Transcriptome of the Deep-Sea Black Scabbardfish, Aphanopus carbo (Perciformes: Trichiuridae): Tissue-Specific Expression Patterns and Candidate Genes Associated to Depth Adaptation
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 wer...
Saved in:
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wiley
2014-01-01
|
| Series: | International Journal of Genomics |
| Online Access: | http://dx.doi.org/10.1155/2014/267482 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832551532692766720 |
|---|---|
| author | Sergio Stefanni Raul Bettencourt Miguel Pinheiro Gianluca De Moro Lucia Bongiorni Alberto Pallavicini |
| author_facet | Sergio Stefanni Raul Bettencourt Miguel Pinheiro Gianluca De Moro Lucia Bongiorni Alberto Pallavicini |
| author_sort | Sergio Stefanni |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-57c7d8e3e87947d5af8c2973761ea543 |
| institution | Kabale University |
| issn | 2314-436X 2314-4378 |
| language | English |
| publishDate | 2014-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | International Journal of Genomics |
| spelling | doaj-art-57c7d8e3e87947d5af8c2973761ea5432025-02-03T06:01:17ZengWileyInternational Journal of Genomics2314-436X2314-43782014-01-01201410.1155/2014/267482267482Transcriptome of the Deep-Sea Black Scabbardfish, Aphanopus carbo (Perciformes: Trichiuridae): Tissue-Specific Expression Patterns and Candidate Genes Associated to Depth AdaptationSergio Stefanni0Raul Bettencourt1Miguel Pinheiro2Gianluca De Moro3Lucia Bongiorni4Alberto Pallavicini5ISSIA-CNR, Via de Marini 6, 16149 Genova, ItalyLARSyS, 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, PortugalSchool of Medicine, University of St Andrews, North Haugh, St Andrews KY16 9TF, UKDepartment of Life Sciences, University of Trieste, Piazzale Valmaura, 9, 34148 Trieste, ItalyInstitute of Marine Sciences, National Research Council (ISMAR-CNR), Castello 2437/F, 30122 Venezia, ItalyDepartment of Life Sciences, University of Trieste, Piazzale Valmaura, 9, 34148 Trieste, ItalyDeep-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.http://dx.doi.org/10.1155/2014/267482 |
| spellingShingle | Sergio Stefanni Raul Bettencourt Miguel Pinheiro Gianluca De Moro Lucia Bongiorni Alberto Pallavicini 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 |
| title | Transcriptome of the Deep-Sea Black Scabbardfish, Aphanopus carbo (Perciformes: Trichiuridae): Tissue-Specific Expression Patterns and Candidate Genes Associated to Depth Adaptation |
| title_full | Transcriptome of the Deep-Sea Black Scabbardfish, Aphanopus carbo (Perciformes: Trichiuridae): Tissue-Specific Expression Patterns and Candidate Genes Associated to Depth Adaptation |
| title_fullStr | Transcriptome of the Deep-Sea Black Scabbardfish, Aphanopus carbo (Perciformes: Trichiuridae): Tissue-Specific Expression Patterns and Candidate Genes Associated to Depth Adaptation |
| title_full_unstemmed | Transcriptome of the Deep-Sea Black Scabbardfish, Aphanopus carbo (Perciformes: Trichiuridae): Tissue-Specific Expression Patterns and Candidate Genes Associated to Depth Adaptation |
| title_short | Transcriptome of the Deep-Sea Black Scabbardfish, Aphanopus carbo (Perciformes: Trichiuridae): Tissue-Specific Expression Patterns and Candidate Genes Associated to Depth Adaptation |
| title_sort | transcriptome of the deep sea black scabbardfish aphanopus carbo perciformes trichiuridae tissue specific expression patterns and candidate genes associated to depth adaptation |
| url | http://dx.doi.org/10.1155/2014/267482 |
| work_keys_str_mv | AT sergiostefanni transcriptomeofthedeepseablackscabbardfishaphanopuscarboperciformestrichiuridaetissuespecificexpressionpatternsandcandidategenesassociatedtodepthadaptation AT raulbettencourt transcriptomeofthedeepseablackscabbardfishaphanopuscarboperciformestrichiuridaetissuespecificexpressionpatternsandcandidategenesassociatedtodepthadaptation AT miguelpinheiro transcriptomeofthedeepseablackscabbardfishaphanopuscarboperciformestrichiuridaetissuespecificexpressionpatternsandcandidategenesassociatedtodepthadaptation AT gianlucademoro transcriptomeofthedeepseablackscabbardfishaphanopuscarboperciformestrichiuridaetissuespecificexpressionpatternsandcandidategenesassociatedtodepthadaptation AT luciabongiorni transcriptomeofthedeepseablackscabbardfishaphanopuscarboperciformestrichiuridaetissuespecificexpressionpatternsandcandidategenesassociatedtodepthadaptation AT albertopallavicini transcriptomeofthedeepseablackscabbardfishaphanopuscarboperciformestrichiuridaetissuespecificexpressionpatternsandcandidategenesassociatedtodepthadaptation |