High-throughput sequence analysis of turbot (Scophthalmus maximus) transcriptome using 454- pyrosequencing for the discovery of antiviral immune genes
17 páginas, 7 tablas, 12 figuras Background: Turbot (Scophthalmus maximus L.) is an important aquacultural resource both in Europe and Asia. However, there is little information on gene sequences available in public databases. Currently, one of the main problems affecting the culture of this flatfis...
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ftcsic:oai:digital.csic.es:10261/51954 2024-02-11T10:08:26+01:00 High-throughput sequence analysis of turbot (Scophthalmus maximus) transcriptome using 454- pyrosequencing for the discovery of antiviral immune genes Pereiro, Patricia Balseiro, P. Romero Jódar, Alejandro Dios, S. Forn-Cuni, Gabriel Fusté, Berta Planas, Josep V. Beltrán, Sergi Novoa, Beatriz Figueras Huerta, Antonio 2012 http://hdl.handle.net/10261/51954 https://doi.org/10.1371/journal.pone.0035369 en eng Public Library of Science Publisher’s version http://dx.doi.org/10.1371/journal.pone.0035369 PLoS ONE 7(5): e35369 (2012) http://hdl.handle.net/10261/51954 doi:10.1371/journal.pone.0035369 1932-6203 22629298 open artículo http://purl.org/coar/resource_type/c_6501 2012 ftcsic https://doi.org/10.1371/journal.pone.0035369 2024-01-16T09:38:49Z 17 páginas, 7 tablas, 12 figuras Background: Turbot (Scophthalmus maximus L.) is an important aquacultural resource both in Europe and Asia. However, there is little information on gene sequences available in public databases. Currently, one of the main problems affecting the culture of this flatfish is mortality due to several pathogens, especially viral diseases which are not treatable. In order to identify new genes involved in immune defense, we conducted 454-pyrosequencing of the turbot transcriptome after different immune stimulations. Methodology/Principal Findings: Turbot were injected with viral stimuli to increase the expression level of immune-related genes. High-throughput deep sequencing using 454-pyrosequencing technology yielded 915,256 high-quality reads. These sequences were assembled into 55,404 contigs that were subjected to annotation steps. Intriguingly, 55.16% of the deduced protein was not significantly similar to any sequences in the databases used for the annotation and only 0.85% of the BLASTx top-hits matched S. maximus protein sequences. This relatively low level of annotation is possibly due to the limited information for this specie and other flatfish in the database. These results suggest the identification of a large number of new genes in turbot and in fish in general. A more detailed analysis showed the presence of putative members of several innate and specific immune pathways. Conclusions/Significance: To our knowledge, this study is the first transcriptome analysis using 454-pyrosequencing for turbot. Previously, there were only 12,471 EST and less of 1,500 nucleotide sequences for S. maximus in NCBI database. Our results provide a rich source of data (55,404 contigs and 181,845 singletons) for discovering and identifying new genes, which will serve as a basis for microarray construction, gene expression characterization and for identification of genetic markers to be used in several applications. Immune stimulation in turbot was very effective, obtaining an enormous ... Article in Journal/Newspaper Scophthalmus maximus Turbot Digital.CSIC (Spanish National Research Council) PLoS ONE 7 5 e35369 |
institution |
Open Polar |
collection |
Digital.CSIC (Spanish National Research Council) |
op_collection_id |
ftcsic |
language |
English |
description |
17 páginas, 7 tablas, 12 figuras Background: Turbot (Scophthalmus maximus L.) is an important aquacultural resource both in Europe and Asia. However, there is little information on gene sequences available in public databases. Currently, one of the main problems affecting the culture of this flatfish is mortality due to several pathogens, especially viral diseases which are not treatable. In order to identify new genes involved in immune defense, we conducted 454-pyrosequencing of the turbot transcriptome after different immune stimulations. Methodology/Principal Findings: Turbot were injected with viral stimuli to increase the expression level of immune-related genes. High-throughput deep sequencing using 454-pyrosequencing technology yielded 915,256 high-quality reads. These sequences were assembled into 55,404 contigs that were subjected to annotation steps. Intriguingly, 55.16% of the deduced protein was not significantly similar to any sequences in the databases used for the annotation and only 0.85% of the BLASTx top-hits matched S. maximus protein sequences. This relatively low level of annotation is possibly due to the limited information for this specie and other flatfish in the database. These results suggest the identification of a large number of new genes in turbot and in fish in general. A more detailed analysis showed the presence of putative members of several innate and specific immune pathways. Conclusions/Significance: To our knowledge, this study is the first transcriptome analysis using 454-pyrosequencing for turbot. Previously, there were only 12,471 EST and less of 1,500 nucleotide sequences for S. maximus in NCBI database. Our results provide a rich source of data (55,404 contigs and 181,845 singletons) for discovering and identifying new genes, which will serve as a basis for microarray construction, gene expression characterization and for identification of genetic markers to be used in several applications. Immune stimulation in turbot was very effective, obtaining an enormous ... |
format |
Article in Journal/Newspaper |
author |
Pereiro, Patricia Balseiro, P. Romero Jódar, Alejandro Dios, S. Forn-Cuni, Gabriel Fusté, Berta Planas, Josep V. Beltrán, Sergi Novoa, Beatriz Figueras Huerta, Antonio |
spellingShingle |
Pereiro, Patricia Balseiro, P. Romero Jódar, Alejandro Dios, S. Forn-Cuni, Gabriel Fusté, Berta Planas, Josep V. Beltrán, Sergi Novoa, Beatriz Figueras Huerta, Antonio High-throughput sequence analysis of turbot (Scophthalmus maximus) transcriptome using 454- pyrosequencing for the discovery of antiviral immune genes |
author_facet |
Pereiro, Patricia Balseiro, P. Romero Jódar, Alejandro Dios, S. Forn-Cuni, Gabriel Fusté, Berta Planas, Josep V. Beltrán, Sergi Novoa, Beatriz Figueras Huerta, Antonio |
author_sort |
Pereiro, Patricia |
title |
High-throughput sequence analysis of turbot (Scophthalmus maximus) transcriptome using 454- pyrosequencing for the discovery of antiviral immune genes |
title_short |
High-throughput sequence analysis of turbot (Scophthalmus maximus) transcriptome using 454- pyrosequencing for the discovery of antiviral immune genes |
title_full |
High-throughput sequence analysis of turbot (Scophthalmus maximus) transcriptome using 454- pyrosequencing for the discovery of antiviral immune genes |
title_fullStr |
High-throughput sequence analysis of turbot (Scophthalmus maximus) transcriptome using 454- pyrosequencing for the discovery of antiviral immune genes |
title_full_unstemmed |
High-throughput sequence analysis of turbot (Scophthalmus maximus) transcriptome using 454- pyrosequencing for the discovery of antiviral immune genes |
title_sort |
high-throughput sequence analysis of turbot (scophthalmus maximus) transcriptome using 454- pyrosequencing for the discovery of antiviral immune genes |
publisher |
Public Library of Science |
publishDate |
2012 |
url |
http://hdl.handle.net/10261/51954 https://doi.org/10.1371/journal.pone.0035369 |
genre |
Scophthalmus maximus Turbot |
genre_facet |
Scophthalmus maximus Turbot |
op_relation |
Publisher’s version http://dx.doi.org/10.1371/journal.pone.0035369 PLoS ONE 7(5): e35369 (2012) http://hdl.handle.net/10261/51954 doi:10.1371/journal.pone.0035369 1932-6203 22629298 |
op_rights |
open |
op_doi |
https://doi.org/10.1371/journal.pone.0035369 |
container_title |
PLoS ONE |
container_volume |
7 |
container_issue |
5 |
container_start_page |
e35369 |
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1790607773695737856 |