STORRE Collection: Electronic copies of Aquaculture journal articles.Electronic copies of Aquaculture journal articles.http://hdl.handle.net/1893/2172024-03-29T08:45:39Z2024-03-29T08:45:39ZLooking for Local Adaptation: Convergent Microevolution in Aleppo Pine (Pinus halepensis)Ruiz Daniels, RoseTaylor, Richard SGonzález-Martínez, Santiago CVendramin, Giovanni GFady, BrunoOddou-Muratorio, SylviePiotti, AndreaSimioni, GuillaumeGrivet, DelphineBeaumont, Mark Ahttp://hdl.handle.net/1893/358892024-03-29T01:11:49Z2019-01-01T00:00:00ZTitle: Looking for Local Adaptation: Convergent Microevolution in Aleppo Pine (Pinus halepensis)
Author(s): Ruiz Daniels, Rose; Taylor, Richard S; González-Martínez, Santiago C; Vendramin, Giovanni G; Fady, Bruno; Oddou-Muratorio, Sylvie; Piotti, Andrea; Simioni, Guillaume; Grivet, Delphine; Beaumont, Mark A
Abstract: Finding outlier loci underlying local adaptation is challenging and is best approached by suitable sampling design and rigorous method selection. In this study, we aimed to detect outlier loci (single nucleotide polymorphisms, SNPs) at the local scale by using Aleppo pine (Pinus halepensis), a drought resistant conifer that has colonized many habitats in the Mediterranean Basin, as the model species. We used a nested sampling approach that considered replicated altitudinal gradients for three contrasting sites. We genotyped samples at 294 SNPs located in genomic regions selected to maximize outlier detection. We then applied three different statistical methodologies—Two Bayesian outlier methods and one latent factor principal component method—To identify outlier loci. No SNP was an outlier for all three methods, while eight SNPs were detected by at least two methods and 17 were detected only by one method. From the intersection of outlier SNPs, only one presented an allelic frequency pattern associated with the elevational gradient across the three sites. In a context of multiple populations under similar selective pressures, our results underline the need for careful examination of outliers detected in genomic scans before considering them as candidates for convergent adaptation.2019-01-01T00:00:00ZGenomic Epidemiology of Salmonid Alphavirus in Norwegian Aquaculture Reveals Recent Subtype-2 Transmission Dynamics and Novel Subtype-3 LineagesMacqueen, Daniel JEve, OliverGundappa, Manu KumarDaniels, Rose RuizGallagher, Michael DAlexandersen, SveinKarlsen, Mariushttp://hdl.handle.net/1893/358882024-03-29T01:11:23Z2021-01-01T00:00:00ZTitle: Genomic Epidemiology of Salmonid Alphavirus in Norwegian Aquaculture Reveals Recent Subtype-2 Transmission Dynamics and Novel Subtype-3 Lineages
Author(s): Macqueen, Daniel J; Eve, Oliver; Gundappa, Manu Kumar; Daniels, Rose Ruiz; Gallagher, Michael D; Alexandersen, Svein; Karlsen, Marius
Abstract: 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.2021-01-01T00:00:00ZAnalysing responsible innovation along a value chain-A single- cell protein case studyFlight, Monica HoyosTait, JoyceChronopoulos, TheoBetancor, MonicaWischhusen, PaulineBurton, EmilyMasey O'Neill, HelenVan Der Heul, KimHays, JohnRowe, Peterhttp://hdl.handle.net/1893/358762024-03-29T01:06:40Z2024-03-20T00:00:00ZTitle: Analysing responsible innovation along a value chain-A single- cell protein case study
Author(s): Flight, Monica Hoyos; Tait, Joyce; Chronopoulos, Theo; Betancor, Monica; Wischhusen, Pauline; Burton, Emily; Masey O'Neill, Helen; Van Der Heul, Kim; Hays, John; Rowe, Peter
Abstract: The British Standards Institution's Publicly Available Specification 440 (PAS 440) provides a Responsible Innovation Framework (RIF) that companies can use to continuously monitor the societal, environmental and health benefits and risks of their innovations, as well as relevant changes to the supply chain and regulations. PAS 440 is intended to help companies achieve the benefits of innovation in a timely manner and avoid any potential harm or unintended misuse of a new product, process or service. Here, the authors have applied the PAS 440 RIF to a novel single-cell protein (SCP) animal feed ingredient taking into consideration the perspectives of the value chain partners (VCPs), companies and laboratories involved in an Innovate UK research project. The authors' findings show how VCPs can use PAS440 to demonstrate that they are innovating responsibly. Using this approach to responsible innovation along the value chain-from manufacturing scale-up, through regulatory approval, to incorporation in animal feed and from there to food on supermarket shelves-can support the development of innovations that contribute to the economic and environmental sustainability of the animal feed sector. The authors conclude that the PAS 440 Guide can facilitate the progress of a new product throughout a value chain and contribute to coordinating responsible behaviour among companies involved in the value chain.2024-03-20T00:00:00ZMapping the cellular landscape of Atlantic salmon head kidney by single cell and single nucleus transcriptomicsAndresen, Adriana M.S.Taylor, Richard S.Grimholt, UnniDaniels, Rose RuizSun, JianxuanDobie, RossHenderson, Neil C.Martin, Samuel A.M.Macqueen, Daniel J.Fosse, Johanna H.http://hdl.handle.net/1893/358622024-03-20T01:01:04Z2024-03-01T00:00:00ZTitle: Mapping the cellular landscape of Atlantic salmon head kidney by single cell and single nucleus transcriptomics
Author(s): Andresen, Adriana M.S.; Taylor, Richard S.; Grimholt, Unni; Daniels, Rose Ruiz; Sun, Jianxuan; Dobie, Ross; Henderson, Neil C.; Martin, Samuel A.M.; Macqueen, Daniel J.; Fosse, Johanna H.
Abstract: Single-cell transcriptomics is the current gold standard for global gene expression profiling, not only in mammals and model species, but also in non-model fish species. This is a rapidly expanding field, creating a deeper understanding of tissue heterogeneity and the distinct functions of individual cells, making it possible to explore the complexities of immunology and gene expression on a highly resolved level. In this study, we compared two single cell transcriptomic approaches to investigate cellular heterogeneity within the head kidney of healthy farmed Atlantic salmon (Salmo salar). We compared 14,149 cell transcriptomes assayed by single cell RNA-seq (scRNA-seq) with 18,067 nuclei transcriptomes captured by single nucleus RNA-Seq (snRNA-seq). Both approaches detected eight major cell populations in common: granulocytes, heamatopoietic stem cells, erythrocytes, mononuclear phagocytes, thrombocytes, B cells, NK-like cells, and T cells. Four additional cell types, endothelial, epithelial, interrenal, and mesenchymal cells, were detected in the snRNA-seq dataset, but appeared to be lost during preparation of the single cell suspension submitted for scRNA-seq library generation. We identified additional heterogeneity and subpopulations within the B cells, T cells, and endothelial cells, and revealed developmental trajectories of heamatopoietic stem cells into differentiated granulocyte and mononuclear phagocyte populations. Gene expression profiles of B cell subtypes revealed distinct IgM and IgT-skewed resting B cell lineages and provided insights into the regulation of B cell lymphopoiesis. The analysis revealed eleven T cell sub-populations, displaying a level of T cell heterogeneity in salmon head kidney comparable to that observed in mammals, including distinct subsets of cd4/cd8-negative T cells, such as tcrγ positive, progenitor-like, and cytotoxic cells. Although snRNA-seq and scRNA-seq were both useful to resolve cell type-specific expression in the Atlantic salmon head kidney, the snRNA-seq pipeline was overall more robust in identifying several cell types and subpopulations. While scRNA-seq displayed higher levels of ribosomal and mitochondrial genes, snRNA-seq captured more transcription factor genes. However, only scRNA-seq-generated data was useful for cell trajectory inference within the myeloid lineage. In conclusion, this study systematically outlines the relative merits of scRNA-seq and snRNA-seq in Atlantic salmon, enhances understanding of teleost immune cell lineages, and provides a comprehensive list of markers for identifying major cell populations in the head kidney with significant immune relevance.2024-03-01T00:00:00Z