ArticleZoological letters2016
Bivalve-specific gene expansion in the pearl oyster genome: implications of adaptation to a sessile lifestyle.
Article in Zoological letters, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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Who cites it
69 citing papers in PubMed, 160 citations in OpenAlex.
- Quantitative Proteomic Profiling of Pinctada fucata Shell Nacre Defines a Solubility-Based Type Classification of Shell Matrix Proteins.Marine biotechnology (New York, N.Y.) · 2026Article
- An improved chromosome-level genome assembly of a deep-sea limpet (Bathyacmaea lactea).Scientific data · 2025Article
- Diversification of von Willebrand Factor A and Chitin-Binding Domains in Pif/BMSPs Among Mollusks.Journal of molecular evolution · 2024Article
- The First High-Quality Genome Assembly of Freshwater Pearl MusselInternational journal of molecular sciences · 2024Article
- Article
- Expansion of the HSP70 gene family in Tegillarca granosa and expression profiles in response to zinc toxicity.Cell stress & chaperones · 2024Article
- A novel birnavirus identified as the causative agent of summer atrophy of pearl oyster (PeerJ · 2024Article
- Comparative Analysis of Bivalve and Sea Urchin Genetics and Development: Investigating the Dichotomy in Bilateria.International journal of molecular sciences · 2023Review
- Invertebrate C1q Domain-Containing Proteins: Molecular Structure, Functional Properties and Biomedical Potential.Marine drugs · 2023Review
- The environmental cellular stress response: the intertidal as a multistressor model.Cell stress & chaperones · 2023Review
- A Genomic and Transcriptomic Analysis of the C-Type Lectin Gene Family Reveals Highly Expanded and Diversified Repertoires in Bivalves.Marine drugs · 2023Article
- Immune diversity in lophotrochozoans, with a focus on recognition and effector systems.Computational and structural biotechnology journal · 2023Review
- A high-quality, haplotype-phased genome reconstruction reveals unexpected haplotype diversity in a pearl oyster.DNA research : an international journal for rapid publication of reports on genes and genomes · 2022Article
- Reference genome for the California ribbed mussel, Mytilus californianus, an ecosystem engineer.The Journal of heredity · 2022Article
- Gene Recruitments and Dismissals in the Argonaut Genome Provide Insights into Pelagic Lifestyle Adaptation and Shell-like Eggcase Reacquisition.Genome biology and evolution · 2022Article
- Convergent evolution of barnacles and molluscs sheds lights in origin and diversification of calcareous shell and sessile lifestyle.Proceedings. Biological sciences · 2022Article
- Chromosome-Level Genome Assembly of the Butter Clam Saxidomus purpuratus.Genome biology and evolution · 2022Article
- Evolution of Epidermal Growth Factor (EGF)-like and Zona Pellucida Domains Containing Shell Matrix Proteins in Mollusks.Molecular biology and evolution · 2022Article
- Exosome-derived small non-coding RNAs reveal immune response upon grafting transplantation inOpen biology · 2022Article
- Genome-Wide Analyses of Heat Shock Protein Superfamily Provide New Insights on Adaptation to Sulfide-Rich Environments inInternational journal of molecular sciences · 2022Article
9 more citing papers are in PubMed but not listed here.
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Authors and funding
19 authors at 5 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
introductionBivalve molluscs have flourished in marine environments, and many species constitute important aquatic resources. Recently, whole genome sequences from two bivalves, the pearl oyster, Pinctada fucata, and the Pacific oyster, Crassostrea gigas, have been decoded, making it possible to compare genomic sequences among molluscs, and to explore general and lineage-specific genetic features and trends in bivalves. In order to improve the quality of sequence data for these purposes, we have updated the entire P. fucata genome assembly.
resultsWe present a new genome assembly of the pearl oyster, Pinctada fucata (version 2.0). To update the assembly, we conducted additional sequencing, obtaining accumulated sequence data amounting to 193× the P. fucata genome. Sequence redundancy in contigs that was caused by heterozygosity was removed in silico, which significantly improved subsequent scaffolding. Gene model version 2.0 was generated with the aid of manual gene annotations supplied by the P. fucata research community. Comparison of mollusc and other bilaterian genomes shows that gene arrangements of Hox, ParaHox, and Wnt clusters in the P. fucata genome are similar to those of other molluscs. Like the Pacific oyster, P. fucata possesses many genes involved in environmental responses and in immune defense. Phylogenetic analyses of heat shock protein70 and C1q domain-containing protein families indicate that extensive expansion of genes occurred independently in each lineage. Several gene duplication events prior to the split between the pearl oyster and the Pacific oyster are also evident. In addition, a number of tandem duplications of genes that encode shell matrix proteins are also well characterized in the P. fucata genome.
conclusionsBoth the Pinctada and Crassostrea lineages have expanded specific gene families in a lineage-specific manner. Frequent duplication of genes responsible for shell formation in the P. fucata genome explains the diversity of mollusc shell structures. These duplications reveal dynamic genome evolution to forge the complex physiology that enables bivalves to employ a sessile lifestyle in the intertidal zone.
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