Pacific Geoduck Panopea Generosa Research Articles

Chromosome-level genome assembly of the Pacific geoduck Panopea generosa reveals major inter- and intrachromosomal rearrangements and substantial expansion of the copine gene family.

The Pacific geoduck Panopea generosa (class Bivalvia, order Adapedonta, family Hiatellidae, genus Panopea) is the largest known burrowing bivalve with considerable commercial value. Pacific geoduck and other geoduck clams play important roles in maintaining ecosystem health for their filter feeding habit and coupling pelagic and benthic processes. Here, we report a high-quality chromosome-level genome assembly of P. generosa to characterize its phylogeny and molecular mechanisms of its life strategies. The assembled P. generosa genome consists of 19 chromosomes with a size of 1.47 Gb, a contig N50 length of 1.6 Mb, and a scaffold N50 length of 73.8 Mb. The BUSCO test of the genome assembly showed 93.0% completeness. Constructed chromosome synteny revealed many occurrences of inter- and intrachromosomal rearrangements between P. generosa and Sinonovacula constricta. Of the 35,034 predicted protein-coding genes, 30,700 (87.6%) could be functionally annotated in public databases, indicating the high quality of genome annotation. Comparison of gene copy numbers of gene families among P. generosa and 11 selected species identified 507 rapidly expanded P. generosa gene families that are functionally enriched in immune and gonad development and may be involved in its complex survival strategies. In particular, genes carrying the copine domains underwent additional duplications in P. generosa, which might be important for neuronal development and immune response. The availability of a fully annotated chromosome-level genome provides a valuable dataset for genetic breeding of P. generosa.

Acclimatory gene expression of primed clams enhances robustness to elevated pCO2.

Sublethal exposure to environmental challenges may enhance ability to cope with chronic or repeated change, a process known as priming. In a previous study, pre-exposure to seawater enriched with pCO2 improved growth and reduced antioxidant capacity of juvenile Pacific geoduck Panopea generosa clams, suggesting that transcriptional shifts may drive phenotypic modifications post-priming. To this end, juvenile clams were sampled and TagSeq gene expression data were analysed after (i) a 110-day acclimation under ambient (921 μatm, naïve) and moderately elevated pCO2 (2870 μatm, pre-exposed); then following (ii) a second 7-day exposure to three pCO2 treatments (ambient: 754 μatm; moderately elevated: 2750μatm; severely elevated: 4940 μatm), a 7-day return to ambient pCO2 and a third 7-day exposure to two pCO2 treatments (ambient: 967 μatm; moderately elevated: 3030 μatm). Pre-exposed geoducks frontloaded genes for stress and apoptosis/innate immune response, homeostatic processes, protein degradation and transcriptional modifiers. Pre-exposed geoducks were also responsive to subsequent encounters, with gene sets enriched for mitochondrial recycling and immune defence under elevated pCO2 and energy metabolism and biosynthesis under ambient recovery. In contrast, gene sets with higher expression in naïve clams were enriched for fatty-acid degradation and glutathione components, suggesting naïve clams could be depleting endogenous fuels, with unsustainable energetic requirements if changes in carbonate chemistry persist. Collectively, our transcriptomic data indicate that pCO2 priming during post-larval periods could, via gene expression regulation, enhance robustness in bivalves to environmental change. Such priming approaches may be beneficial for aquaculture, as seafood demand intensifies concurrent with increasing climate change in marine systems.

Metabolic recovery and compensatory shell growth of juvenile Pacific geoduck Panopea generosa following short-term exposure to acidified seawater.

While acute stressors can be detrimental, environmental stress conditioning can improve performance. To test the hypothesis that physiological status is altered by stress conditioning, we subjected juvenile Pacific geoduck, Panopea generosa, to repeated exposures of elevated pCO2 in a commercial hatchery setting followed by a period in ambient common garden. Respiration rate and shell length were measured for juvenile geoduck periodically throughout short-term repeated reciprocal exposure periods in ambient (~550 μatm) or elevated (~2400 μatm) pCO2 treatments and in common, ambient conditions, 5 months after exposure. Short-term exposure periods comprised an initial 10-day exposure followed by 14 days in ambient before a secondary 6-day reciprocal exposure. The initial exposure to elevated pCO2 significantly reduced respiration rate by 25% relative to ambient conditions, but no effect on shell growth was detected. Following 14 days in common garden, ambient conditions, reciprocal exposure to elevated or ambient pCO2 did not alter juvenile respiration rates, indicating ability for metabolic recovery under subsequent conditions. Shell growth was negatively affected during the reciprocal treatment in both exposure histories; however, clams exposed to the initial elevated pCO2 showed compensatory growth with 5.8% greater shell length (on average between the two secondary exposures) after 5 months in ambient conditions. Additionally, clams exposed to the secondary elevated pCO2 showed 52.4% increase in respiration rate after 5 months in ambient conditions. Early exposure to low pH appears to trigger carryover effects suggesting bioenergetic re-allocation facilitates growth compensation. Life stage-specific exposures to stress can determine when it may be especially detrimental, or advantageous, to apply stress conditioning for commercial production of this long-lived burrowing clam.

Geographic Variation in the Life History and Morphology of the Pacific Geoduck Panopea generosa

Evaluating the spatial scale of biological variation in marine species aids understanding of the ways in which environmental selection pressures can shape life histories, population demography, and morphological traits. The Pacific geoduck Panopea generosa is an ideal candidate to investigate patterns of life history variation and morphological plasticity, as the species occurs over a large geographic range, inhabits different marine environments, and experiences intense fishing pressure in some locations. Six populations were sampled from Washington to Baja California (Mexico), from a mix of subtidal and intertidal habitats, to evaluate evidence for geographic variation in demography, life history, and shell morphology. Results provided evidence for a latitudinal cline with larger clams occurring in locations characterized by colder water temperature. Von Bertalanffy growth model analyses revealed significant spatial variation in asymptotic lengths across sampling locations. Correlations between environmental variables (sea surface temperatures and chlorophyll a) and growth parameters indicated that clams reached larger sizes at locations that were cooler and had higher primary productivity. Age structure and longevity analyses demonstrated that life expectancy was significantly lower at intertidal sites than at subtidal sites, potentially in response to increased fishing pressure at sites more easily accessed by humans at low tide. Morphological analyses (i.e., geometric morphometrics) revealed significant spatial differences in shell shape that did not follow a latitudinal pattern, but may be better explained by site-specific differences in sediment characteristics or other selective pressures in the environment. In a management context, these results may inform efforts to develop spatially explicit regulations for the Pacific geoduck fishery. Finally, this study provides a general framework for evaluating demographic variability in shellfish populations across large spatial scales.

First Description of Symbionts, Parasites, and Diseases of the Pacific GeoduckPanopea generosafrom the Pacific Coast of Baja California, Mexico

The Pacific geoduck Panopea generosa is distributed along the Pacific coast of the peninsula of Baja California, Mexico. Because of its high market value, this species has been under an intensive fishery pressure during the last few years, whereas its experimental aquaculture production is still developing. The fishery and culture practices point to the movement of clams as a risk factor for dispersion of symbionts, parasites, and diseases. Wild geoduck clams from fishery captures are sent to facilities that maintain clams alive, before marketing. Some of them show external abnormalities such as weakness and flaccidity, blisters, and darkening and thickening of the mantle surface and siphon. The objective of this study was to determinate if these abnormalities were related to parasites or diseases through conventional parasitological and histological analyses. The parasitological analysis showed two species of copepods, Pseudomyicola spinosus and a calanoid species in the mantle cavity and gills; additionally, a turbellarian species was also observed in the mantle cavity, none of these symbionts were related to tissue damage. The histological analysis showed that some weak-flaccid clams were in a postspawning condition. The dark and thick areas of the siphon and mantle suffered a dramatic transformation of the periostracum into a cavernous structure with numerous protozoans in different developmental stages. Fungi were occasionally observed in the external area of the periostracum. Unusual mortalities were reported by producers in clams with this abnormality. Rickettsia-like inclusions and trematodes were found in the digestive gland associated with limited damage to the host. The darkening and thickening of the siphon represent a major issue because of the negative appearance of the clams, which prevents its sale and is possibly related to the unusual mortality episodes. Detailed field and laboratory studies are needed to determine the origin of this pathology as well as its distribution and effect on the survival of the host. Moreover, field studies on the distribution, prevalence, and intensity of the other symbionts and parasites here detected are needed. These data constitute the first record for organisms associated with P. generosa in Mexico and a baseline for future studies.

Assessing Potential Benthic Impacts of Harvesting the Pacific Geoduck ClamPanopea generosain Intertidal and Subtidal Sites in British Columbia, Canada

ABSTRACT The Pacific geoduck Panopea generosa is the largest burrowing clam in the world and adults can live up to a meter below the sediment surface. To extract these clams, harvesters use pressurized water jets to dislodge surrounding sediments. This type of disturbance could have significant effects on the local benthic environment, but has been little examined. The present study was conducted on one intertidal and one subtidal plot to assess potential effects of commercial-scale geoduck harvesting on the sedimentary benthic environment and nearby eelgrass beds. Sediment samples were collected inside the impacted plots and at intervals up to 75 m away while eelgrass sampleswere collected adjacent to the impacted plots and at intervals up to 50maway, seasonally over 2 y.Harvest of the subtidal plot occurred at one year and mock harvest of the intertidal plot occurred after one preimpact sample. Sediment and infaunal qualities examined included: grain size, percent organics, total nitrogen, total organic...

GeoduckPanopea generosaGrowth at Its Southern Distribution Limit in North America using a Multimodel Inference Approach

The Pacific geoduck Panopea generosa is distributed throughout the North Pacific temperate zone from Alaska to Baja California and is described as a species that reaches large sizes, has prolonged longevity, and exhibits slow growth. This study assessed the individual growth and population structure of the P. generosa population located at its southernmost geographic distribution limit. Shell length and total weight data were obtained from a commercial fishery established on Punta Canoas, Baja California. Individual age was determined by counting growth lines for 243 organisms. The results revealed the following averages: shell length (SL), 113.5 mm; total weight, 511.8 g; age, 12.5 y. The relationship of SL to total weight showed negative allometric growth (b = 2.16). Size-at-age data were adjusted to von Bertalanffy, Gompertz, logistic, Johnson, and Schnute growth models according to the multimodel inference (MMI) approach. The best candidate growth model was selected based on the Akaike information criterion (AIC) and the Schwartz—Bayesian criterion (SBC). The AIC indicated that the Schnute growth model was the best candidate growth model, whereas the SBC showed the Johnson growth model was best. These growth models indicate that between 7 y and 8 y of age, organisms reach 75% of their estimated asymptotic length (SL, ∼103 mm), and although the growth rate decreases subsequently, growth continues up to 25 y (maximum age observed). The MMI approach applied to the analysis of growth in Panopea species identified particular population attributes that are not observable via the von Bertalanffy model. The population of P. generosa from Punta Canoas exhibited smaller mean SL, lower mean weight, an age structure with fewer age classes, and slower growth when compared with northern populations in Washington state and British Columbia, Canada.

Temperature and Food-Ration Optimization in the Hatchery Culture of Juveniles of the Pacific GeoduckPanopea generosa

This research examined the individual effects of temperature and ration on growth and survival of juveniles of the Pacific geoduck Panopea generosa Gould, 1850, in two separate experiments. Growth parameters measured included shell length, daily shell increment, individual total body wet weight, specific growth rate, individual total body dry weight, and total body ash-free dry weight (AFDW). Larvae in all treatments were fed a binary microalgal diet of Chaetoceros muelleri and Tisochrysis lutea mixed at a 1:1 ratio by AFDW. The temperature experiment examined the effect of four temperatures (7°C, 11°C, 15°C, and 19°C) using two geoduck cohorts. One cohort was comprised of larger juveniles (mean initial shell length ± SE, 3.22 ± 0.05 mm) and the other included smaller individuals (0.54 ± 0.01 mm) which were cultured for 28 days and 21 days, respectively. Using a separate cohort, the foodration experiment examined the effect of nine rations (0.0, 1.0, 2.0, 4.0, 8.0, 16.0, 32.0, 64.0, and 128.0 × 106 equivalent T. lutea cells per individual per day) on four size classes of geoduck juveniles obtained from the same spawning batch (mean initial shell length ± SE, size class 1,2.34 ± 0.04 mm; size class 2, 3.32 ± 0.04 mm; size class 3,4.13 ± 0.04 mm; and size class 4, 4.98 ± 0.04 mm) for 7 days. On the final sampling day, there were significant differences among all four temperatures for all growth parameters except AFDW, with each parameter increasing significantly for each increase in temperature. For AFDW, there were no significant differences between 7°C and 19°C, nor between 11°C and 15°C, with the first set of two temperatures producing juveniles with significantly less AFDW than the latter set. In general, optimal ration levels increased with increasing geoduck size. To optimize growth in shell length, individual total body wet weight, and/or individual total body dry weight, the following rations are recommended for size classes 1, 2, 3, and 4, respectively: 4.0 or 8.0, 8.0, 16.0 or 32.0, and 32.0 or 64.0 × 106 equivalent T. lutea cells per individual per day. Refinement of an understanding of optimum juvenile geoduck culture conditions contributes to the general knowledge of the species’ physiology and helps maximize the commercial hatchery production of geoduck seed.

The complete mitochondrial DNA of the Pacific Geoduck clam (Panopea generosa)

The complete mitochondrial genome of the Pacific Geoduck Panopea generosa (Genbank accession KM580067) is 15,585 bp in size and contains the typical 37 genes (13 protein-coding, 2 ribosomal RNA and 22 transfer RNA) found in metazoan mitogenomes, including the rare ATPase subunit 8 gene (ATP8). All genes are coded in the same strand but the gene arrangement is novel among heterodont bivalves. The base composition was: A 25.0%, T 38.7%, C 11.2% and G 25.0%. The genome is structurally similar to that of its congener the Cortes Geoduck Panopea globosa.