Transcriptome of the deep-sea black scabbardfish, Aphanopus carbo (Perciformes: Trichiuridae) : tissue-specific expression patterns and candidate genes associated to depth adaptation
MetadataShow full item record
Altmetrics Handle Statistics
Altmetrics DOI Statistics
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.
Stefanni , S , Bettencourt , R , Monsanto Pinheiro , M , De Moro , G , Bongiorni , L & Pallavicini , A 2014 , ' Transcriptome of the deep-sea black scabbardfish, Aphanopus carbo (Perciformes: Trichiuridae) : tissue-specific expression patterns and candidate genes associated to depth adaptation ' , International Journal of Genomics , vol. 2014 , 267482 . https://doi.org/10.1155/2014/267482
International Journal of Genomics
Copyright © 2014 Sergio Stefanni et al. This is an open access article distributed under the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Items in the St Andrews Research Repository are protected by copyright, with all rights reserved, unless otherwise indicated.