ArticleBMC genomics2011
Transcriptome sequencing and microarray development for the Manila clam, Ruditapes philippinarum: genomic tools for environmental monitoring.
Article in BMC genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed.
- Comparative Genomic Hybridization (CGH) in Genotoxicology: From the Basics to Modern Approaches.Methods in molecular biology (Clifton, N.J.) · 2026Review
- De novo transcriptome analysis of Perna perna L. (Bivalve) with functional and metabolic pathway analysis.Scientific data · 2025Article
- Long-lasting effects of chronic exposure to chemical pollution on the hologenome of the Manila clam.Evolutionary applications · 2021Article
- Transcriptomic analysis provides insights into candidate genes and molecular pathways involved in growth of Manila clam Ruditapes philippinarum.Functional & integrative genomics · 2021Article
- Hyperaccumulation of cadmium by scallop Chlamys farreri revealed by comparative transcriptome analysis.Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine · 2020Article
- The calcitonin-like system is an ancient regulatory system of biomineralization.Scientific reports · 2020Article
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- Clam Genome Sequence Clarifies the Molecular Basis of Its Benthic Adaptation and Extraordinary Shell Color Diversity.iScience · 2019Article
- Evolution and diversity of alpha-carbonic anhydrases in the mantle of the Mediterranean mussel (Mytilus galloprovincialis).Scientific reports · 2019Article
- Salinity stress-induced differentially expressed miRNAs and target genes in sea cucumbers Apostichopus japonicus.Cell stress & chaperones · 2019Article
- Impacts of ocean acidification on carboxylated carbon nanotube effects induced in the clam species Ruditapes philippinarum.Environmental science and pollution research international · 2019Article
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- Metabolomics Study of Immune Responses of New Zealand Greenshell™ Mussels (Perna canaliculus) Infected with Pathogenic Vibrio sp.Marine biotechnology (New York, N.Y.) · 2018Article
- High throughput sequencing of RNA transcriptomes in Ruditapes philippinarum identifies genes involved in osmotic stress response.Scientific reports · 2017Article
- The Whole-Genome and Transcriptome of the Manila Clam (Ruditapes philippinarum).Genome biology and evolution · 2017Article
- Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Manila clam Ruditapes philippinarum.Scientific reports · 2017Article
- A Microarray Study of Carpet-Shell Clam (Frontiers in physiology · 2017Article
- Article
- RNA-Seq in Mytilus galloprovincialis: comparative transcriptomics and expression profiles among different tissues.BMC genomics · 2015Article
- Transcriptome analysis of eyestalk and hemocytes in the ridgetail white prawn Exopalaemon carinicauda: assembly, annotation and marker discovery.Molecular biology reports · 2015Article
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe 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.
resultsA 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.
conclusionsThe 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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