Bivalve Omics: State of the Art and Potential Applications for the Biomonitoring of Harmful Marine Compounds
Abstract
:1. Introduction
2. Leading Edge on Bivalve High-Throughput and NGS Data Analysis
2.1. Bivalve Genomes
2.2. Bivalve Transcriptomes
2.3. Bivalve Proteomes
2.4. Bivalve Metabolomics
2.5. Bivalve Epigenomics
3. Resources for the Study of Bivalve Omic Data
3.1. General Resources
Species | Bioproject | Genome | SRA Datasets | ||||
---|---|---|---|---|---|---|---|
Number | Type | Total | 454 | Illumina | AB SOLiD | ||
Alasmidonta varicosa | 1 | transcriptome/gene expression | YES (no data) | 1 | 1 | - | - |
Arctica islandica | 1 | genome | YES (no data) | 12 | 12 | - | - |
Argopecten irradians | 3 | transcriptome/gene expression | - | 1 | 1 | - | - |
Bankia setacea | 1 | genome | YES (no data) | 1 | 1 | - | - |
Bathymodiolus azoricus | 1 | transcriptome/gene expression | YES (no data) | 1 | 1 | - | - |
Chlamys farreri | 1 | transcriptome/gene expression | - | - | - | - | - |
Chamelea gallina | - | - | - | 1 | 1 | - | - |
Crassostrea angulata | 1 | transcriptome/gene expression | - | - | - | - | - |
Crassostrea gigas | 16 | 1 genome, 15 transcriptome/gene expression | YES (scaffold or contigs status) | 159 | 2 | 155 | 2 |
Crassostrea hongkongensis | 1 | proteome | - | - | - | - | - |
Crassostrea virginica | 3 | transcriptome/gene expression | - | - | - | - | - |
Ennucula tenuis | - | - | - | 1 | 1 | - | - |
Glossus humanus | 1 | exome | YES (no data) | - | - | - | - |
Hyriopsis cumingii | 1 | transcriptome/gene expression | - | 1 | 1 | - | - |
Laternula elliptica | 1 | transcriptome/gene expression | - | 3 | 3 | - | - |
Macoma balthica | - | - | - | 3 | 3 | - | - |
Mercenaria mercenaria | 1 | transcriptome/gene expression | YES (no data) | 2 | - | - | 2 |
Meretrix meretrix | 1 | transcriptome/gene expression | - | 1 | 1 | - | - |
Mizuhopecten (Patinopecten) yessoensis | 1 | transcriptome/gene expression | - | 2 | 2 | - | - |
Mya arenaria | 2 | transcriptome/gene expression | YES (no data) | - | - | - | - |
Mytilus californianus | 4 | transcriptome/gene expression | - | - | - | - | - |
Mytilus edulis | - | - | - | 44 | 44 | - | - |
Mytilus galloprovincialis | 19 | transcriptome/gene expression | - | 12 | 6 | 6 | - |
Nodipecten subnodosus | - | - | - | 2 | 2 | - | - |
Nucula nitidosa | - | - | - | 1 | 1 | - | - |
Ostrea lurida | 2 | transcriptome/gene expression | YES (no data) | 1 | - | 1 | - |
Pinctada fucata | 1 | transcriptome/gene expression | YES (no data) | 10 | 7 | 3 | - |
Pinctada margaritifera | 2 | transcriptome/gene expression | YES (no data) | 1 | 1 | - | - |
Pinctada maxima | 7 | transcriptome/gene expression | - | 1 | 1 | - | - |
Pteria penguin | 1 | transcriptome/gene expression | YES (no data) | - | - | - | - |
Ruditapes decussatus | 3 | transcriptome/gene expression | - | - | - | - | - |
Ruditapes philippinarum | 6 | transcriptome/gene expression | - | 28 | 2 | 26 | - |
Solemya velum | - | - | - | 2 | 1 | 1 | - |
Spisula solidissima | 1 | genome | YES (no data) | - | - | - | - |
Tegillarca granosa | 1 | transcriptome/gene expression | - | 1 | 1 | - | - |
Yoldia limatula | - | - | - | 1 | 1 | - | - |
3.2. Specialized Resources
3.2.1. Databases and Knowledge Repositories
Database | Organism/# Sequences | Tissues/URL | |
---|---|---|---|
Species-centered | |||
Mytibase | M. galloprovincialis 7112 | Digestive gland, gills, hemocytes [95] | |
GigasDatabase | C. gigas 29745 | Digestive gland, gills, gonad, hemocytes, mantle-edge, muscle [96] | |
RuphiBase | R. philippinarum 32606 | Mixed tissues [97] | |
ChameleaBase | C. gallina 36422 | Muscle [98] | |
DeepSeaVent | B. azoricus 35903 | Gills [99] | |
Functionally-centered | |||
Chromevaloa | M.galloprovincialis 14408 | Digestive gland [100] |
3.2.2. Array Technology
4. Bivalve Omic Approaches for the Biomonitoring of Marine Compounds
4.1. Bivalve Transcriptomes as Biomonitoring Tools
4.2. Toxin Biomonitoring during Harmful Algae Blooms
4.3. Evaluation of the Harmful Effects of Anthropic Pollutants
4.4. Proteomic Biomonitoring of Harmful Marine Compounds
5. Conclusions
Acknowledgments
Conflicts of Interest
References
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Suárez-Ulloa, V.; Fernández-Tajes, J.; Manfrin, C.; Gerdol, M.; Venier, P.; Eirín-López, J.M. Bivalve Omics: State of the Art and Potential Applications for the Biomonitoring of Harmful Marine Compounds. Mar. Drugs 2013, 11, 4370-4389. https://doi.org/10.3390/md11114370
Suárez-Ulloa V, Fernández-Tajes J, Manfrin C, Gerdol M, Venier P, Eirín-López JM. Bivalve Omics: State of the Art and Potential Applications for the Biomonitoring of Harmful Marine Compounds. Marine Drugs. 2013; 11(11):4370-4389. https://doi.org/10.3390/md11114370
Chicago/Turabian StyleSuárez-Ulloa, Victoria, Juan Fernández-Tajes, Chiara Manfrin, Marco Gerdol, Paola Venier, and José M. Eirín-López. 2013. "Bivalve Omics: State of the Art and Potential Applications for the Biomonitoring of Harmful Marine Compounds" Marine Drugs 11, no. 11: 4370-4389. https://doi.org/10.3390/md11114370