The rainbow trout genome, an important landmark for aquaculture and genome evolution

Bobe, Julien; Marandel, Lucie; Panserat, Stéphane; Boudinot, Pierre; Berthelot, Camille; Quillet, Edwige; Volff, Jean‐Nicolas; Genêt, Carine; Jaillon, Olivier; Crollius, Hugues Roest; Guiguen, Yann

doi:10.1016/b978-0-12-801418-9.00002-0

Cited by 4 publications

(3 citation statements)

References 107 publications

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“…Contiguity and completeness is likely most affected in regions with high residual tetraploidy or incomplete rediploidization. While long-read based assemblies (and future sequencing technologies) are likely to generate a more complete picture, the current genome assembly represents a valuable resource for chum salmon on par with those available for Chinook, sockeye, and longstanding assemblies for Atlantic salmon and rainbow trout that allowed a transformation in genomic understanding of these commercially and culturally specific species (e.g., [101]).…”

Section: Discussionmentioning

confidence: 99%

Genome assembly, transcriptome and SNP database for chum salmon (Oncorhynchus keta)

Rondeau

Christensen

Sakhrani

et al. 2021

Preprint

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Chum salmon (Oncorhynchus keta) is the species with the widest geographic range of the anadromous Pacific salmonids,. Chum salmon is the second largest of the Pacific salmon, behind Chinook salmon, and considered the most plentiful Pacific salmon by overall biomass. This species is of significant commercial and economic importance: on average the commercial chum salmon fishery has the second highest processed value of the Pacific salmon within British Columbia. The aim of this work was to establish genomic baseline resources for this species. Our first step to accomplish this goal was to generate a chum salmon reference genome assembly from a doubled-haploid chum salmon. Gene annotation of this genome was facilitated by an extensive RNA-seq database we were able to create from multiple tissues. Range-wide resequencing of chum salmon genomes allowed us to categorize genome-wide geographic variation, which in turn reinforced the idea that genetic differentiation was best described on a regional, rather than at a stock-specific, level. Within British Columbia, chum salmon regional groupings were described at the conservation unit (CU) level, and there may be substructure within particular CUs. Genome wide associations of phenotypic sex to SNP genetic markers identified two clear peaks, a very strong peak on Linkage Group 15, and another on Linkage Group 3. With these new resources, we were better able to characterize the sex-determining region and gain further insights into sex determination in chum salmon and the general biology of this species.

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Section: Discussionmentioning

confidence: 99%

Genome assembly, transcriptome and SNP database for chum salmon (Oncorhynchus keta)

Rondeau

Christensen

Sakhrani

et al. 2021

Preprint

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“…As a potential substitution for UV‐328, UV‐327 has a similar molecular weight, structure, log K OW (6.91 compared to 7.25 for UV‐328), and environmental omnipresence (summarized in Supporting Information S1, Table S2; Cantwell et al, 2015). Rainbow trout was selected as a model organism due to the species’ economic and scientific importance, while also being an integral part in environmental risk assessments (Bobe et al, 2016; D'Agaro et al, 2022). Newly fertilized embryos were microinjected with UV‐327 at environmentally relevant concentrations (nominally ≤429 ng UV‐327 g −1 egg; Brorström‐Lundén et al, 2009; Nakata et al, 2012; Wick et al, 2016) and sampled throughout the developmental period until compete yolk absorption.…”

Section: Introductionmentioning

confidence: 99%

Embryonic Exposure to Benzotriazole Ultraviolet Stabilizer 327 Alters Behavior of Rainbow Trout Alevin

Eriksson,

Dubiel,

Zink

et al. 2024

Enviro Toxic and Chemistry

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Benzotriazole ultraviolet stabilizers (BUVSs) are used in great quantities during industrial production of a variety of consumer and industrial goods. Due to leaching and spill, BUVSs are detectable ubiquitously in the environment. As of May 2023, citing concerns related to bioaccumulation, biomagnification, and environmental persistence, (B)UV(S)‐328 was recommended to be listed under Annex A of the Stockholm Convention on Persistent Organic Pollutants. However, a phase out of UV‐328 could result in a regrettable substitution, as the replacement chemical(s) could cause similar or unpredicted toxicity in vivo, relative to the UV‐328. Therefore, the influence of UV‐327, a potential replacement of UV‐328, was investigated with respected to early life development of newly fertilized rainbow trout embryos (Oncorhynchus mykiss), microinjected with environmentally relevant concentrations of UV‐327. Developmental parameters (standard length), energy consumption (yolk area), heart function, blue sac disease, mortality, and behaviour were investigated. Alevins at 14 days post‐hatching, exposed to 107 ng UV‐327 g‐1 egg, presented significant signs of hyperactivity, as they moved on average 1.8‐fold the distance and at 1.5‐fold the velocity of controls. Although a substantial reduction in body burden of UV‐327 was observed at hatching, it is postulated that UV‐327, due to its lipophilic properties, interfered with neurological development and signaling from the onset of neurogenesis. If these results hold true across multiple taxa and species, a potential contributor to neurodevelopmental disorders might have been identified. These findings suggest that UV‐327 pose an unknown hazard to rainbow trout embryos and alevins, rendering UV‐327 a potential regrettable substitution to UV‐328. However, a qualified statement on a regrettable substitution requires a comparative investigation on the teratogenic effects between the two BUVSs.

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“…The rainbow trout (Oncorhynchus mykiss) is an economic fish that has been cultured worldwide for more than 100 years [1]. With the public concern for nutrition and food security, the high demand for rainbow trout has promoted the development of intensive cultures, yielding about 920,000 tons of global production per year [2].…”

Section: Introductionmentioning

confidence: 99%

Effects of Dietary Supplementation with Endogenous Probiotics Bacillus subtilis on Growth Performance, Immune Response and Intestinal Histomorphology of Juvenile Rainbow Trout (Oncorhynchus mykiss)

Wang,

Fan,

Zhao

et al. 2024

Fishes

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The rainbow trout (Oncorhynchus mykiss) is an important commercial fish. Studies have shown that probiotics can promote the healthy growth of fish. In this study, we assessed the impact of an endogenous Bacillus subtilis strain (RT-BS07) on the growth, survival and immunological response of juvenile rainbow trout. Additionally, the morphology of rainbow trout’s intestinal tissue was measured. Control (CT) and experimental groups (B) were fed with conventional and probiotic-supplemented diets (1.0 × 108 CFU per gram) for 42 days, respectively. Following feeding, a challenge experiment was carried out with Aeromonas hydrophila at 1.0 × 107 CFU/mL to determine the experimental fish’s tolerance to the bacteria. The results showed that the weight gain rate (WGR) in group B was 118.2%, which was significantly higher than that in group CT (54.86%) after 42 days. The height of intestinal villi and the number of goblet cells increased in group B, thus increasing the resistance of rainbow trout to pathogenic bacteria. The alkaline phosphatase (AKP) activity (U/mg prot) in the liver, spleen and intestinal tissues of group B was significantly higher than that in the CT group. The expression of interleukin-1β (IL-1β) in the intestinal tissue of group B was 6-fold higher than that in group CT. Furthermore, the expression of growth hormone-2 (GH-2) in the spleen was 3-fold higher than that in group CT. After 12 days of A. hydrophila injection, the survival rate was 40% and 70% in group CT and group B, respectively. Collectively, the present study demonstrated that the addition of endogenous B. subtilis strain (1.0 × 108 CFU per gram) to the feed can effectively promote the growth of rainbow trout and enhance immunity, which is beneficial to rainbow trout culture.

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The rainbow trout genome, an important landmark for aquaculture and genome evolution

Cited by 4 publications

References 107 publications

Genome assembly, transcriptome and SNP database for chum salmon (Oncorhynchus keta)

Genome assembly, transcriptome and SNP database for chum salmon (Oncorhynchus keta)

Embryonic Exposure to Benzotriazole Ultraviolet Stabilizer 327 Alters Behavior of Rainbow Trout Alevin

Effects of Dietary Supplementation with Endogenous Probiotics Bacillus subtilis on Growth Performance, Immune Response and Intestinal Histomorphology of Juvenile Rainbow Trout (Oncorhynchus mykiss)

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