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      Bivalve Omics: State of the Art and Potential Applications for the Biomonitoring of Harmful Marine Compounds

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          Abstract

          The extraordinary progress experienced by sequencing technologies and bioinformatics has made the development of omic studies virtually ubiquitous in all fields of life sciences nowadays. However, scientific attention has been quite unevenly distributed throughout the different branches of the tree of life, leaving molluscs, one of the most diverse animal groups, relatively unexplored and without representation within the narrow collection of well established model organisms. Within this Phylum, bivalve molluscs play a fundamental role in the functioning of the marine ecosystem, constitute very valuable commercial resources in aquaculture, and have been widely used as sentinel organisms in the biomonitoring of marine pollution. Yet, it has only been very recently that this complex group of organisms became a preferential subject for omic studies, posing new challenges for their integrative characterization. The present contribution aims to give a detailed insight into the state of the art of the omic studies and functional information analysis of bivalve molluscs, providing a timely perspective on the available data resources and on the current and prospective applications for the biomonitoring of harmful marine compounds.

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          GenBank

          GenBank® is a comprehensive database that contains publicly available nucleotide sequences for more than 380 000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system that integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov.
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            The beginning of the end for microarrays?

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              Draft Genome of the Pearl Oyster Pinctada fucata: A Platform for Understanding Bivalve Biology

              The study of the pearl oyster Pinctada fucata is key to increasing our understanding of the molecular mechanisms involved in pearl biosynthesis and biology of bivalve molluscs. We sequenced ∼1150-Mb genome at ∼40-fold coverage using the Roche 454 GS-FLX and Illumina GAIIx sequencers. The sequences were assembled into contigs with N50 = 1.6 kb (total contig assembly reached to 1024 Mb) and scaffolds with N50 = 14.5 kb. The pearl oyster genome is AT-rich, with a GC content of 34%. DNA transposons, retrotransposons, and tandem repeat elements occupied 0.4, 1.5, and 7.9% of the genome, respectively (a total of 9.8%). Version 1.0 of the P. fucata draft genome contains 23 257 complete gene models, 70% of which are supported by the corresponding expressed sequence tags. The genes include those reported to have an association with bio-mineralization. Genes encoding transcription factors and signal transduction molecules are present in numbers comparable with genomes of other metazoans. Genome-wide molecular phylogeny suggests that the lophotrochozoan represents a distinct clade from ecdysozoans. Our draft genome of the pearl oyster thus provides a platform for the identification of selection markers and genes for calcification, knowledge of which will be important in the pearl industry.
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                Author and article information

                Journal
                Mar Drugs
                Mar Drugs
                marinedrugs
                Marine Drugs
                MDPI
                1660-3397
                01 November 2013
                November 2013
                : 11
                : 11
                : 4370-4389
                Affiliations
                [1 ]Chromatin Structure and Evolution (CHROMEVOL) Group, Department of Biological Sciences, Florida International University, North Miami, FL 33181, USA; E-Mail: msuarezu@ 123456fiu.edu
                [2 ]Wellcome Trust Center for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; E-Mail: jfertaj@ 123456well.ox.ac.uk
                [3 ]Department of Life Sciences, University of Trieste, Trieste 34127, Italy; E-Mails: cmanfrin@ 123456units.it (C.M.); mgerdol@ 123456units.it (M.G.)
                [4 ]Department of Biology, University of Padova, Padova 35121, Italy; E-Mail: paola.venier@ 123456unipd.it
                Author notes
                [* ] Author to whom correspondence should be addressed; E-Mail: jeirinlo@ 123456fiu.edu ; Tel.: +1-305-919-4000; Fax: +1-305-919-4030.
                Article
                marinedrugs-11-04370
                10.3390/md11114370
                3853733
                24189277
                e23e4924-2555-4264-8e89-b726d964fb06
                © 2013 by the authors; licensee MDPI, Basel, Switzerland.

                This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license ( http://creativecommons.org/licenses/by/3.0/).

                History
                : 10 July 2013
                : 27 September 2013
                : 09 October 2013
                Categories
                Review

                Pharmacology & Pharmaceutical medicine
                marine invertebrates,pollution,omics,pahs,bioinformatics,biomonitoring,heavy metals,biotoxins

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