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Population genetics of the Manila clam (Ruditapes philippinarum) in East Asia.

ABSTRACT: The Manila clam Ruditapes philippinarum is the world's second most important bivalve mollusk commercially farmed, whose indigenous populations are mainly distributed in the coastal areas of East Asia. However, with the development of commercialization, mixture of populations and loss of local germplasm have become prominent problems. Here, genetic differentiation of seven Manila clam populations from East Asia was investigated through analyzing the polymorphism of the mitochondrial cytochrome C oxidase subunit I (COI) gene as well as 20 simple sequence repeat (SSR) molecular loci. In total, 40 haplotypes were identified, among which 31 were unique. Moreover, two main haplotypes were detected with several radiating derived haplotypes. Populations in Japan-North Korea shared haplotype Hap_31, and populations in China shared haplotype Hap_7, suggesting that the natural geographical isolation of the Yangtze River and the Yalu River might have divided the East Asian indigenous populations into three groups, which were located in South China, North China, and Japan-North Korea, respectively. The Aquaculture breeding activities from South to North in China might have promoted gene exchange among Manila clam populations. Population in Laizhou had the highest genetic diversity and therefore could be an excellent germplasm source.

SUBMITTER: Tan Y

PROVIDER: S-EPMC7736867 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Population genetics of the Manila clam (Ruditapes philippinarum) introduced in North America and Europe.

Project description:Globally, the Manila clam (Ruditapes philippinarum) stands as the second most important bivalve species in fisheries and aquaculture. Native to the Pacific coast of Asia, it is now well-established in North America and Europe, where its on-going management reflects local economic interests. The historic record of transfers spans the 20th century and suggests sequential movement from Japan to North America, as a hitch-hiker on oysters, and then intentional introduction in Europe, but global genetic data are missing. We have studied mitochondrial DNA and microsatellite markers in nine populations from Asia, North America and Europe. The results from the two types of markers indicated a good concordance of present-day genetic structure with the reported history of clam transfers across continents, and no evidence of relevant concealed introductions from continental Asia in Europe and North America. However, European populations showed a loss of genetic variability and significant genetic differentiation as compared to their American counterparts. Our study shows that in spite of the increasing ease for species to spread out of their native range, in the case of the Manila clam this has not resulted in new invasion waves in the two studied continents.

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The Whole-Genome and Transcriptome of the Manila Clam (Ruditapes philippinarum).

Project description:The manila clam, Ruditapes philippinarum, is an important bivalve species in worldwide aquaculture including Korea. The aquaculture production of R. philippinarum is under threat from diverse environmental factors including viruses, microorganisms, parasites, and water conditions with subsequently declining production. In spite of its importance as a marine resource, the reference genome of R. philippinarum for comprehensive genetic studies is largely unexplored. Here, we report the de novo whole-genome and transcriptome assembly of R. philippinarum across three different tissues (foot, gill, and adductor muscle), and provide the basic data for advanced studies in selective breeding and disease control in order to obtain successful aquaculture systems. An approximately 2.56 Gb high quality whole-genome was assembled with various library construction methods. A total of 108,034 protein coding gene models were predicted and repetitive elements including simple sequence repeats and noncoding RNAs were identified to further understanding of the genetic background of R. philippinarum for genomics-assisted breeding. Comparative analysis with the bivalve marine invertebrates uncover that the gene family related to complement C1q was enriched. Furthermore, we performed transcriptome analysis with three different tissues in order to support genome annotation and then identified 41,275 transcripts which were annotated. The R. philippinarum genome resource will markedly advance a wide range of potential genetic studies, a reference genome for comparative analysis of bivalve species and unraveling mechanisms of biological processes in molluscs. We believe that the R. philippinarum genome will serve as an initial platform for breeding better-quality clams using a genomic approach.

| S-EPMC5499747 | biostudies-literature

Filtration rates of the manila clam, Ruditapes philippinarum, in tidal flats with different hydrographic regimes.

Project description:The manila clam Ruditapes philippinarum is widely distributed in the sandy mud sediments of tidal flats and plays a role in seawater purification by filtering suspended organic matter. This study was designed to evaluate differences in seawater purification based on the filtration rate of the manila clam in terms of particulate organic matter (POM) between two tidal flats with different hydrographic regimes. In situ experiments were carried out at Geunso and Sihwa tidal flats, along the west coast of Korea. The amount of POM removed from the water column by the feeding activity of the clam was measured in the field using a closed circulation chamber. The filtration rate of clams for POM at Sihwa tidal flat (2.86 for POC, 2.29 for PON and 5.46 L h-1 gDW-1 for Chl a) was higher than that at Geunso tidal flat (0.61 for POC, 0.89 for PON and 2.54 L h-1 gDW-1 for Chl a) which resulted from differences in the hydrographic regime, including tide characteristics, current speed and submergence time, and food quantity and quality. The current speed was much greater at Geunso tidal flat than at Sihwa tidal flat, but the submergence time by tide was longer at the latter site than the former, resulting in different feeding times for clams. The food quantity in terms of chlorophyll a was higher at Sihwa tidal flat than at Geunso tidal flat, and the food quality based on the C/N ratio of POM was better at the former site than the latter, with values of 12.8 and 15.6, respectively. These findings suggest that hydrographic regime could be important in understanding in situ filtration rates of R. philippinarum.

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Effects of hypoxia on survival, behavior, metabolism and cellular damage of Manila clam (Ruditapes philippinarum).

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Ruditapes philippinarum cultivar:manila clam

Project description:Ruditapes philippinarum cultivar:manila clam Raw sequence reads

| PRJNA579230 | ENA

Exploring the Dynamic of Bacterial Communities in Manila Clam (<i>Ruditapes philippinarum</i>) During Refrigerated Storage.

Project description:Microorganism contamination is one of the most important factors affecting the spoilage and food safety of Manila clams. This study aimed to gain insights into bacterial composition and the dynamic change of bacterial communities on retailed Manila clam during refrigerated storage within the edible period. High-throughput sequencing was conducted to monitor the bacterial population with the prolongation of storage time of Day 0, Day 1, and Day 3. Result demonstrated that phyla of Proteobacteria, Actinobacteriota, Acidobacteriota, and Chloroflexi composed the majority of bacterial communities during the whole observation process. Furthermore, the increase of Proteobacteria showed a positive correlation with the storage time, whereas Acidobacteriota and Chloroflexi continued to decline in storage. For genus annotation, none of genus obtained dominant population in storage. From Day 0 to Day 1, the genera of Streptomyces, Bradyrhizobium, and Mycobacterium significantly increased; meanwhile, 12 genera significantly decreased. Compared with samples at Day 0, a total of 15 genera significantly decreased with the reduced proportion ranging from 0.50 to 4.40% at Day 3. At the end of the storage, the genus Crossiella became the most redundant population. Both the richness and diversity decreased at the start of storage at Day 1, and then slightly increased at Day 3 was observed. Based on the result in this study, strategy targeting the increased bacteria could be tested to improve the consumption quality and safety of refrigerated clam.

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Transcriptome sequencing and microarray development for the Manila clam, Ruditapes philippinarum: genomic tools for environmental monitoring.

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Ruditapes philippinarum strain:wild population | cultivar:manila clam

Project description:Ruditapes philippinarum strain:wild population | cultivar:manila clam Raw sequence reads

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Project description:Ruditapes philippinarum strain:wild population | cultivar:manila clam Raw sequence reads

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