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International Journal of Genomics
Volume 2014, Article ID 267482, 21 pages
Research Article

Transcriptome of the Deep-Sea Black Scabbardfish, Aphanopus carbo (Perciformes: Trichiuridae): Tissue-Specific Expression Patterns and Candidate Genes Associated to Depth Adaptation

1ISSIA-CNR, Via de Marini 6, 16149 Genova, Italy
2LARSyS, Associated Laboratory & Centre of IMAR of the University of the Azores, Department of Oceanography and Fisheries, Rua Prof. Frederico Machado 4, 9901-862 Horta, Azores, Portugal
3School of Medicine, University of St Andrews, North Haugh, St Andrews KY16 9TF, UK
4Department of Life Sciences, University of Trieste, Piazzale Valmaura, 9, 34148 Trieste, Italy
5Institute of Marine Sciences, National Research Council (ISMAR-CNR), Castello 2437/F, 30122 Venezia, Italy

Received 25 May 2014; Accepted 19 July 2014; Published 17 September 2014

Academic Editor: Elena Pasyukova

Copyright © 2014 Sergio Stefanni et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Deep-sea fishes provide a unique opportunity to study the physiology and evolutionary adaptation to extreme environments. We carried out a high throughput sequencing analysis on a 454 GS-FLX titanium plate using unnormalized cDNA libraries from six tissues of A. carbo. Assemblage and annotations were performed by Newbler and InterPro/Pfam analyses, respectively. The assembly of 544,491 high quality reads provided 8,319 contigs, 55.6% of which retrieved blast hits against the NCBI nonredundant database or were annotated with ESTscan. Comparison of functional genes at both the protein sequences and protein stability levels, associated with adaptations to depth, revealed similarities between A. carbo and other bathypelagic fishes. A selection of putative genes was standardized to evaluate the correlation between number of contigs and their normalized expression, as determined by qPCR amplification. The screening of the libraries contributed to the identification of new EST simple-sequence repeats (SSRs) and to the design of primer pairs suitable for population genetic studies as well as for tagging and mapping of genes. The characterization of the deep-sea fish A. carbo first transcriptome is expected to provide abundant resources for genetic, evolutionary, and ecological studies of this species and the basis for further investigation of depth-related adaptation processes in fishes.