iIRSL dating of K-feldspar

BACKGROUND: The eye has evolved across 13 separate lineages of molluscs. Yet, there have been very few studies examining the molecular machinary underlying eye function of this group, which is due, in part, to a lack of genomic resources. The scallop (Bivalvia: Pectinidae) represents a compeling molluscan model to study photoreception due to its morphologically novel and separately evolved mirror-type eye. We sequenced the adult eye transcriptome of two scallop species to: 1) identify the phototransduction pathway components; 2) identify any additional light detection functions; and 3) test the hypothesis that molluscs possess genes not found in other animal lineages. RESULTS: A total of 3,039 contigs from the bay scallop, Argopecten irradians and 26,395 contigs from the sea scallop, Placopecten magellanicus were produced by 454 sequencing. Targeted BLAST searches and functional annotation using Gene Ontology (GO) terms and KEGG pathways identified transcripts from three light detection systems: two phototransduction pathways and the circadian clock, a previously unrecognized function of the scallop eye. By comparing the scallop transcriptomes to molluscan and non-molluscan genomes, we discovered that a large proportion of the transcripts (7,776 sequences) may be specific to the scallop lineage. Nearly one-third of these contain transmembrane protein domains, suggesting these unannotated transcripts may be sensory receptors. CONCLUSIONS: Our data provide the most comprehensive transcriptomic resource currently available from a single molluscan eye type. Candidate genes potentially involved in sensory reception were identified, and are worthy of further investigation. This resource, combined with recent phylogenetic and genomic data, provides a strong foundation for future investigations of the function and evolution of molluscan photosensory systems in this morphologically and taxonomically diverse phylum

Major categories of protein domains identified by InterProScan for <i>A. irradians</i> and <i>P. magellanicus</i> adult eye transcriptomes.

<p>Major categories of protein domains identified by InterProScan for <i>A. irradians</i> and <i>P. magellanicus</i> adult eye transcriptomes.</p

Venn diagram of <i>P.</i><i>magellanicus</i> transcriptome sequences with significant blast hits against other animal genomes.

<p>The labels in each circle represent the animal genomes the <i>P. magellanicus</i> eye transcriptome was blasted against: the pacific oyster, <i>Crassostrea gigas</i> (green), the owl limpet, <i>Lottia gigantea</i> (red), and two non-mollusc genomes, <i>Drosophila melanogaster</i> and <i>Mus musculus</i> (blue). The number of sequences from <i>P. magellanicus</i> that did not match any other animal genome and are putatively unique to scallops are shown in a separate circle (black).</p

Distribution of Gene Ontology (GO) term categories in <i>A.</i><i>irradians</i> and <i>P. magellancius</i> eye transcriptomes.

<p>Bars show the percent of sequences with a GO term annotation for each category.</p

Sequence of analyses performed to assemble and annotate scallop eye transcriptomes.

<p>Sequence of analyses performed to assemble and annotate scallop eye transcriptomes.</p

Protein domain annotation of <i>A. irradians</i> and <i>P. magellanicus</i> adult eye transcriptomes.

a<p>Putative genes are based on isogroups constructed during the assembly of the transcriptome. Because the <i>A. irradians</i> dataset was constructed from a combination of Sanger and 454 sequences, isogroups were not calculated for these data.</p>b<p>Putative genes based on homology were identified by blastx blasts to the predicted gene models of the <i>Lottia gigantea</i> genome (E-value cutoff of E-3.</p

Presence of key phototransduction and circadian clock genes in scallop eye transcriptomes.

<p>Gene presence is indicated by the letters <i>B</i>, <i>G</i>, or <i>K</i>, which describes method of identification (<i>B</i> = BLAST, <i>G</i> = GO terms, <i>K</i> = KEGG pathway analysis).</p

Scallop BLAST hit distributions.

<p>Percent hits in each major category of proteins examined (“Known” = annotated nuclear proteins; “Unknown” = proteins described as putative, hypothetical, unknown, or a species mRNA clone; “Mitochondrial genome” = annotated mitochondrial proteins; “Ribosomal” = ribosomal genes).</p