Publisher Correction: Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Manila clam Ruditapes philippinarum.
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SUBMITTER: Nie H
PROVIDER: S-EPMC6081410 | biostudies-literature | 2018 Aug
REPOSITORIES: biostudies-literature
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Publisher Correction: Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Manila clam Ruditapes philippinarum.
Nie Hongtao H Yan Xiwu X Huo Zhongming Z Jiang Liwen L Chen Peng P Liu Hui H Ding Jianfeng J Yang Feng F
Scientific reports 20180807 1
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Project description:Genetic linkage maps are indispensable tools in a wide range of genetic and genomic research. With the advancement of genotyping-by-sequencing (GBS) methods, the construction of a high-density linkage maps has become achievable in marine organisms lacking sufficient genomic resources, such as mollusks. In this study, high-density linkage map was constructed for an ecologically and commercially important clam species, Ruditapes philippinarum. For the consensus linkage map, a total of 9658 markers spanning 1926.98?cM were mapped to 18 sex-averaged linkage groups, with an average marker distance of 0.42?cM. Based on the high-density linkage map, ten QTLs for growth-related traits and shell color were detected. The coverage and density of the current map are sufficient for us to effectively detect QTL for segregating traits, and two QTL positions were all coincident with the closest markers. This high-density genetic linkage map reveals basic genomic architecture and will be useful for comparative genomics research, genome assembly and genetic improvement of R. philippinarum and other bivalve molluscan species.
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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.
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Project description: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.
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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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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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Project description:The Manila clam Ruditapes philippinarum has become a common and dominant macrobenthic species in coastal areas of the northwestern Pacific and temperate waters of Europe; it is also a major cultured shellfish, with annual worldwide production exceeding 3.3 million tonnes. This species faces greater risk of exposure to hypoxia as eutrophication worsens throughout its coastal habitats; however, its tolerance to hypoxia remains unclear, and the toxicological indicators including LC50 and LT50 have not yet been assessed. Previous studies on the effects of hypoxia on marine benthos have focused largely on functional responses, such as metabolism and gene expression, leaving potential structural damage to the mitochondria or the cells unknown. In this study we assessed the effects of hypoxia on Manila clam in terms of survival, behavior, metabolism and cellular damage, using a newly designed automated hypoxia simulation device that features exceptional accuracy and good stability. The clams exhibited strong tolerance to hypoxia as the 20-day LC50 for dissolved oxygen (DO) was estimated to be 0.57 mg L-1, and the LT50 at 0.5 mg L-1 DO was 422 hours. Adaptations included fewer buried clams and a depressed metabolism, while the unexpected rise in the activities of key enzymes involved in glycolysis may indicate a diverse strategy of shellfish under hypoxia. Cellular damage was observed as collapse of the mitochondrial cristae and both cellular and mitochondrial vacuolization. This multi-level study complements and updates our knowledge of the effects of hypoxia on marine benthos, by improving our understanding of the potential for marine ecological transformation under hypoxic conditions and providing useful information for Manila clam farming.
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Project description:BACKGROUND: The Manila clam, Ruditapes philippinarum, is one of the major aquaculture species in the world and a potential sentinel organism for monitoring the status of marine ecosystems. However, genomic resources for R. philippinarum are still extremely limited. Global analysis of gene expression profiles is increasingly used to evaluate the biological effects of various environmental stressors on aquatic animals under either artificial conditions or in the wild. Here, we report on the development of a transcriptomic platform for global gene expression profiling in the Manila clam. RESULTS: A normalized cDNA library representing a mixture of adult tissues was sequenced using a ultra high-throughput sequencing technology (Roche 454). A database consisting of 32,606 unique transcripts was constructed, 9,747 (30%) of which could be annotated by similarity. An oligo-DNA microarray platform was designed and applied to profile gene expression of digestive gland and gills. Functional annotation of differentially expressed genes between different tissues was performed by enrichment analysis. Expression of Natural Antisense Transcripts (NAT) analysis was also performed and bi-directional transcription appears a common phenomenon in the R. philippinarum transcriptome. A preliminary study on clam samples collected in a highly polluted area of the Venice Lagoon demonstrated the applicability of genomic tools to environmental monitoring. CONCLUSIONS: The transcriptomic platform developed for the Manila clam confirmed the high level of reproducibility of current microarray technology. Next-generation sequencing provided a good representation of the clam transcriptome. Despite the known limitations in transcript annotation and sequence coverage for non model species, sufficient information was obtained to identify a large set of genes potentially involved in cellular response to environmental stress.
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Project description:Ruditapes philippinarum cultivar:manila clam Raw sequence reads
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Project description:BACKGROUND: The Manila clam (Ruditapes philippinarum) is a worldwide cultured bivalve species with important commercial value. Diseases affecting this species can result in large economic losses. Because knowledge of the molecular mechanisms of the immune response in bivalves, especially clams, is scarce and fragmentary, we sequenced RNA from immune-stimulated R. philippinarum hemocytes by 454-pyrosequencing to identify genes involved in their immune defense against infectious diseases. METHODOLOGY AND PRINCIPAL FINDINGS: High-throughput deep sequencing of R. philippinarum using 454 pyrosequencing technology yielded 974,976 high-quality reads with an average read length of 250 bp. The reads were assembled into 51,265 contigs and the 44.7% of the translated nucleotide sequences into protein were annotated successfully. The 35 most frequently found contigs included a large number of immune-related genes, and a more detailed analysis showed the presence of putative members of several immune pathways and processes like the apoptosis, the toll like signaling pathway and the complement cascade. We have found sequences from molecules never described in bivalves before, especially in the complement pathway where almost all the components are present. CONCLUSIONS: This study represents the first transcriptome analysis using 454-pyrosequencing conducted on R. philippinarum focused on its immune system. Our results will provide a rich source of data to discover and identify new genes, which will serve as a basis for microarray construction and the study of gene expression as well as for the identification of genetic markers. The discovery of new immune sequences was very productive and resulted in a large variety of contigs that may play a role in the defense mechanisms of Ruditapes philippinarum.
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Project description:Gymnophallid metacercariae found in the Manila clam Ruditapes philippinarum ('Banjirak' in Korean) from Gochang-gun, Jeollabuk-do, Korea were morphologically and molecularly confirmed to be Parvatrema duboisi (Dollfus, 1923) Bartoli, 1974. The metacercariae were morphologically characterized by having a large oral sucker, small ventral sucker, genital pore some distance anterior to the ventral sucker, no ventral pit, and 1 compact or slightly lobed vitellarium, which were all compatible with P. duboisi. Some of the metacercariae were experimentally fed to mice, and adult flukes were recovered at day 7 post-infection. The morphology of the adult flukes was basically the same as that of the metacercariae except for the presence of uterine eggs; the uterus was filled with up to 40 eggs. The nucleotide sequences (1,193 bp) from ITS regions (ITS1, 5.8S rDNA, and ITS2) of the metacercariae showed 99.7% identity with P. duboisi and 75.7% identity with Gymnophalloides seoi deposited in GenBank. These results confirmed the presence of P. duboisi metacercariae in the Manila clam R. philippinarum in an estuary region of Gochang-gun, Korea.
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