Evolution of duplicated IgH loci in Atlantic salmon, Salmo salar

<p>Abstract</p> <p>Background</p> <p>The Atlantic salmon (<it>Salmo salar</it>) immunoglobulin heavy chain (<it>IgH</it>) locus possesses two parallel <it>IgH </it>isoloci (<it>IGH-A </it>and <it>IGH-B</it>), that are related to the genomic duplication event in the family Salmonidae. These duplicated <it>IgH </it>loci in Atlantic salmon provide a unique opportunity to examine the mechanisms of genome diversity and genome evolution of the <it>IgH </it>loci in vertebrates. In this study, we defined the structure of these loci in Atlantic salmon, and sequenced 24 bacterial artificial chromosome (BAC) clones that were assembled into the <it>IGH-A </it>(1.1 Mb) and <it>IGH-B </it>(0.9 Mb) loci. In addition, over 7,000 cDNA clones from the <it>IgH </it>variable (V<smcaps>H</smcaps>) region have been sequenced and analyzed.</p> <p>Results</p> <p>The present study shows that the genomic organization of the duplicated <it>IgH </it>loci in Atlantic salmon differs from that in other teleosts and other vertebrates. The loci possess multiple Cτ genes upstream of the Cμ region, with three of the Cτ genes being functional. Moreover, the duplicated loci possess over 300 V<smcaps>H</smcaps> segments which could be classified into 18 families. This is the largest number of V<smcaps>H</smcaps> families currently defined in any vertebrate. There were significant structural differences between the two loci, indicating that both <it>IGH-A </it>and <it>-B </it>loci have evolved independently in the short time after the recent genome duplication approximately 60 mya.</p> <p>Conclusions</p> <p>Our results indicate that the duplication of the <it>IgH </it>loci in Atlantic salmon significantly contributes to the increased diversity of the antibody repertoire, as compared with the single <it>IgH </it>locus in other vertebrates.</p

Reference genome of Lumpfish Cyclopterus lumpus Linnaeus provides evidence of male heterogametic sex determination through the AMH pathway

acceptedVersio

Genomic evidence of recent European introgression into North American farmed and wild Atlantic salmon

publishedVersio

Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome

<p>Abstract</p> <p>Background</p> <p>Salmonids are one of the most intensely studied fish, in part due to their economic and environmental importance, and in part due to a recent whole genome duplication in the common ancestor of salmonids. This duplication greatly impacts species diversification, functional specialization, and adaptation. Extensive new genomic resources have recently become available for Atlantic salmon (<it>Salmo salar</it>), but documentation of allelic versus duplicate reference genes remains a major uncertainty in the complete characterization of its genome and its evolution.</p> <p>Results</p> <p>From existing expressed sequence tag (EST) resources and three new full-length cDNA libraries, 9,057 reference quality full-length gene insert clones were identified for Atlantic salmon. A further 1,365 reference full-length clones were annotated from 29,221 northern pike (<it>Esox lucius</it>) ESTs. Pairwise d_N/d_Scomparisons within each of 408 sets of duplicated salmon genes using northern pike as a diploid out-group show asymmetric relaxation of selection on salmon duplicates.</p> <p>Conclusions</p> <p>9,057 full-length reference genes were characterized in <it>S. salar </it>and can be used to identify alleles and gene family members. Comparisons of duplicated genes show that while purifying selection is the predominant force acting on both duplicates, consistent with retention of functionality in both copies, some relaxation of pressure on gene duplicates can be identified. In addition, there is evidence that evolution has acted asymmetrically on paralogs, allowing one of the pair to diverge at a faster rate.</p

Genomic evidence of past and future climate-linked loss in a migratory Arctic fish

Acknowledgements We thank staff of the Newfoundland DFO Salmonids section, Parks Canada, the Nunatsiavut Government, the NunatuKavut Community Council, the Sivunivut Inuit Community Corporation, the Innu Nation, the Labrador Hunting and Fishing Association and fishers for their support, participation and tissue collections and the staff of the Aquatic Biotechnology Lab at the Bedford Institute of Oceanography for DNA extractions. This study was supported by the Ocean Frontier Institute, a Genomics Research and Development Initiative (GRDI) Grant, a Natural Sciences and Engineering Research Council (NSERC) Discovery Grant and Strategic Project Grant to I.R.B., the Weston Family Award for research at the Torngat Mountains Base Camp and an Atlantic Canada Opportunities Agency and Department of Tourism, Culture, Industry and Innovation grant allocated to the Labrador Institute. Author Correction: Layton, K.K.S., Snelgrove, P.V.R., Dempson, J.B. et al. Author Correction: Genomic evidence of past and future climate-linked loss in a migratory Arctic fish. Nat. Clim. Chang. 11, 551 (2021). https://doi.org/10.1038/s41558-021-01023-8Peer reviewedPostprin

Resolving fine-scale population structure and fishery exploitation using sequenced microsatellites in a northern fish

Funding Information Natural Sciences and Engineering Research Council of Canada (NSERC) Strategic Project Atlantic Canada Opportunities Agency and Department of Tourism, Culture, Industry and Innovation grants allocated to the Labrador Institute (MC) Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Genomics Research and Development Initiative (GRDI) Weston Family AwardPeer reviewedPublisher PD

Feeding rates and abundance of marine invertebrate planktonic larvae under harmful algal bloom conditions off Vancouver Island

13 pages, 7 figures, 6 tablesThe interactions between toxic phytoplankton and their potential grazers are poorly understood aspects of the ecology of harmful algal blooms. In this study, we determined the feeding rates, prey selection and trophic impact of different marine invertebrate planktonic larvae on the natural bloom of Heterosigma akashiwo and Prorocentrum triestinum which occurred on the west coast of Vancouver Island in July of 2006. Additionally, we estimated the abundance, biomass and composition of zooplankton before and during the harmful algal bloom. Feeding experiments were performed with polychaete (Serpula columbiana), echinoderm (Stronglyocentratus purpuratus) and cirripede (Balanus crenatus) larvae obtained from laboratory cultures, and bivalve and gastropod larvae collected from the study site by plankton tows. All larvae fed on H. akashiwo whereas only cirripede nauplii and echinoderm larvae fed on P. triestinum. H. akashiwo was the main component of all larval diets (>64%). We observed a positive relationship between prey availability in the food assemblages and their contribution to all larval diets. The potential trophic impact of meroplanktonic larvae on bloom forming phytoplankton species was low (<1.5%). The ingestion of bloom forming phytoplankton did not appear to have any adverse effects on the studied grazers after 48 h of incubation. In contrast, field abundance of planktonic larvae and other zooplankton continuously decreased throughout the progression of the bloom, with losses approaching 75% in comparison to their pre-bloom abundance. The presence of H. akashiwo negatively affected the abundance of meroplanktonic larvae, despite efficient grazing of these larvae. Therefore, grazing pressure was reduced which likely contributed to the growth and persistence of the bloom. The reduction in meroplanktonic larvae and other zooplankton abundance associated with the H. akashiwo bloom may have potential impacts on benthic recruitment and energy transfers to higher trophic levels in marine food websA Ph.D. fellowship to RA (BES-2005-7491) from the Spanish Ministry of Science and Innovation (MICINN) and a TRU CUEF award to AMM funded this work. The research was also supported by MICROROL (CTM2004-02775) research project from MICINN to RA and an NSERC Discovery grant to LAGPeer reviewe

Molecular and phylogenetic identification of unique isolates of hammerhead viroid-like RNA from 'Pacific Gala' apple (Malus domestica) in Canada

[EN] Ten isolates of apple hammerhead viroid-like RNA (AHVd RNA) were detected by next-generation sequencing (NGS) and/or by RT-PCR analysis of apple (Malus domestica) 'Pacific Gala' (PG) from Canada. All consisted of 433 nucleotides in size, and their circular structure and sequence were supported by reverse transcription amplification with two separate pairs of abutted primers, cloning and sequencing. Two regions were defined for the computer-predicted secondary structure of AHVd RNA-PG isolates - a hammerhead region (HHR) and a loop-rich region (LRR). The HHR contained the core and flanking nucleotides typical of natural hammerhead ribozymes. The secondary structure associated with the LRR was distinct from that predicted for the corresponding region of AHVd RNA isolates previously described in 'Fuji' apple in China. However, both structures share conserved stem-loops in the LRR, identified as S1, S2, S3 and S4.This work was supported by the Canadian Food Inspection Agency; Ministerio de Economia y Competitividad [BFU2014-56812-P].Messmer, A.; Sanderson, D.; Braun, G.; Flores Pedauye, R.; Serra Alfonso, P.; James, D. (2017). Molecular and phylogenetic identification of unique isolates of hammerhead viroid-like RNA from 'Pacific Gala' apple (Malus domestica) in Canada. Canadian Journal of Plant Pathology. 39(3):342-353. doi:10.1080/07060661.2017.1354334S34235339