO2 (pCO2), and its associated microbial communities to the surface. Anecdotally, these events impact shellfish hatcheries and farms, warranting improved understanding of changes in composition and activity of marine microbial communities in relation to environmental processes. To characterize both compositional and functional changes associated with abiotic factors, here we generate a reference metatranscriptome from the Strait of Georgia over representative seasons and analyze metatranscriptomic profiles of the microorganisms present within intake water containing different pCO2 levels at a shellfish hatchery in British Columbia from June through October. Abiotic factors studied include pH, temperature, alkalinity, aragonite, calcite and pCO2. Community composition changes were observed to occur at broad taxonomic levels, and most notably to vary with temperature and pCO2. Functional gene expression profiles indicated a strong difference between early (June-July) and late summer (August-October) associated with viral activity. The taxonomic data suggests this could be due to the termination of cyanobacteria and phytoplankton blooms by viral lysis in the late season. Functional analysis indicated fewer differentially expressed transcripts associated with abiotic variables (e.g., pCO2) than with the temporal effect. Microbial composition and activity in these waters varies with both short-term effects observed alongside abiotic variation as well as long-term effects observed across seasons. The analysis of both taxonomy and functional gene expression simultaneously in the same samples by environmental RNA (eRNA metatranscriptomics) provided a more comprehensive view for monitoring water bodies than either would in isolation.

genetics↗

bioRxiv2021

In-field genetic stock identification of overwintering coho salmon in the Gulf of Alaska: Evaluation of Nanopore sequencing for remote real-time deployment

Genetic stock identification (GSI) by single nucleotide polymorphism (SNP) sequencing has become the gold standard for stock identification in Pacific salmon, which are found in mixed-stocks during the oceanic phase of their lifecycle. Sequencing platforms currently applied require large batch sizes and multi-day processing in specialized facilities to perform genotyping by the thousands. However, recent advances in third-generation single-molecule sequencing platforms, like the Oxford Nanopore minION, provide base calling on portable, pocket-sized sequencers and hold promise for the application of real-time, in-field stock identification on variable batch sizes. Here we report and evaluate utility and comparability of at-sea stock identification of coho salmon Oncorhynchus kisutch based on targeted SNP amplicon sequencing on the minION platform during the International Year of the Salmon Signature Expedition to the Gulf of Alaska in the winter of 2019. Long read sequencers are not optimized for short amplicons, therefore we concatenate amplicons to increase coverage and throughput. Nanopore sequencing at-sea yielded stock assignment for 50 of the 80 assessed individuals. Nanopore-based SNP calls agreed with Ion Torrent based genotypes in 83.25%, but assignment of individuals to stock of origin only agreed in 61.5% of individuals highlighting inherent challenges of Nanopore sequencing, such as resolution of homopolymer tracts and indels. However, poor representation of assayed coho salmon in the queried baseline dataset contributed to poor assignment confidence on both platforms. Future improvements will focus on lowering turnaround time, accuracy, throughput, and cost, as well as augmentation of the existing baselines, specifically in stocks from coastal northern BC and Alaska. If successfully implemented, Nanopore sequencing will provide an alternative method to the large-scale laboratory approach. Genotyping by amplicon sequencing in the hands of diverse stakeholders could inform management decisions over a broad expanse of the coast by allowing the analysis of small batches in remote areas in near real-time.

genetics↗

bioRxiv2020

Population structure of eulachon Thaleichthys pacificus from Northern California to Alaska using single nucleotide polymorphisms from direct amplicon sequencing

Eulachon Thaleichthys pacificus, a culturally and ecologically important anadromous smelt (Family Osmeridae), ranges from Northern California to the southeast Bering Sea. In recent decades, some populations have experienced declines. Here we use a contig-level genome assembly combined with previously published RADseq-derived markers to construct an amplicon panel for eulachon. Using this panel, we develop a filtered genetic baseline of 521 variant loci genotyped in 1,989 individuals from 14 populations ranging from Northern California through Central Alaska. Consistent with prior genetic studies, the strongest separation occurs among three main regions: from Northern California up to and including the Fraser River; north of the Fraser River to southeast Alaska; and within the Gulf of Alaska. Separating the Fraser River from southern US populations, and refining additional substructure within the central coast may be possible in mixed-stock analysis; this will be addressed in future work. The amplicon panel outperformed the previous microsatellite panel, and thus will be used in future mixed-stock analyses of eulachon in order to provide new insights for management and conservation of eulachon.

genetics↗

bioRxiv2020

Identification of hypoxia-specific biomarkers in salmonids using RNA-sequencing and validation using high-throughput qPCR

Identifying early gene expression responses to hypoxia (i.e., low dissolved oxygen) as a tool to assess the degree of exposure to this stressor is crucial for salmonids, because they are increasingly exposed to hypoxic stress due to anthropogenic habitat change, e.g., global warming, excessive nutrient loading, and persistent algal blooms. Our goal was to discover and validate gill gene expression biomarkers specific to the hypoxia response in salmonids across multi-stressor conditions. Gill tissue was collected from 24 freshwater juvenile Chinook salmon (Oncorhynchus tshawytscha), held in normoxia [dissolved oxygen (DO) > 8 mg L-1] and hypoxia (DO = 4{square}5 mg L-1) in 10 and 18{degrees}C temperatures for up to six days. RNA-sequencing (RNA-seq) was then used to discover 240 differentially expressed genes between hypoxic and normoxic conditions, but not affected by temperature. The most significantly differentially expressed genes had functional roles in the cell cycle and suppression of cell proliferation associated with hypoxic conditions. The most significant genes (n = 30) were selected for real-time qPCR assay development. These assays demonstrated a strong correlation (r = 0.88; p < 0.001) between the expression values from RNA-seq and the fold changes from qPCR. Further, qPCR of the 30 candidate hypoxia biomarkers was applied to an additional 322 Chinook salmon exposed to hypoxic and normoxic conditions to reveal the top biomarkers to define hypoxic stress. Multivariate analyses revealed that smolt stage, water salinity, and morbidity status were relevant factors to consider with the expression of these genes in relation to hypoxic stress. These hypoxia candidate genes will be put into application screening Chinook salmon to determine the identity of stressors impacting the fish.

genomics↗

bioRxiv2019

Relative genomic impacts of translocation history, hatchery practices, and farm selection in Pacific oyster Crassostrea gigas throughout the Northern Hemisphere

Pacific oyster Crassostrea gigas, endemic to coastal Asia, has been translocated globally throughout the past century, resulting in self-sustaining introduced populations (naturalized). Oyster aquaculture industries in many parts of the world depend on commercially available seed (hatchery-farmed) or naturalized/wild oysters to move onto a farm (naturalized-farmed). It is therefore important to understand genetic variation among populations and farm types. Here we genotype naturalized/wild populations from France, Japan, China, and most extensively in coastal British Columbia, Canada. We also genotype cultured populations from throughout the Northern Hemisphere to compare with naturalized populations. In total, 16,942 markers were identified using double-digest RAD-sequencing in 182 naturalized, 112 hatchery-farmed, and 72 naturalized-farmed oysters (n = 366). Consistent with previous studies, very low genetic differentiation was observed around Vancouver Island (mean FST = 0.0019), and low differentiation between countries in the Japan-Canada-France historical translocation lineage (France-Canada FST = 0.0024; Japan-Canada FST = 0.0060). Chinese populations were more differentiated (China-Japan FST = 0.0241). Hatchery-propagated populations had higher inter-individual relatedness suggesting family structure. Within-population inbreeding was not detected on farms, but nucleotide diversity and polymorphism rate was lower in one farm population. Moving oysters from nature onto farms did not result in strong within-generation selection. Private alleles at substantial frequency were identified in several hatchery populations grown in BC, suggesting non-local origins. Tests of selection identified outlier loci consistent with selective differences associated with domestication, in some cases consistently identified in multiple farms. Top outlier candidates were nearby genes involved in calcium signaling and calmodulin activity. Implications of potential introgression from hatchery-farmed oysters depends on whether naturalized populations are valued as a locally-adapted resource or as an introduced, invasive species. Given the value of the industry in BC and the challenges the industry faces (e.g., climate change, crop losses, biotic stressors), this remains an important question.

genetics↗

bioRxiv2019

Comparative genomic analyses and a novel linkage map for cisco (Coregonus artedi) provides insight into chromosomal evolution and rediploidization across salmonids

Whole-genome duplication (WGD) is hypothesized to be an important evolutionary mechanism that can facilitate adaptation and speciation. Genomes that exist in states of both diploidy and residual tetraploidy are of particular interest, as mechanisms that maintain the ploidy mosaic after WGD may provide important insights into evolutionary processes. The Salmonidae family exhibits residual tetraploidy, and this, combined with the evolutionary diversity formed after an ancestral autotetraploidization event, makes this group a useful study system. In this study, we generate a novel linkage map for cisco (Coregonus artedi), an economically and culturally important fish in North America and a member of the subfamily Coregoninae, which previously lacked a high-density haploid linkage map. We also conduct comparative genomic analyses to refine our understanding of chromosomal fusion/fission history across salmonids. To facilitate this comparative approach, we use the naming strategy of protokaryotype identifiers (PKs) to associate duplicated chromosomes to their putative ancestral state. The female linkage map for cisco contains 20,292 loci, 3,225 of which are likely within residually tetraploid regions. Comparative genomic analyses revealed that patterns of residual tetrasomy are generally conserved across species, although interspecific variation persists. To determine the broad-scale retention of residual tetrasomy across the salmonids, we analyze sequence similarity of currently available genomes and find evidence of residual tetrasomy in seven of the eight chromosomes that have been previously hypothesized to show this pattern. This interspecific variation in extent of rediploidization may have important implications for understanding salmonid evolutionary histories and informing future conservation efforts.

genomics↗

bioRxiv2019

Combining metabarcoding and morphological approaches to identify phytoplankton taxa associated with harmful algal blooms

Molecular techniques are expected to be highly useful in detecting taxa causing harmful algal blooms (HABs). This is the first report in Canada evaluating HABs-related species identification using a combination of morphological and molecular approaches. Microscopy, quantitative polymerase chain reaction (qPCR), and metabarcoding with multiple markers (i.e. 16S, 18S-dinoflagellate and 18S-diatom, large subunit (28S) rDNA) were applied on samples (n=54) containing suspected harmful algae (e.g. Alexandrium spp., Chattonella sp., Chrysochromulina spp., Dictyocha spp., Heterosigma akashiwo, Protoceratium reticulatum, Pseudochattonella verruculosa, Pseudo-nitzschia spp., Pseudopedinella sp.). Due to methodology limitations, qPCR result interpretation was limited, although good detectability occurred using previously published assays for Alexandrium tamarense, H. akashiwo, and P. verruculosa. Overall, the multiple-marker metabarcoding results were superior to the morphology-based methods, with the exception of taxa from the silicoflagellate group. The combined results using both 18S markers and the 28S marker together closely corresponded with morphological identification of targeted species, providing the best overall taxonomic coverage and resolution. The most numerous unique taxa were identified using the 18S-dinoflagellate amplicon, and the best resolution to the species level occurred using the 28S amplicon. Molecular techniques are therefore highly useful for HABs taxa detection, but currently depend on deploying multiple markers for metabarcoding.

genetics↗

bioRxiv2018

Sex-specific and conserved gene co-expression networks underlie phenotypes within the paleopolyploid Salvelinus genus (Family Salmonidae)

Networks of co-expressed genes produce complex phenotypes associated with functional novelty. Sex differences in gene expression levels or in the structure of gene co-expression networks can cause sexual dimorphism and may resolve sexually antagonistic selection. Here we used RNA-sequencing in the paleopolyploid salmonid Brook Charr Salvelinus fontinalis to characterize sex-specific co-expression networks in the liver of 35 female and 51 male offspring. In both networks, modules were characterized for functional enrichment, hub gene identification, and associations with 15 growth, reproduction, and stress-related phenotypes. Modules were then evaluated for preservation in the opposite sex, and in the congener Arctic Charr Salvelinus alpinus. Overall, more transcripts were assigned to a module in the female network than in the male network, which coincided with higher inter-individual gene expression and phenotype variation in the females. Most modules were preserved between sexes and species, including those involved in conserved cellular processes (e.g. translation, immune pathways). However, two sex-specific male modules were identified, and these may contribute to sexual dimorphism. To compare with the network analysis, differentially expressed transcripts were identified between the sexes, finding a total of 16% of expressed transcripts as sex-biased. For both sexes, there was no overrepresentation of sex-biased genes or sex-specific modules on the putative sex chromosome. Sex-biased transcripts were also not overrepresented in sex-specific modules, and in fact highly male-biased transcripts were enriched in preserved modules. Comparative network analysis and differential expression analyses identified different aspects of sex differences in gene expression, and both provided new insights on the genes underlying sexual dimorphism in the salmonid Brook Charr.

genomics↗