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High-Throughput Sequence Analysis of Turbot (Scophthalmus maximus) Transcriptome Using 454-Pyrosequencing for the Discovery of Antiviral Immune Genes

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 pat...

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Autores principales: Pereiro, Patricia, Balseiro, Pablo, Romero, Alejandro, Dios, Sonia, Forn-Cuni, Gabriel, Fuste, Berta, Planas, Josep V., Beltran, Sergi, Novoa, Beatriz, Figueras, Antonio
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3356354/
https://www.ncbi.nlm.nih.gov/pubmed/22629298
http://dx.doi.org/10.1371/journal.pone.0035369
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author Pereiro, Patricia
Balseiro, Pablo
Romero, Alejandro
Dios, Sonia
Forn-Cuni, Gabriel
Fuste, Berta
Planas, Josep V.
Beltran, Sergi
Novoa, Beatriz
Figueras, Antonio
author_facet Pereiro, Patricia
Balseiro, Pablo
Romero, Alejandro
Dios, Sonia
Forn-Cuni, Gabriel
Fuste, Berta
Planas, Josep V.
Beltran, Sergi
Novoa, Beatriz
Figueras, Antonio
author_sort Pereiro, Patricia
collection PubMed
description 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 variety of sequences belonging to genes involved in the defense mechanisms.
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spelling pubmed-33563542012-05-24 High-Throughput Sequence Analysis of Turbot (Scophthalmus maximus) Transcriptome Using 454-Pyrosequencing for the Discovery of Antiviral Immune Genes Pereiro, Patricia Balseiro, Pablo Romero, Alejandro Dios, Sonia Forn-Cuni, Gabriel Fuste, Berta Planas, Josep V. Beltran, Sergi Novoa, Beatriz Figueras, Antonio PLoS One Research Article 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 variety of sequences belonging to genes involved in the defense mechanisms. Public Library of Science 2012-05-18 /pmc/articles/PMC3356354/ /pubmed/22629298 http://dx.doi.org/10.1371/journal.pone.0035369 Text en Pereiro et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Pereiro, Patricia
Balseiro, Pablo
Romero, Alejandro
Dios, Sonia
Forn-Cuni, Gabriel
Fuste, Berta
Planas, Josep V.
Beltran, Sergi
Novoa, Beatriz
Figueras, Antonio
High-Throughput Sequence Analysis of Turbot (Scophthalmus maximus) Transcriptome Using 454-Pyrosequencing for the Discovery of Antiviral Immune Genes
title 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_short 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
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3356354/
https://www.ncbi.nlm.nih.gov/pubmed/22629298
http://dx.doi.org/10.1371/journal.pone.0035369
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