Hokkaido-wide eDNA Monitoring for Sakhalin Taimen, Endangered Salmonid Species

Patterns of genetic variation among lake trout (Salvelinus namaycush) of eastern Lake Superior were examined using starch gel electrophoresis. We used 484 individuals sampled from three areas, representing three morphological types (leans, humpers, and siscowets). Of 50 loci examined, 44 were monomorphic in all groups sampled. Genetic variation occurs at six loci AAT-1,2, MDH-3,4, ME-1, and SOD-1. The average heterozygosity found (H = 0.015) is low relative to other salmonid species. A significant amount of heterogeneity exists among the 10 lake trout samples. These differences are due to variation within as well as between morphological types. The significance and management implications of these data are discussed.Key words: genetic variation, lake trout, Salvelinus namaycush, Lake Superior

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Relationship between vitellogenin and its related egg yolk proteins in Sakhalin taimen (Hucho perryi)

Comparative Biochemistry and Physiology Part A Physiology ◽

10.1016/0300-9629(96)00055-2 ◽

1996 ◽

Vol 115 (3) ◽

pp. 243-251 ◽

Cited By ~ 56

Author(s):

Naoshi Hiramatsu ◽

Akihiko Hara

Keyword(s):

Egg Yolk ◽

Yolk Proteins ◽

Hucho Perryi ◽

Sakhalin Taimen

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Earlier Migration Timing, Decreasing Phenotypic Variation, and Biocomplexity in Multiple Salmonid Species

PLoS ONE ◽

10.1371/journal.pone.0053807 ◽

2013 ◽

Vol 8 (1) ◽

pp. e53807 ◽

Cited By ~ 61

Author(s):

Ryan P. Kovach ◽

John E. Joyce ◽

Jesse D. Echave ◽

Mark S. Lindberg ◽

David A. Tallmon

Keyword(s):

Phenotypic Variation ◽

Migration Timing ◽

Salmonid Species

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Salmon lice evasion, susceptibility, retention, and development differ amongst host salmonid species

ICES Journal of Marine Science ◽

10.1093/icesjms/fsx222 ◽

2017 ◽

Vol 75 (3) ◽

pp. 1071-1079 ◽

Cited By ~ 2

Author(s):

Samantha Bui ◽

Elina Halttunen ◽

Agnes M Mohn ◽

Tone Vågseth ◽

Frode Oppedal

Keyword(s):

Atlantic Salmon ◽

Chinook Salmon ◽

Salmo Trutta ◽

Parasite Development ◽

Lepeophtheirus Salmonis ◽

Sea Trout ◽

Salmon Lice ◽

Salmonid Species ◽

Host Parasite ◽

Temporal Overlap

Abstract With different ecological characteristics amongst salmonid species, their response to parasitic infestation is likely to vary according to their spatial and temporal overlap with the parasite. This study investigated the host–parasite interactions amongst three species of salmonids and the ectoparasitic salmon louse, Lepeophtheirus salmonis. To determine any variation in infestation parameters amongst salmonids, single population groups of Atlantic salmon (Salmo salar), chinook salmon (Onchorhynchus tshawytscha), and previously-infested and naïve sea trout (Salmo trutta) were exposed to a controlled infestation challenge. We found that chinook salmon and both sea trout groups were more susceptible to acquiring lice than Atlantic salmon. Behavioural responses during infestation were more pronounced in Atlantic and chinook salmon. Parasite development was similar in lice attached to Atlantic salmon and sea trout, but hindered on chinook salmon. At 16 days post-infestation, chinook salmon had reduced lice loads to the same level as Atlantic salmon, whilst sea trout retained their lice. These results demonstrate differences in interactions with L. salmonis amongst these species, and highlight the vulnerability of sea trout to infestation.

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A chromosome-anchored genome assembly for Lake Trout (Salvelinus namaycush)

10.22541/au.161792605.50398568/v1 ◽

2021 ◽

Author(s):

Seth Smith ◽

Eric Normandeau ◽

Haig Djambazian ◽

Pubudu Nawarathna ◽

Pierre Berube ◽

...

Keyword(s):

Genome Assembly ◽

Lake Trout ◽

Single Copy ◽

Salvelinus Namaycush ◽

Genomic Research ◽

Total Size ◽

Salmonid Species ◽

Long Read ◽

Potential Applications ◽

Conservation Concern

Here we present an annotated, chromosome-anchored, genome assembly for Lake Trout (Salvelinus namaycush) – a highly diverse salmonid species of notable conservation concern and an excellent model for research on adaptation and speciation. We leveraged Pacific Biosciences long-read sequencing, paired-end Illumina sequencing, proximity ligation (Hi-C), and a previously published linkage map to produce a highly contiguous assembly composed of 7,378 contigs (contig N50 = 1.8 mb) assigned to 4,120 scaffolds (scaffold N50 = 44.975 mb). 84.7% of the genome was assigned to 42 chromosome-sized scaffolds and 93.2% of Benchmarking Universal Single Copy Orthologs were recovered, putting this assembly on par with the best currently available salmonid genomes. Estimates of genome size based on k-mer frequency analysis were highly similar to the total size of the finished genome, suggesting that the entirety of the genome was recovered. A mitome assembly was also produced. Self-vs-self synteny analysis allowed us to identify homeologs resulting from the Salmonid specific autotetraploid event (Ss4R) and alignment with three other salmonid species allowed us to identify homologous chromosomes in other species. We also generated multiple resources useful for future genomic research on Lake Trout including a repeat library and a sex averaged recombination map. A novel RNA sequencing dataset was also used to produce a publicly available set of gene annotations using the National Center for Biotechnology Information Eukaryotic Genome Annotation Pipeline. Potential applications of these resources to population genetics and the conservation of native populations are discussed.

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Efficient genome editing in multiple salmonid cell lines using ribonucleoprotein complexes

10.1101/2020.04.03.022038 ◽

2020 ◽

Author(s):

Remi L. Gratacap ◽

Ye Hwa Jin ◽

Marina Mantsopoulou ◽

Ross D. Houston

Keyword(s):

Rainbow Trout ◽

Atlantic Salmon ◽

Infectious Diseases ◽

Genome Editing ◽

Cell Lines ◽

Chinook Salmon ◽

Model Systems ◽

Fish Cell ◽

Ribonucleoprotein Complexes ◽

Salmonid Species

AbstractInfectious and parasitic diseases have major negative economic and animal welfare impacts on aquaculture of salmonid species. Improved knowledge of the functional basis of host response and genetic resistance to these diseases is key to developing preventative and treatment options. Cell lines provide a valuable model to study infectious diseases in salmonids, and genome editing using CRISPR provides an exciting avenue to evaluate the function of specific genes in those systems. While CRISPR/Cas9 has been successfully performed in a Chinook salmon cell line (CHSE-214), there are no reports to date of editing of cell lines derived from the most commercially relevant salmonid species Atlantic salmon and rainbow trout, which are difficult to transduce and therefore edit using lentivirus-mediated methods. In the current study, a method of genome editing of salmonid cell lines using ribonucleoprotein (RNP) complexes was optimised and tested in the most commonly-used salmonid fish cell lines; Atlantic salmon (SHK-1 and ASK cell lines), rainbow trout (RTG-2) and Chinook salmon (CHSE-214). Electroporation of RNP based on either Cas9 or Cas12a was efficient at targeted editing of all the tested lines (typically > 90 % cells edited), and the choice of enzyme expands the number of potential target sites for editing within the genomes of these species. These optimised protocols will facilitate functional genetic studies in salmonid cell lines, which are widely used as model systems for infectious diseases in aquaculture.

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Characterization of Collagen from Sakhalin Taimen Skin as Useful Biomass

Food Technology and Biotechnology ◽

10.17113/ftb.58.04.20.6734 ◽

2020 ◽

Vol 58 (4) ◽

Author(s):

Takeshi Nagai ◽

Masataka Saito ◽

Yasuhiro Tanoue ◽

Norihisa Kai ◽

Nobutaka Suzuki

Keyword(s):

Structural Changes ◽

Polyacrylamide Gel Electrophoresis ◽

High Yield ◽

Collagen Molecule ◽

Edible Portion ◽

Sakhalin Taimen ◽

Skin Collagen ◽

Modification Technique ◽

Cold Acetone ◽

Α Helix

Research background. Animal collagen has been widely utilized in foods, cosmetics, and biomedical fields. The non-edible portion, such as fish skins and bones, are generated during cooking processes. Most of them are currently discarded as wastes, although the nutritional values of the skins and bones are high. It needs to utilize the non-edible portion for the reduction of environmental impact, as it may be one of source of environmental pollution. Experimental approach. Collagen was prepared from Sakhalin taimen skins as wastes generated during cooking processes. Next, the color, SDS-polyacrylamide gel electrophoresis, ultraviolet absorption, subunit composition, amino acid composition, denaturation temperature, and attenuated total reflectance-Fourier transform infrared spectroscopy analysis were conducted to explore the properties of the collagen. Lastly, it tried to improve the functional properties of the collagen using chemical modification technique for future applications. Results and conclusions. Cold acetone treatment made it possible to easily remove the fats and pigments from skins. The odorless and pure-white collagen was obtained with high-yield. The α3 chain did not exist in the collagen. Sakhalin taimen skin collagen had rich α-helix and low β-sheet structures. Succinylation caused the secondary structural changes of the collagen molecule. Moreover, succinylation made it possible not only to increase the viscosity of collagen solution and but also to improve the solubility of collagen in the physiological conditions around pH=6. Novelty and scientific contribution. This finding was the first report on the absence of the α3 chain in Salmonid fish skin collagens. The succinylated collagen from Sakhalin taimen skins as useful biomass has potential to utilize in foods, cosmetics, and its related industries.

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Critical Habitat and the Conservation Ecology of the Freshwater Parasitic Lamprey, Lampetra macrostoma

The Canadian Field-Naturalist ◽

10.22621/cfn.v122i4.640 ◽

2008 ◽

Vol 122 (4) ◽

pp. 327 ◽

Cited By ~ 5

Author(s):

R. J. Beamish ◽

J. Wade

Keyword(s):

British Columbia ◽

Initial Study ◽

Vancouver Island ◽

Larval Rearing ◽

Fishing Pressure ◽

Critical Habitat ◽

Conservation Ecology ◽

Salmonid Species ◽

Rivers And Streams

Lampetra macrostoma, the Cowichan Lamprey, is a freshwater parasitic lamprey that probably evolved from L. tridentata within the last 10 000 years. It is unique to the Cowichan Lake watershed on Vancouver Island, British Columbia, Canada. Larval rearing in Mesachie and Cowichan lakes occurs in shallow, silt-covered gravel areas at the mouths of rivers and streams flowing into the lakes. Spawning occurs over a protracted period from early May until about late July. Shallow areas with small gravel along the shore of the lakes, near the mouths of rivers are essential for successful spawning. Adults prey on a variety of salmonid species within the lake. There has been considerable development around Mesachie Lake and reported increased fishing pressure on prey in Mesachie and Cowichan lakes. It is not known if the size of the population of L. macrostoma has changed since an initial study in the early 1980s, but a study in 2008 captured very few spawning lamprey in Mesachie Lake, possibly indicating that the population is declining.

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De novo assembly of the Brown trout (Salmo trutta m. fario) brain and muscle transcriptome: transcript annotation, tissue differential expression profile and SNP discovery

BMC Research Notes ◽

10.1186/s13104-020-05351-4 ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

J. Fibla ◽

N. Oromi ◽

M. Pascual-Pons ◽

J. L. Royo ◽

A. Palau ◽

...

Keyword(s):

Differential Expression ◽

Brown Trout ◽

Salmo Trutta ◽

De Novo ◽

Transcriptome Assembly ◽

Differential Expression Analysis ◽

Cdna Libraries ◽

Significant Differential Expression ◽

Reference Transcriptome ◽

Salmonid Species

Abstract Objectives The Brown trout is a salmonid species with a high commercial value in Europe. Life history and spawning behaviour include resident (Salmo trutta m. fario) and migratory (Salmo trutta m. trutta) ecotypes. The main objective is to apply RNA-seq technology in order to obtain a reference transcriptome of two key tissues, brain and muscle, of the riverine trout Salmo trutta m. fario. Having a reference transcriptome of the resident form will complement genomic resources of salmonid species. Data description We generate two cDNA libraries from pooled RNA samples, isolated from muscle and brain tissues of adult individuals of Salmo trutta m. fario, which were sequenced by Illumina technology. Raw reads were subjected to de-novo transcriptome assembly using Trinity, and coding regions were predicted by TransDecoder. A final set of 35,049 non-redundant ORF unigenes were annotated. Tissue differential expression analysis was evaluated by Cuffdiff. A False Discovery Rate (FDR) ≤ 0.01 was considered for significant differential expression, allowing to identify key differentially expressed unigenes. Finally, we have identified SNP variants that will be useful tools for population genomic studies.

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