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 path...
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ftdoajarticles:oai:doaj.org/article:5775e41877e1454e895a98d44e82ffec 2023-05-15T18:15:46+02:00 High-throughput sequence analysis of turbot (Scophthalmus maximus) transcriptome using 454-pyrosequencing for the discovery of antiviral immune genes. Patricia Pereiro Pablo Balseiro Alejandro Romero Sonia Dios Gabriel Forn-Cuni Berta Fuste Josep V Planas Sergi Beltran Beatriz Novoa Antonio Figueras 2012-01-01T00:00:00Z https://doi.org/10.1371/journal.pone.0035369 https://doaj.org/article/5775e41877e1454e895a98d44e82ffec EN eng Public Library of Science (PLoS) https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22629298/pdf/?tool=EBI https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0035369 https://doaj.org/article/5775e41877e1454e895a98d44e82ffec PLoS ONE, Vol 7, Iss 5, p e35369 (2012) Medicine R Science Q article 2012 ftdoajarticles https://doi.org/10.1371/journal.pone.0035369 2022-12-31T05:21:47Z 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 ... Article in Journal/Newspaper Scophthalmus maximus Turbot Directory of Open Access Journals: DOAJ Articles PLoS ONE 7 5 e35369 |
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Directory of Open Access Journals: DOAJ Articles |
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topic |
Medicine R Science Q |
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Medicine R Science Q Patricia Pereiro Pablo Balseiro Alejandro Romero Sonia Dios Gabriel Forn-Cuni Berta Fuste Josep V Planas Sergi Beltran Beatriz Novoa Antonio Figueras High-throughput sequence analysis of turbot (Scophthalmus maximus) transcriptome using 454-pyrosequencing for the discovery of antiviral immune genes. |
topic_facet |
Medicine R Science Q |
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 ... |
format |
Article in Journal/Newspaper |
author |
Patricia Pereiro Pablo Balseiro Alejandro Romero Sonia Dios Gabriel Forn-Cuni Berta Fuste Josep V Planas Sergi Beltran Beatriz Novoa Antonio Figueras |
author_facet |
Patricia Pereiro Pablo Balseiro Alejandro Romero Sonia Dios Gabriel Forn-Cuni Berta Fuste Josep V Planas Sergi Beltran Beatriz Novoa Antonio Figueras |
author_sort |
Patricia Pereiro |
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 (PLoS) |
publishDate |
2012 |
url |
https://doi.org/10.1371/journal.pone.0035369 https://doaj.org/article/5775e41877e1454e895a98d44e82ffec |
genre |
Scophthalmus maximus Turbot |
genre_facet |
Scophthalmus maximus Turbot |
op_source |
PLoS ONE, Vol 7, Iss 5, p e35369 (2012) |
op_relation |
https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22629298/pdf/?tool=EBI https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0035369 https://doaj.org/article/5775e41877e1454e895a98d44e82ffec |
op_doi |
https://doi.org/10.1371/journal.pone.0035369 |
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PLoS ONE |
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7 |
container_issue |
5 |
container_start_page |
e35369 |
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