Biology subjects

Bean, T. P.

Publications and source records attributed to Bean, T. P..

13 recordsLinked to original sources

bioRxiv2026

A Single-Nucleus Transcriptomic Atlas Reveals Cell-Type-Specific Responses to OsHV-1 Infection in the Pacific Oyster

BackgroundThe Pacific oyster (Crassostrea/Magallana gigas) is increasingly recognised as a model marine invertebrate. Valued for both ecological and commercial importance, Pacific oysters are farmed widely, supporting global food security by providing a sustainable nutrient-rich source of protein. Despite the significant and recurring economic losses caused by Ostreid herpesvirus (OsHV-1) outbreaks, only a limited number of studies have examined host-pathogen interplay at single-cell resolution. The few available studies largely focus on circulating immune cells (haemocytes), thereby overlooking the complexity of host responses across different tissues and organs. ResultsWe present a detailed single-nucleus transcriptomic atlas of the whole Pacific oysters, including during OsHV-1 infection. A total of 18 distinct transcriptomic clusters were resolved, capturing major cell populations from the gill, mantle, hepatopancreas, adductor muscle, and haemocytes. Notably, three populations- gill ciliary cells, hepatopancreas cells, and an immune-enriched cluster 1- exhibited pronounced transcriptomic responses to OsHV-1 infection. Across the 6, 24, 72, and 96 hours post-infection (hpi) time course, viral transcripts were detected almost exclusively at 72 hpi, with enrichment primarily in adductor muscle cells and two immune cell populations- immature haemocytes, and hyalinocytes. ConclusionsOur findings suggest potential entry portals and tissue-specific replication sites for the OsHV-1 virus in Pacific oysters. This atlas resource provides a high-resolution cellular framework for understanding host-virus interactions and establishes a foundation for future investigations into herpesvirus pathogenesis in marine invertebrates.

genomics↗

bioRxiv2025

Transcriptomic study of WSSV infection in Litopenaeus vannamei lymphoid organ via single nuclei RNA sequencing

BackgroundAquaculture is the fastest growing farmed food sector and is a key part of global food security. Crustacean aquaculture, while being one of the most profitable sectors, is threatened by pathogenic diseases such as white spot disease (WSD), which results in severe stock losses and threatens animal health and welfare. In this study, we used novel techniques to study the impact of white spot syndrome virus (WSSV), the causative agent of WSD, on Pacific whiteleg shrimp (Litopenaeus vannamei), and uncover additional information that may be used in creating WSSV-resistant shrimp stocks. ResultsWe successfully developed a novel nuclei isolation protocol optimized for shrimp tissues to prepare our samples for single nuclei RNA-sequencing following a pathogen challenge comprising of 32 adult whiteleg shrimp infected with WSSV either through their feed or by injection. We constructed the first penaeid shrimp lymphoid organ cell atlas to improve our understanding of the characteristics of this immune organ, constructed the UMAPs and identified marker genes that define distinct cell clusters to reveal the biological functions of different cell types within this organ. ConclusionBy comparing gene expression between the control and WSSV-infected samples we uncovered multiple genes of interest that that have the potential to be used as targets for CRISPR gene editing for WSSV-resistance in Pacific whiteleg shrimp. These genes have the potential to be valuable assets for future gene editing studies in commercially important penaeid shrimp species. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/693182v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1be071org.highwire.dtl.DTLVardef@2c3da6org.highwire.dtl.DTLVardef@835e67org.highwire.dtl.DTLVardef@aacff1_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2025

Gene editing without a genome: generation and validation of F0 CRISPR mutants in gastropod mollusc Crepidula fornicata

BackgroundCRISPR-Cas9 gene editing is a powerful tool to study gene function but to date is mostly applied in traditional model organisms. Due to specific challenges in spiralian genomics such as genome size, complexity, proportion of repetitive regions and high inter individual genome variation, applications of CRISPR-Cas9 in spiralian models have been limited. Within the Spiralia, molluscs are a strikingly diverse phylum with many unique gene family expansions and novelties, yet there are relatively few applications of CRISPR-Cas9 to unravel gene function. ResultsWe generated pax6 knockout F0 CRISPR-Cas9 mutants in the gastropod mollusc Crepidula fornicata using a de novo transcriptome to design single guide RNAs and genotyping primers. In lieu of an assembled genome, alignments with closely related species were used to determine putative intron-exon boundaries and successfully target gene editing to a specific exon of pax6 containing a homeodomain. F0 pax6 knockout mutants had an eye-loss phenotype. Successful CRISPR-Cas9 gene editing was confirmed genotypically using Sanger sequencing and Interference of CRISPR Edits (ICE) analysis. ConclusionsThe generation of F0 CRISPR-Cas9 knockout mutants with a clear phenotype in a mollusc without an assembled genome enhances the applicability of CRISPR for functional genomics in non-traditional emerging model systems. pax6 is highly conserved and is required for eye development across metazoans, including the snail C. fornicata. The pax6 mutants developed in this study suggests the pax6 homeodomain is specifically required for eye formation in gastropods and sheds light on the evolution of eye development in animals.

developmental biology↗

bioRxiv2025

Development of long-term oyster tissue cultures reveals cellular plasticity, regenerative potential, and sustained physiological activity

Molluscs are ecologically and economically significant, yet progress in understanding their cellular biology has been constrained by the lack of reliable molluscan cell culture systems. Insights into key molluscan biology such as immunity, biomineralization, and host-pathogen interactions, has previously been limited by short term survival of primary culture systems. Here, we establish reproducible long-term in vitro and ex vivo cultures of cells and tissues from the oyster, Ostrea edulis, including whole heart, visceral mass, mantle, and gill explants. Explanted tissues remained viable for over two months, with whole hearts maintaining rhythmic, stimulus-responsive contractions for up to nine months. Cultures maintained structural and functional features while uncovering cellular plasticity, including haemocyte granule turnover, auricular epithelial remodelling with novel ciliation, and the emergence of de novo multicellular microtissues. Previously under-characterized tissue-specific cell types were maintained in culture, including adipocytes from the visceral mass and myocytes from the mantle, thereby expanding the cellular repertoire accessible in vitro. Mineralized structures were observed across tissue cultures, highlighting the potential of this system for studying biomineralization. By sustaining diverse cell types in vitro, these cultures provide a novel tractable platform for studying molluscan diseases, while also laying the foundation for deeper investigation into comparative invertebrate biology and the development of immortalised molluscan cell lines.

cell biology↗

bioRxiv2025

A high-quality reference genome and tissue expression atlas for the European lobster (Homarus gammarus)

The European lobster (Homarus gammarus) and its sister species, the American lobster (Homarus americanus), are notable for their remarkable immunity and longevity, with lifespans reaching up to 80 years in the wild. A reference genome is available for the American lobster, but not yet for the European lobster, despite its ecological significance, and importance to fisheries and aquaculture. Here, we present a high-quality genome assembly and annotation for the European lobster. The assembly spans 1.76 Gb, with a scaffold N50 of 1.82 Mb and a BUSCO completeness of 97.6%. As observed in the American lobster, the total assembly span is substantially smaller than genome size estimates derived from flow cytometry, performed using independently sampled European lobsters (3.18 - 3.42 Gb). This discrepancy may reflect the highly repetitive nature of decapod genomes, with 51.8% of the H. gammarus assembly consisting of repetitive elements. Leveraging a comprehensive multi-tissue RNA-seq dataset, we annotated 23,223 protein-coding genes and characterised gene expression across ten tissues to generate a tissue-level gene expression atlas, available at www.LobsterGeneX.com. Using single-copy orthologs, we estimated a divergence time of 26 Mya (95% HPD 22 - 30 Mya) between H. gammarus and H. americanus, corresponding to the Oligocene-Miocene boundary. We also identified Homarus-specific gene duplications with roles in immunity and longevity, including telomere maintenance. The reported genomic resources can facilitate future research into lobster biology, support sustainable fisheries and aquaculture management practices, and enable investigations of the evolutionary mechanisms underlying basic biological processes, notably immunity and longevity in Homarid lobsters. Significance StatementThe European lobster (Homarus gammarus) and the American lobster (Homarus americanus) are large benthic decapod crustaceans with significant seafood value, known for their remarkable longevity, with typical lifespans of 30-55 years in the wild and maximum lifespans of up to 80 years. Lobsters grow, reproduce and regenerate limbs throughout their life, and there are very few reports of tumours or age-related diseases. We generated and herein share a high-quality genome assembly and annotation for the European lobster alongside a tissue expression atlas, LobsterGeneX, which enables the visualisation of gene expression profiles across ten tissue types. Based on the genetic information generated, we also provide an estimated time for the divergence between H. gammarus and H. americanus (26 Mya) and identify duplication events for genes related to immunity and longevity. The European lobster reference genome will facilitate further research for investigations into local adaptation in lobster populations, genomic mixing in Homarid hybrids, and identification of genes of interest in aquaculture, ageing, regeneration, disease and cancer resistance.

genomics↗

bioRxiv2024

Thermal selection shifts genetic diversity and performance in blue mussel juveniles

Mussels from the genus Mytilus, key inhabitants of the benthos, are important for the aquaculture industry and one of the most sustainable sources of animal protein available. Species within the Mytilus edulis complex (M. edulis, M. galloprovincialis and M. trossulus) are commonly found in temperate regions globally and can easily hybridise whenever their geographic distributions overlap. In the Baltic Sea, populations are formed by M. edulis and M. trossulus hybrids with low levels of M. galloprovincialis introgression. Given the economic and ecological relevance of mussels, this study aimed to investigate mechanisms through which their resilience towards global warming may be fast-tracked. For this, we developed two cohorts of juvenile mussels (i.e. recently settled animals) from the Baltic Sea (Kiel, Germany), one exposed to an extreme heat event early in life and one naive to this stressor. Both cohorts were then exposed to experimental temperatures at the proposed upper thermal limit for this population, 21{degrees}C to 26{degrees}C, with animal performance measured after 25 days. We then assessed the impacts of thermal stress on the genetic composition of each cohort by genotyping 50 individuals using the blue mussel 60K SNP-array. We observed a significant increase in M. edulis genotypes together with a decrease in M. trossulus in the S cohort in comparison with NS juveniles. We also found that exposure to high temperature has an effect on the performance of mussel cohorts, reducing dry tissue weight of the selected individuals. Results from this study provide relevant insights on how selection through thermal stress impacts performance and genetic composition of blue mussel juveniles, with key implications for understanding and managing mussel populations under future warming scenarios.

genomics↗

bioRxiv2024

Laboratory in vitro replication of Ostreid Herpes Virus (OsHV-1) using Pacific oyster tissue explants

Pacific oysters (Crassostrea or Magallana gigas) are one of the most economically important aquaculture species globally. Over the past two decades, ostreid herpesvirus (OsHV-1), has become a major pathogen of cultured Pacific oysters resulting in widespread mortality with a global distribution. Experimental use of OsHV-1 is challenging for many reasons, including both complexity and relative obscurity of host pathogen dynamics, and a lack of functioning model systems. The goal of this study was to improve the tools available for working with OsHV-1 in both whole animals and in tissue explants established ex vivo from oysters and maintained in controlled laboratory conditions. Tissue explants were taken from oysters originating from two different sources that have different levels of mortality in OsHV-1 challenges and were used in disease challenges alongside whole animals for comparison. Quantitative PCR, histology and electron microscopy were used to confirm that the explants were capable of replicating OsHV-1. Furthermore, the quantitative PCR results suggests that the source of the oysters was significant in determining the outcome of infection in the explants, supporting the validity of the explant model for OsHV-1 infection. This approach for studying OsHV-1 allows for the control of confounding factors in disease outcome that is not possible in whole animal challenges, providing a new tool for studying OsHV-1 in Pacific oysters.

microbiology↗

bioRxiv2023

Vibrio aestuarianus Clade A and Clade B isolates are associated with Pacific oyster (Crassostrea gigas) disease outbreaks across Ireland

2.Bacteria from the Vibrionaceae family have been implicated in mass mortalities of farmed Pacific oysters (Crassostrea gigas) in multiple countries, leading to substantial impairment for growth in the sector. In Ireland there has been concern that Vibrio have been involved in serious summer outbreaks. There is evidence that Vibrio aestuarianus is increasingly becoming the main pathogen of concern for the Pacific Oyster industry in Ireland. While bacteria belonging to the Vibrio splendidus clade are also detected frequently in mortality episodes, their role in the outbreaks of summer mortality are not well understood. To identify and characterise strains involved in these outbreaks, 43 Vibrio isolates were recovered from Pacific oyster summer mass mortality episodes in Ireland from 2008-2015 and these were whole genome sequenced. Among these, 25 were found to be V. aestuarianus (implicated in disease) and 18 V. splendidus sensu lato (role in disease undetermined). Two distinct clades of V. aestuarianus - Clade A and Clade B - were found that had previously been described as circulating within French oyster culture. The high degree of similarity between the Irish and French V. aestuarianus isolates points to translocation of the pathogen between Europes two major oyster producing countries, probably via trade in spat and other age classes. V. splendidus isolates were more diverse, but the data reveal a single clone of this species that has spread across oyster farms in Ireland. This underscores that Vibrio could be transmitted readily across oyster farms. The presence of V. aestuarianus Clades A and B in not only France but also Ireland adds weight to growing concern that this pathogen is spreading and impacting Pacific oyster production within Europe. 3. OutcomePacific oyster culture in Ireland has increasingly suffered from summer mass mortality events. Many of these mortalities in recent years have been associated with Vibrio aestuarianus; the role of another pathogen, Vibrio splendidus has, so far, remained inconclusive. Here we show that two clades of V. aestuarianus are circulating in Ireland, and that these are members of two clades that have previously caused extensive oyster die offs in France. Their discovery in Ireland is consistent with transport of infected oyster stock between the two countries. Although V. splendidus-like strains in Ireland were highly diverse, a small clonal group was detected that appears to have spread rapidly from a single source to disparate locations in Ireland. Combined, these findings highlight the appearance of a highly pathogenic Vibrio in Ireland, and the risk of transmission between interconnected oyster production industries in Europe. 4. Data summarySequences generated in this study were deposited on the NCBI. Accession number: PRJNA797364. Publicly accessed genomes are listed in Table S2. The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

microbiology↗

bioRxiv2022

A blue mussel chromosome-scale assembly and genomic resources for aquaculture, marine ecology and evolution

The blue mussel, Mytilus edulis is part of the Mytilus edulis species complex, encompassing at least three putative species: M. edulis, M. galloprovincialis and M. trossulus. These three species occur on both sides of the Atlantic and hybridize in nature, and both M. edulis and M. galloprovincialis are important aquaculture species. They are also invasive species in many parts of the world. Here, we present a chromosome-level assembly of Mytilus edulis. We used a combination of PacBio sequencing and Dovetails Omni-C technology to generate an assembly with 14 long scaffolds containing 94% of the predicted length of the M. edulis genome (1.6 out of 1.7 Gb). Assembly statistics were total length 1.65 Gb, N50 = 116 Mb, L50 = 7 and, L90 = 13. BUSCO analysis showed 92.55% eukaryote BUSCOs identified. AB-Initio annotation using RNA-seq from mantle, gills, muscle and foot predicted 47,128 genes. These gene models were combined with Isoseq validation resulting in 65,505 gene models and 129,708 isoforms. Using GBS and shotgun sequencing, we also sequenced 3 North American populations of Mytilus to characterize single-nucleotide as well as structural variance. This high-quality genome for M. edulis provides a platform to develop tools that can be used in breeding, molecular ecology and evolution to address questions of both commercial and environmental perspectives.

genomics↗

bioRxiv2022

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

The European flat oyster (Ostrea edulis L.) is a bivalve naturally distributed across Europe that was an integral part of human diets for centuries, until anthropogenic activities and disease outbreaks severely reduced wild populations. Despite a growing interest in genetic applications to support population management and aquaculture, a reference genome for this species is lacking to date. Here we report a chromosome-level assembly and annotation for the European Flat oyster genome, generated using Oxford Nanopore, Illumina, Dovetail OmniC proximity ligation and RNA sequencing. A contig assembly (N50: 2.38Mb) was scaffolded into the expected karyotype of 10 pseudo-chromosomes. The final assembly is 935.13 Mb, with a scaffold-N50 of 95.56 Mb, with a predicted repeat landscape dominated by unclassified elements specific to O. edulis. The assembly was verified for accuracy and completeness using multiple approaches, including a novel linkage map built with ddRAD-Seq technology, comprising 4,016 SNPs from four full-sib families (8 parents and 163 F1 offspring). Annotation of the genome integrating multi-tissue transcriptome data, comparative protein evidence and ab-initio gene prediction identified 35,699 protein-coding genes. Chromosome level synteny was demonstrated against multiple high-quality bivalve genome assemblies, including an O. edulis genome generated independently for a French O. edulis individual. Comparative genomics was used to characterize gene family expansions during Ostrea evolution that potentially facilitated adaptation. This new reference genome for European flat oyster will enable high-resolution genomics in support of conservation and aquaculture initiatives, and improves our understanding of bivalve genome evolution.

genomics↗

bioRxiv2022

Genome-wide association and genomic prediction of growth traits in the European flat oyster (Ostrea edulis)

The European flat oyster (Ostrea edulis) is a bivalve mollusc that was once widely distributed in Europe and represented an important food resource for humans for centuries. Populations of O. edulis experienced a severe decline across their biogeographic range mainly due to anthropogenic activities and disease outbreaks. To restore the economic and ecological benefits of European flat oyster populations, extensive protection and restoration efforts are in place within Europe. In line with the increasing interest in supporting restoration and oyster farming through the breeding of stocks with enhanced performance, the present study aimed to evaluate the potential of genomic selection for improving growth traits in a European flat oyster population obtained from successive mass-spawning events. Four growth-related traits were evaluated: total weight (TW), shell height (SH), shell width (SW) and shell length (SL). The heritability of the growth traits was moderate-low, with estimates of 0.45, 0.37, 0.22, and 0.32 for TW, SH, SW and SL, respectively. A genome-wide association analysis revealed a largely polygenic genetic architecture for the four growth traits, with two distinct QTLs detected on chromosome 4. To investigate whether genomic selection can be implemented in flat oyster breeding at a reduced cost, the utility of low-density SNP panels (down to 100 SNPs) was assessed. Genomic prediction accuracies using the full density panel were high (>0.83 for all traits). The evaluation of the effect of reducing the number of markers used to predict genomic breeding values revealed that similar selection accuracies could be achieved for all traits with 2K SNPs as for a full panel containing 4,577 SNPs. Only slight reductions in accuracies were observed at the lowest SNP density tested (i.e. 100 SNPs), likely due to a high relatedness between individuals being included in the training and validation sets during cross-validation. Overall, our results suggest that the genetic improvement of growth traits in oysters is feasible. Nevertheless, and although low-density SNP panels appear as a promising strategy for applying GS at a reduced cost, additional populations with different degrees of genetic relationship should be assessed to derive estimates of prediction accuracies to be expected in practical breeding programmes.

genetics↗

bioRxiv2020

A chromosome-level genome assembly for the Pacific oyster (Crassostrea gigas)

The Pacific oyster (Crassostrea gigas) is a marine bivalve species with vital roles in coastal ecosystems and aquaculture globally. While extensive genomic tools are available for C. gigas, highly contiguous reference genomes are required to support both fundamental and applied research. In the current study, high coverage long and short read sequence data generated on Pacific Biosciences and Illumina platforms from a single female individual specimen was used to generate an initial assembly, which was then scaffolded into 10 pseudo chromosomes using both Hi-C sequencing and a high density SNP linkage map. The final assembly has a scaffold N50 of 58.4 Mb and a contig N50 of 1.8 Mb, representing a step advance on the previously published C. gigas assembly. The new assembly was annotated using Pacific Biosciences Iso-Seq and Illumina RNA-Seq data, identifying 30K putative protein coding genes, with an average of 3.9 transcripts per gene. Annotation of putative repeat elements highlighted an inverse relationship with gene density, and identified putative centromeres of the metacentric chromosomes. An enrichment of Helitron rolling circle transponsable elements was observed, suggesting their potential role in shaping the evolution of the C. gigas genome. This new chromosome-level assembly will be an enabling resource for genetics and genomics studies to support fundamental insight into bivalve biology, as well as for genetic improvement of C. gigas in aquaculture breeding programmes.

genomics↗

bioRxiv2017

A genome-wide association study for host resistance to Ostreid Herpesvirus in Pacific oysters (Crassostrea gigas)

Ostreid herpesvirus (OsHV) can cause mass mortality events in Pacific oyster aquaculture. While various factors impact on the severity of outbreaks, it is clear that genetic resistance of the host is an important determinant of mortality levels. This raises the possibility of selective breeding strategies to improve the genetic resistance of farmed oyster stocks, thereby contributing to disease control. Traditional selective breeding can be augmented by use of genetic markers, either via marker-assisted or genomic selection. The aim of the current study was to investigate the genetic architecture of resistance to OsHV in Pacific oyster, to identify genomic regions containing putative resistance genes, and to inform the use of genomics to enhance efforts to breed for resistance. To achieve this, a population of ~1,000 juvenile oysters were experimentally challenged with a virulent form of OsHV, with samples taken from mortalities and survivors for genotyping and qPCR measurement of viral load. The samples were genotyped using a recently-developed SNP array, and the genotype data were used to reconstruct the pedigree. Using these pedigree and genotype data, the first high density linkage map was constructed for Pacific oyster, containing 20,353 SNPs mapped to the ten pairs of chromosomes. Genetic parameters for resistance to OsHV were estimated, indicating a significant but low heritability for the binary trait of survival and also for viral load measures (h2 0.12 - 0.25). A genome-wide association study highlighted a region of linkage group 6 containing a significant QTL affecting host resistance. These results are an important step towards identification of genes underlying resistance to OsHV in oyster, and a step towards applying genomic data to enhance selective breeding for disease resistance in oyster aquaculture.

genomics↗