Biology subjects

Plough, L. V.

Publications and source records attributed to Plough, L. V..

4 recordsLinked to original sources

bioRxiv2026

Chromosome-level genome assembly of the Olympia oyster (Ostrea lurida), the only oyster species native to the West Coast of North America

The Olympia oyster (Ostrea lurida) was once a major food source and a key component of coastal marine ecosystems and culture on the US West Coast. Overfishing and habitat contamination in the early to mid-20th century severely depleted populations of Olympia oysters, and the species is currently considered a species of concern. Although multiple restoration efforts are underway, progress understanding the species biology and recovery potential has been limited by the historical lack of genomic resources. Here, we report a chromosome-level assembly of the Olympia oyster. The assembly was built using Oxford Nanopore reads and Hi-C to obtain a highly contiguous 1.03 Gb-assembly consisting of 10 chromosomes. RNA from gills, mantle, adductor muscle, and a mix of brooding eggs and larvae were also sequenced as 150 nt long paired-end reads which were used to guide the genome annotation. Over 52 K genes were predicted in the genome, of which 34K were protein-coding. A BUSCO analysis on the assembly showed 98.9% of the mollusca_odb12 gene set were complete (with 2.1% duplicated, and 0.8% missing). The short RNA reads were also used to identify tissue-level gene expression signatures in adductor muscles, egg and brooding larvae, and mantle. Development-related genes were highly expressed in eggs and brooding larvae whereas many xenobiotic metabolism genes were present in mantle tissues, highlighting mantles role in the interaction of the oyster with external environments. This new genomic resource will greatly advance our understanding of this keystone mollusk and provide a critical tool for guiding restoration efforts and the development of sustainable commercial production.

genomics↗

bioRxiv2022

Linking mesozooplankton and SAR11 bacteria in Oxygen Deficient Zones and the open ocean

The gravitational biological pump is not large enough to account for microbial heterotrophic activity in the mesopelagic ocean. Migrating zooplankton may be a key source of organic matter transport to depth. Here we show signatures of zooplankton in the suspended organic matter at the zooplankton vertical migration depth in the Eastern Tropical North Pacific Oxygen Deficient Zone (ETNP ODZ). We examine the mesozooplankton community in metagenomic depth profiles using the mitochondrial cytochrome c oxidase (COI) gene as a marker in the ETNP and Eastern Tropical South Pacific (ETSP) ODZs and at the oxic Hawaii Ocean Timeseries (HOT). Additionally, eukaryotic transcripts (polyA-selected) were examined for zooplankton in the ETNP. While zooplankton eDNA increased in the ODZ, zooplankton eRNA decreased in the ODZ, similar to previous net-based data, implying that eDNA is better preserved under anoxia. At all stations, Cnidaria, often missed in net-based data, contributed greatly to the zooplankton eDNA/eRNA. SAR11 abundance, determined from the single-copy core gene (rpoB), significantly correlated with zooplankton eDNA, with R2 values >0.8 at all stations. Strong correlations between SAR11 and zooplankton have not been previously reported, but are logical as SAR11 bacteria consume and zooplankton excrete simple dissolved organic compounds. SAR11 bacteria possessed genes to utilize urea and taurine in the ODZ, both compounds known to be excreted by zooplankton. In ODZs, SAR11 bacteria preferentially used the taurine degradation pathway leading to C and N assimilation, not the pathway for organic S assimilation, probably due to additional sources of organic S in ODZs.

microbiology↗

bioRxiv2020

Are bivalves susceptible to domestication selection? Using starvation tolerance to test for potential trait changes in eastern oyster larvae

Conservation efforts are increasingly being challenged by a rapidly changing environment, and for some aquatic species the use of captive rearing or selective breeding is an attractive option. However, captivity itself can impose unintended artificial selection known as domestication selection (adaptation to culture conditions). For most marine species, it is not known to what degree domestication selection affects traits related to fitness in the wild. To test for domestication selection in a marine bivalve, we focused on a fitness-related trait (larval starvation resistance) that could be altered under artificial selection. Using larvae produced from a wild population of Crassostrea virginica and a selectively bred, disease-resistant line we measured growth and survival during starvation versus standard algal diet (control) conditions. Larvae from both lineages showed a remarkable resilience to food limitation, possibly mediated by an ability to uptake and utilize dissolved organic matter for somatic maintenance. Water chemistry analysis showed dissolved organic carbon in filtered tank water to be at concentrations similar to natural river water. We observed that survival in larvae produced from the aquaculture line was significantly lower compared to larvae produced from wild broodstock (8 {+/-} 3% and 21 {+/-} 2%, respectively) near the end of a 10-day period with no food (phytoplankton). All larval cohorts had arrested growth during the starvation period and took at least two days to recover once food was reintroduced before resuming growth. Phenotypic differences between the wild and aquaculture lines suggest potential differences in the capacity to sustain extended food limitation, but this work requires replication with multiple selection lines and wild populations to make more general inferences about domestication selection. With this contribution we explore the potential for domestication selection in bivalves, discuss the physiological and fitness implications of reduced starvation tolerance, and aim to inspire further research on the topic.

evolutionary biology↗

bioRxiv2016

Fine-scale temporal analysis of genotype-dependent mortality at settlement in the Pacific oyster Crassostrea gigas

Settlement and metamorphosis mark a critical transition in the life cycle of marine invertebrates, during which larvae undergo substantial morphological, sensory, and genetic changes. High mortality during or after metamorphosis is commonly observed in both wild and hatchery settings, however, the underlying causes of this mortality remain poorly understood. Previous pair-crossing experiments with the Pacific oyster, Crassostrea gigas showed that substantial genotype-dependent mortality (GDM) occurs around metamorphosis, but, owing to sparse temporal sampling, it remains unknown whether mortality occurs just before, during, or after settlement. In this laboratory study, microsatellite marker segregation ratios were followed daily throughout the settlement and metamorphosis of an inbred, F2 cross of the Pacific oyster to examine the fine-scale patterns of GDM in larvae and spat. Genetic control of settlement timing was also examined using a quantitative trait locus (QTL) mapping approach. Settlement occurred over nine days (day 18 to day 27 post-fertilization) with 68% of individuals settling on an early (day 19) and a late (day 24) time point. Tracking the survival of spat for 40 days after initial settlement revealed almost no post-settlement mortality. Temporal analysis revealed that three of 11 loci exhibited segregation distortion at metamorphosis, one of which (Cg205) was followed throughout settlement. Alternative temporal patterns of selection against each homozygote at Cg205 suggest possible defects in both the competency pathway (inability to initiate metamorphosis) and the morphogenesis pathway (mortality during the metamorphic transition). QTL mapping of settlement timing identified three individual and one epistatic QTL (29% of the variance explained), however, two of these loci were closely linked to markers exhibiting GDM at metamorphosis, thus making it difficult to distinguish between genetic variance in settlement timing and differential mortality early or late in settlement. Overall, results from this study highlight the complex temporal patterns of viability selection during metamorphosis and show that endogenous mortality during the larval-juvenile transition appears to be focused during or just prior to metamorphosis. Fine-scale experimental analysis of settlement can reveal important genetic insights into larval settlement behavior and the sources of larval mortality, and future studies should be able to further dissect the functional targets of selection during metamorphosis.

genetics↗