Biology subjects

van Aerle, R.

Publications and source records attributed to van Aerle, R..

7 recordsLinked to original sources

bioRxiv2026

Inference of nodavirus zoonotic transmission networks from publicly available sequencing data

The potential for nodavirus zoonosis has been known for many decades. However, diseases associated with nodavirus infection in mammals has only been documented recently. Natural infection with nodaviruses have been observed in human handlers of aquatic animal tissues (covert mortality nodavirus), and in pigs (porcine nodavirus). Here, we infer the potential networks of transmission of these nodaviruses and explore their genetic diversity by mining publicly available datasets.

genomics↗

bioRxiv2025

Developmental priming increases copper-tolerance in a model fish species via epigenetic-and microbiome-mediated mechanisms

Pollution is a significant threat to aquatic ecosystems globally and, in order to survive, natural populations depend upon their ability to rapidly develop tolerance to chemical stressors. We examined whether early-life priming enhances life-long copper-tolerance in a model fish species via developmental plasticity. Stickleback (Gasterosteus aculeatus) embryos were pre-exposed to a low concentration of copper (10 {micro}g/L) during early development, reared in clean water for nine months alongside a control group, and then exposed to copper (0,10 and 20 {micro}g/L) for 96 h as adults. Priming markedly reduced evidence of copper-toxicity in adult gills at the transcriptional level (including reduced cellular stress response (CSR) and disruption of ion-homeostasis) and increased inducibility of the metal-binding protein, metallothionein. In parallel, we identified epigenetic and microbiome-mediated mechanisms likely contributing to this tolerance. Pre-exposure induced persistent DNA methylation changes, consistent with priming of CSR and ion-homeostasis pathways. We identified enhanced copper-tolerance in the gill microbiota of primed fish that likely also contributed to host tolerance. These findings provide critical evidence for developmental plasticity induced by chemical stressors in animals, highlight the importance of integrated microbiome and epigenetic responses, and enhance our understanding of how natural populations cope with pollution in their environment.

evolutionary 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↗

bioRxiv2025

Detection of Macrobrachium rosenbergii golda virus (MrGV) in giant river prawn larvae across Asia through NCBI sequence read archive (SRA) data mining

1Macrobrachium rosenbergii golda virus (MrGV) was first characterised in Macrobrachium rosenbergii larvae in 2020, associated with mass mortalities in multiple Southern Bangladesh prawn hatcheries. MrGV has since been detected in two metatranscriptomic datasets from M. rosenbergii in China and in relation to a larval mortality event in India. The major objective of this study was to further characterise the geographical spread of the virus by mining the NCBI Sequence Read Archive (SRA) database. Utilising a new database, Logan, generated from assembling each SRA dataset, and a custom Snakemake pipeline, we discovered MrGV sequence data in M. rosenbergii SRA datasets from China, Thailand, and India, and determined that presence and relative abundance of MrGV is mostly associated with the larval life stage of M. rosenbergii. These results provide insights into the current prevalence of MrGV globally, suggest the life stages of prawn that should be screened to prevent spread of the virus, and demonstrate how the Logan database can be used to inform epidemiological studies.

bioinformatics↗

bioRxiv2022

De novo assembly and annotation of the Patagonian toothfish (Dissostichus eleginoides) genome

Patagonian toothfish (Dissostichus eleginoides) is an economically and ecologically important fish species in the family Nototheniidae, found at depths between 70 and 2,500 meters on the southern shelves and slopes around the sub-Antarctic islands of the Southern Ocean. Genomic sequence data for this species is limited. Here, we report a high-quality assembly and annotation of the D. eleginoides genome, generated using a combination of Illumina, PacBio and Omni-C sequencing technologies. To aid the genome annotation, the transcriptome derived from a variety of toothfish tissues was also generated using both short and long read sequencing methods. The final genome assembly was 797.8 Mb with a N50 scaffold length of 3.5 Mb. Approximately 31.7% of the genome consisted of repetitive elements. A total of 35,543 putative protein-coding regions were identified, of which 50% have been functionally annotated. Transcriptomics analysis showed that approximately 64% of the predicted genes (22,617 genes) were found to be expressed in the tissues sampled. Comparative genomics analysis revealed that the anti-freeze glycoprotein (AFGP) locus of D. eleginoides does not contain any AFGP proteins compared to the same locus in the Antarctic toothfish (Dissostichus mawsoni). This is in agreement with previously published results looking at hybridization signals and confirms that Patagonian toothfish do not possess AFGP coding sequences in their genome. The high-quality genome assembly of the Patagonian toothfish will provide a valuable genetic resource for ecological and evolutionary studies on this and other closely related species.

genomics↗

bioRxiv2021

Social partner cooperativeness influences brain oxytocin transcription in Trinidadian guppies (Poecilia reticulata)

For non-kin cooperation to be maintained, individuals need to respond adaptively to the cooperative behaviour of their social partners. Currently, however, little is known about the biological responses of individuals to experiencing cooperation. Here, we quantify the neuroregulatory response of Trinidadian guppies (Poecilia reticulata) experiencing cooperation or defection by examining the transcriptional response of the oxytocin gene (oxt; also known as isotocin), which has been implicated in cooperative decision-making. We exposed wild-caught females to social environments where partners either cooperated or defected during predator inspection, or to a control (non-predator inspection) context, and quantified the relative transcription of the oxt gene. We tested an experimental group, originating from a site where individuals are under high predation threat and have previous experience of large aquatic predators (HP), and a control group, where individuals are under low predation threat and naive to large aquatic predators (LP). In HP, but not LP, fish brain mid-section oxt relative transcription varied depending on social partner behaviour. HP fish experiencing cooperation during predator inspection had lower oxt transcription than those experiencing defection. This effect was not present in the control population or in the control context, where the behaviour of social partners did not affect oxt transcription. Our findings provide insight into the neuromodulation underpinning behavioural responses to social experiences, and ultimately to the proximate mechanisms underlying social decision-making.

animal behavior and cognition↗

bioRxiv2020

A novel RNA virus, Macrobrachium rosenbergii Golda virus (MrGV), linked to mass mortalities of the larval giant freshwater prawn in Bangladesh

1Mass mortalities of the larval stage of the giant freshwater prawn, Macrobrachium rosenbergii, have been occurring in Bangladesh since 2011. Mortalities can reach 100% and have resulted in an 80% decline in the number of hatcheries actively producing M. rosenbergii. To investigate a causative agent for the mortalities, a disease challenge was carried out using infected material from a hatchery experiencing mortalities. Moribund larvae from the challenge were prepared for metatranscriptomic sequencing. De novo virus assembly revealed a 29 kb single-stranded positive-sense RNA virus with similarities in key protein motif sequences to yellow head virus (YHV), an RNA virus that causes mass mortalities in marine shrimp aquaculture, and other viruses in the Nidovirales order. Primers were designed against the novel virus and used to screen cDNA from larvae sampled from hatcheries in the South of Bangladesh from two consecutive years. Larvae from all hatcheries screened from both years were positive by PCR for the novel virus, including larvae from a hatchery that at the point of sampling appeared healthy, but later experienced mortalities. These screens suggest that the virus is widespread in M. rosenbergii hatchery culture in southern Bangladesh, and that early detection of the virus can be achieved by PCR. The hypothesised protein motifs of MrGV suggest that it is likely to be a new species within the Nidovirales order. Biosecurity measures should be taken in order to mitigate global spread through the movement of post-larvae within and between countries, which has previously been linked to other virus outbreaks in crustacean aquaculture.

molecular biology↗