title: Transcriptome of the Deep-Sea Black Scabbardfish, Aphanopus carbo (Perciformes: Trichiuridae): Tissue-Specific Expression Patterns and Candidate Genes Associated to Depth Adaptation.
abstract: 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.
authors.affiliation: ISSIA-CNR, Via de Marini 6, 16149 Genova, Italy ; LARSyS, 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.
authors.forename: Sergio
authors.initials: S
authors.lastname: Stefanni
authors.affiliation: LARSyS, 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.
authors.forename: Raul
authors.initials: R
authors.lastname: Bettencourt
authors.affiliation: School of Medicine, University of St Andrews, North Haugh, St Andrews KY16 9TF, UK.
authors.forename: Miguel
authors.initials: M
authors.lastname: Pinheiro
authors.affiliation: Department of Life Sciences, University of Trieste, Piazzale Valmaura, 9, 34148 Trieste, Italy.
authors.forename: Gianluca De
authors.initials: GD
authors.lastname: Moro
authors.affiliation: Institute of Marine Sciences, National Research Council (ISMAR-CNR), Castello 2437/F, 30122 Venezia, Italy.
authors.forename: Lucia
authors.initials: L
authors.lastname: Bongiorni
authors.affiliation: Department of Life Sciences, University of Trieste, Piazzale Valmaura, 9, 34148 Trieste, Italy.
authors.forename: Alberto
authors.initials: A
authors.lastname: Pallavicini