Abstract
The striped venus Chamelea gallina (Linnaeus 1758) is a species of substantial economic importance, distributed along the Mediterranean coast and the Eastern Atlantic coasts. Due to an intensive trade activity since the 1970’s, this species has experienced a rapid decline in the last 30 years, still exacerbated by irregular mortality events due to undetermined triggers. Global profiling of gene expression has the potential to disentangle the biological effects of various environmental stressors causing severe landings decline or mortality events. In this study, we report the development of a C. gallina-specific oligo-microarray, a first transcriptomic platform for global gene expression profiling in the striped venus. This tool was applied to compare gene expression profiles of clams collected in different periods along the Abruzzo coast in a reference site (T7) and in a site subject to mortality events (T4). Our results reveal substantial transcriptional modifications among the investigated sites and the significant up-regulation of several genes involved in the immune response in the T4 site. The transcriptomic differences between clams from the two investigated sites endorse distinct health and metabolic status under different environmental stressors. Overall, this approach provides a preliminary indication about the potential causes of periodic localized mortality affecting C. gallina.
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Acknowledgments
This work is part of the project F.E.P. 01/POI/13 (Studio di soluzioni per contrastare la flessione produttiva di vongole [Chamelea gallina] del Compartimento Marittimo di Ortona) financed by the Italian Abruzzo region with determination DH 32/24 of 5 April 2013; Project manager: Prof. Giuseppe Martino.
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This article contains studies with animals (Chamelea gallina), from commercial fishery harvesting. All applicable international, national and/or institutional guidelines for the care and use of animals were followed.
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Massimo Milan and Fiorentina Palazzo have contributed equally to this work.
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Supplementary File S1
List of differentially expressed genes obtained by two-way ANOVA analysis considering “sampling time” factor. For each probe, the table reports: the p value, the annotation considering SwissProt, Homo sapiens Ensembl protein database, Danio rerio Ensembl protein database, and Crassostrea gigas Ensembl protein database. (PDF 2447 kb)
Supplementary File S2
Enriched Biological Processes (BPs) and KEGG pathways (KPs) obtained by DAVID functional analyses of significant genes obtained by two-way ANOVA considering “sampling time” factor (see Supplementary File S1). GO terms and KEGG pathways, gene count (number of significant genes for each process), p value and fold enrichment are also reported. (PDF 311 kb)
Supplementary File S3
List of differentially expressed genes identified by two-way ANOVA analysis considering “sampling site” factor. For each probe the table reports: the p value, the fold change at each sampling time comparing T4 and T7 sites, the annotation considering SwissProt, Homo sapiens Ensembl protein database, Danio rerio Ensembl protein database, and Crassostrea gigas Ensembl protein database. Significant transcripts showing a Fold Change FC>1.5 are reported in bolt green (over-expressed in T4 compared to T7), or bolt red (over-expressed in T7 compared to T4). (PDF 1012 kb)
Supplementary File S4
Enriched Biological Processes (BPs) and KEGG pathways (KPs) identified by DAVID functional analyses of significant genes obtained considering “sampling site” factor (see Supplementary File S3). Enrichment analysis was performed separately for up-regulated genes in T4 and T7 clams. GO terms and KEGG pathways, gene count (number of significant genes for each process), p value and fold enrichment are also reported. (PDF 327 kb)
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Milan, M., Palazzo, F., Papetti, C. et al. Transcriptomic profiling of Chamelea gallina from sites along the Abruzzo coast (Italy), subject to periodic localized mortality events. Mar Biol 163, 196 (2016). https://doi.org/10.1007/s00227-016-2971-2
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DOI: https://doi.org/10.1007/s00227-016-2971-2