ArticleGenome biology and evolution2017
The Whole-Genome and Transcriptome of the Manila Clam (Ruditapes philippinarum).
Article in Genome biology and evolution, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Protective effect of Glutamicibacter sp. ZY1 against Vibrio parahaemolyticus YDE17 pathogenicity in the clam Ruditapes philippinarum.World journal of microbiology & biotechnology · 2026Article
- Genome-Wide Resequencing Reveals High Connectivity and Localized Adaptive Signals in Manila Clam (Animals : an open access journal from MDPI · 2026Article
- Effects of L-Carnitine on the Developmental Competence of Bovine Oocytes.Animals : an open access journal from MDPI · 2025Article
- Clam Genome and Transcriptomes Provide Insights into Molecular Basis of Morphological Novelties and Adaptations in Mollusks.Biology · 2024Article
- Transcriptome sequencing of the endangered land snail Karaftohelix adamsi from the Island Ulleung: De novo assembly, annotation, valuation of fitness genes and SSR markers.Genes & genomics · 2024Article
- The First High-Quality Genome Assembly of Freshwater Pearl MusselInternational journal of molecular sciences · 2024Article
- Invertebrate C1q Domain-Containing Proteins: Molecular Structure, Functional Properties and Biomedical Potential.Marine drugs · 2023Review
- A review of the endangered mollusks transcriptome under the threatened species initiative of Korea.Genes & genomics · 2023Review
- Immune diversity in lophotrochozoans, with a focus on recognition and effector systems.Computational and structural biotechnology journal · 2023Review
- Chromosomal assembly of the flat oyster (Evolutionary applications · 2022Article
- Comparative analysis of the Mercenaria mercenaria genome provides insights into the diversity of transposable elements and immune molecules in bivalve mollusks.BMC genomics · 2022Article
- A Novel C1q Domain-Containing Protein Isolated from the MolluskMarine drugs · 2021Article
- Draft genome of Semisulcospira libertina, a species of freshwater snail.Genomics & informatics · 2021Article
- Satellitome Analysis of the Pacific OysterInternational journal of molecular sciences · 2021Article
- Exploring Satellite DNAs: Specificities of Bivalve Mollusks Genomes.Progress in molecular and subcellular biology · 2021Article
- Genomic Landscape of Mutational Biases in the Pacific Oyster Crassostrea gigas.Genome biology and evolution · 2020Article
- New insights into the Manila clam and PAMPs interaction based on RNA-seq analysis of clam through in vitro challenges with LPS, PGN, and poly(I:C).BMC genomics · 2020Article
- Chromosome-Level Clam Genome Helps Elucidate the Molecular Basis of Adaptation to a Buried Lifestyle.iScience · 2020Article
- The gene-rich genome of the scallop Pecten maximus.GigaScience · 2020Article
- Organ transcriptomes of the lucinid clam Loripes orbiculatus (Poli, 1791) provide insights into their specialised roles in the biology of a chemosymbiotic bivalve.BMC genomics · 2019Article
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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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