Exploration of the nurse shark (Ginglymostoma cirratum) plasma immunoproteome using high-resolution LC-MS/MS

Funding Information: FKB was supported by a BBSRC-funded EASTBIO Doctoral Training Partnership studentship (grant number BB/M010996/1) awarded to HD. HM is supported by NIH-NIAID predoctoral fellowship F31AI147532. DM received institutional strategic funding from the BBSRC (grants: BBS/E/D/10002071 and BBS/E/D/20002174). For the purpose of open access, the author has applied a Creative Commons Attribution (CC BY) licence to any Author Accepted Manuscript version arising from this submission. Funding Information: We thank Professor Sam Martin (University of Aberdeen) for supporting the supervision of FKB during her PhD. Our thanks also to Luke Tallon and Lisa Sadzewicz at UMBs Institute for Genome Sciences for helpful advice and sharing their expertise during sequencing of the nurse shark transcriptome. Publisher Copyright: Copyright © 2022 Bakke, Gundappa, Matz, Stead, Macqueen and Dooley.Peer reviewedPublisher PD

Zebrafish as a Model to Unveil the Pro-Osteogenic Effects of Boron-Vitamin D3 Synergism

The micronutrient boron (B) plays a key role during the ossification process as suggested by various in vitro and in vivo studies. To deepen our understanding of the molecular mechanism involved in the osteogenicity of B and its possible interaction with vitamin D3 (VD), wild-type AB zebrafish (Danio rerio) were used for morphometric analysis and transcriptomic analysis in addition to taking advantage of the availability of specific zebrafish osteoblast reporter lines. First, osteoactive concentrations of B, VD, and their combinations were established by morphometric analysis of the opercular bone in alizarin red-stained zebrafish larvae exposed to two selected concentrations of B (10 and 100 ng/ml), one concentration of VD (10 pg/ml), and their respective combinations. Bone formation, as measured by opercular bone growth, was significantly increased in the two combination treatments than VD alone. Subsequently, a transcriptomic approach was adopted to unveil the molecular key regulators involved in the synergy. Clustering of differentially expressed genes revealed enrichment toward bone and skeletal functions in the groups co-treated with B and VD. Downstream analysis confirmed mitogen-activated protein kinase as the most regulated pathway by the synergy groups in addition to transforming growth factor-beta signaling, focal adhesion, and calcium signaling. The best-performing synergistic treatment, B at 10 ng/ml and VD at 10 pg/ml, was applied to two zebrafish transgenic lines, Tg(sp7:mCherry) and Tg(bglap:EGFP), at multiple time points to further explore the results of the transcriptomic analysis. The synergistic treatment with B and VD induced enrichment of intermediate (sp7(+)) osteoblast at 6 and 9 days post fertilization (dpf) and of mature (bglap(+)) osteoblasts at 15 dpf. The results obtained validate the role of B in VD-dependent control over bone mineralization and can help to widen the spectrum of therapeutic approaches to alleviate pathological conditions caused by VD deficiency by using low concentrations of B as a nutritional additive.info:eu-repo/semantics/publishedVersio

Genomic epidemiology of salmonid alphavirus in Norwegian aquaculture reveals recent subtype-2 transmission dynamics and novel subtype-3 lineages

Viral disease poses a major barrier to sustainable aquaculture, with outbreaks causing large economic losses and growing concerns for fish welfare. Genomic epidemiology can support disease control by providing rapid inferences on viral evolution and disease transmission. In this study, genomic epidemiology was used to investigate salmonid alphavirus (SAV), the causative agent of pancreas disease (PD) in Atlantic salmon. Our aim was to reconstruct SAV subtype-2 (SAV2) diversity and transmission dynamics in recent Norwegian aquaculture, including the origin of SAV2 in regions where this subtype is not tolerated under current legislation. Using nanopore sequencing, we captured ~90% of the SAV2 genome for n = 68 field isolates from 10 aquaculture production regions sampled between 2018 and 2020. Using time-calibrated phylogenetics, we infer that, following its introduction to Norway around 2010, SAV2 split into two clades (SAV2a and 2b) around 2013. While co-present at the same sites near the boundary of Møre og Romsdal and Trøndelag, SAV2a and 2b were generally detected in non-overlapping locations at more Southern and Northern latitudes, respectively. We provide evidence for recent SAV2 transmission over large distances, revealing a strong connection between Møre og Romsdal and SAV2 detected in 2019/20 in Rogaland. We also demonstrate separate introductions of SAV2a and 2b outside the SAV2 zone in Sognefjorden (Vestland), connected to samples from Møre og Romsdal and Trøndelag, respectively, and a likely 100 km Northward transmission of SAV2b within Trøndelag. Finally, we recovered genomes of SAV2a and SAV3 co-infecting single fish in Rogaland, involving novel SAV3 lineages that diverged from previously characterized strains >25 years ago. Overall, this study demonstrates useful applications of genomic epidemiology for tracking viral disease spread in aquaculture

Chromosome level reference genome for European flat oyster (Ostrea edulis L.)

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Genome-wide reconstruction of rediploidization following autopolyploidization across one hundred million years of salmonid evolution

Acknowledgements: This work was supported by the Biotechnology and Biological Sciences Research Council grant BBS/E/D/10002070 and the Frimedbio program of the Research Council of Norway (grant number 241016). MKG received studentship funding from a University of Aberdeen Elphinstone scholarship with additional support from the Government of Karnataka. We thank Dr Sebastian Beggel, Dr Bernhard C. Stoeckle, Jens-Eike Täuber and Ms Haiyu Ding at the Aquatic Systems Biology Unit, Technical University of Munich for their support in sampling huchen. We thank Dr Torfinn Nome for supporting bioinformatic analyses. We thank Madhusudhan Gundappa (Twitter: @fish_lines) for providing species illustrations in Figure 1. We also thanks Dr Gareth Gillard (Norwegian University of Life Sciences) for support with the RNA-Seq data. The Earlham Institute performed library preparation and sequencing used in the huchen genome assembly.Peer reviewedPublisher PD

Conserved and divergent arms of the antiviral response in the duplicated genomes of salmonid fishes

Funding Information: This work was funded by the European Union's Horizon 2020 research and innovation program under grant agreement No 817923 (AQUAFAANG), by ANR (ANR-21-CE35-0019, LipofishVac), by the Eranet ICRAD-Nucnanofish (ANR_13001498 and BBSRC_ICRAD BB/V019902/1), by the BBSRC Institutional strategic programme award (BBS/E/D/20002174) and by institutional grants from INRAE. We thank Drs Hugues Roest Crollius, Camille Berthelot, Alexandra Louis and Elise Parey for sharing synteny-based corrected data produced by SCORPiOs, and Louis du Pasquier for insightful discussions.Peer reviewedPublisher PD

Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication

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The structural variation landscape in 492 Atlantic salmon genomes

Structural variants (SVs) are a major source of genetic and phenotypic variation, but remain challenging to accurately type and are hence poorly characterized in most species. We present an approach for reliable SV discovery in non-model species using whole genome sequencing and report 15,483 high-confidence SVs in 492 Atlantic salmon (Salmo salar L.) sampled from a broad phylogeographic distribution. These SVs recover population genetic structure with high resolution, include an active DNA transposon, widely affect functional features, and overlap more duplicated genes retained from an ancestral salmonid autotetraploidization event than expected. Changes in SV allele frequency between wild and farmed fish indicate polygenic selection on behavioural traits during domestication, targeting brain-expressed synaptic networks linked to neurological disorders in humans. This study offers novel insights into the role of SVs in genome evolution and the genetic architecture of domestication traits, along with resources supporting reliable SV discovery in non-model species.Peer reviewe

SalMotifDB:a tool for analyzing putative transcription factor binding sites in salmonid genomes

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