A combined strategy involving Sanger and 454 pyrosequencing increases genomic resources to aid in the management of reproduction, disease control and genetic selection in the turbot (Scophthalmus maximus)
Abstract Background Genomic resources for plant and animal species that are under exploitation primarily for human consumption are increasingly important, among other things, for understanding physiological processes and for establishing adequate genetic selection programs. Current available techniq...
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ftbiomed:oai:biomedcentral.com:1471-2164-14-180 2023-05-15T18:15:54+02:00 A combined strategy involving Sanger and 454 pyrosequencing increases genomic resources to aid in the management of reproduction, disease control and genetic selection in the turbot (Scophthalmus maximus) Ribas, Laia Pardo, Belén G Fernández, Carlos Álvarez-Diós, José Gómez-Tato, Antonio Quiroga, María Planas, Josep V Sitjà-Bobadilla, Ariadna Martínez, Paulino Piferrer, Francesc 2013-03-15 http://www.biomedcentral.com/1471-2164/14/180 en eng BioMed Central Ltd. http://www.biomedcentral.com/1471-2164/14/180 Copyright 2013 Ribas et al.; licensee BioMed Central Ltd. Turbot NGS Database Transcriptome Reproduction Immune Genetic Markers SNP Microsatellite Microarray Natural Antisense Transcripts MicroRNA Research article 2013 ftbiomed 2013-07-07T00:12:58Z Abstract Background Genomic resources for plant and animal species that are under exploitation primarily for human consumption are increasingly important, among other things, for understanding physiological processes and for establishing adequate genetic selection programs. Current available techniques for high-throughput sequencing have been implemented in a number of species, including fish, to obtain a proper description of the transcriptome. The objective of this study was to generate a comprehensive transcriptomic database in turbot, a highly priced farmed fish species in Europe, with potential expansion to other areas of the world, for which there are unsolved production bottlenecks, to understand better reproductive- and immune-related functions. This information is essential to implement marker assisted selection programs useful for the turbot industry. Results Expressed sequence tags were generated by Sanger sequencing of cDNA libraries from different immune-related tissues after several parasitic challenges. The resulting database (“Turbot 2 database”) was enlarged with sequences generated from a 454 sequencing run of brain-hypophysis-gonadal axis-derived RNA obtained from turbot at different development stages. The assembly of Sanger and 454 sequences generated 52,427 consensus sequences (“Turbot 3 database”), of which 23,661 were successfully annotated. A total of 1,410 sequences were confirmed to be related to reproduction and key genes involved in sex differentiation and maturation were identified for the first time in turbot ( AR , AMH , SRY -related genes, CYP19A , ZPG s, STAR FSHR, etc.). Similarly, 2,241 sequences were related to the immune system and several novel key immune genes were identified ( BCL , TRAF , NCK , CD28 and TOLLIP, among others). The number of genes of many relevant reproduction- and immune-related pathways present in the database was 50–90% of the total gene count of each pathway. In addition, 1,237 microsatellites and 7,362 single nucleotide polymorphisms (SNPs) were also compiled. Further, 2,976 putative natural antisense transcripts (NATs) including microRNAs were also identified. Conclusions The combined sequencing strategies employed here significantly increased the turbot genomic resources available, including 34,400 novel sequences. The generated database contains a . Article in Journal/Newspaper Scophthalmus maximus Turbot BioMed Central |
institution |
Open Polar |
collection |
BioMed Central |
op_collection_id |
ftbiomed |
language |
English |
topic |
Turbot NGS Database Transcriptome Reproduction Immune Genetic Markers SNP Microsatellite Microarray Natural Antisense Transcripts MicroRNA |
spellingShingle |
Turbot NGS Database Transcriptome Reproduction Immune Genetic Markers SNP Microsatellite Microarray Natural Antisense Transcripts MicroRNA Ribas, Laia Pardo, Belén G Fernández, Carlos Álvarez-Diós, José Gómez-Tato, Antonio Quiroga, María Planas, Josep V Sitjà-Bobadilla, Ariadna Martínez, Paulino Piferrer, Francesc A combined strategy involving Sanger and 454 pyrosequencing increases genomic resources to aid in the management of reproduction, disease control and genetic selection in the turbot (Scophthalmus maximus) |
topic_facet |
Turbot NGS Database Transcriptome Reproduction Immune Genetic Markers SNP Microsatellite Microarray Natural Antisense Transcripts MicroRNA |
description |
Abstract Background Genomic resources for plant and animal species that are under exploitation primarily for human consumption are increasingly important, among other things, for understanding physiological processes and for establishing adequate genetic selection programs. Current available techniques for high-throughput sequencing have been implemented in a number of species, including fish, to obtain a proper description of the transcriptome. The objective of this study was to generate a comprehensive transcriptomic database in turbot, a highly priced farmed fish species in Europe, with potential expansion to other areas of the world, for which there are unsolved production bottlenecks, to understand better reproductive- and immune-related functions. This information is essential to implement marker assisted selection programs useful for the turbot industry. Results Expressed sequence tags were generated by Sanger sequencing of cDNA libraries from different immune-related tissues after several parasitic challenges. The resulting database (“Turbot 2 database”) was enlarged with sequences generated from a 454 sequencing run of brain-hypophysis-gonadal axis-derived RNA obtained from turbot at different development stages. The assembly of Sanger and 454 sequences generated 52,427 consensus sequences (“Turbot 3 database”), of which 23,661 were successfully annotated. A total of 1,410 sequences were confirmed to be related to reproduction and key genes involved in sex differentiation and maturation were identified for the first time in turbot ( AR , AMH , SRY -related genes, CYP19A , ZPG s, STAR FSHR, etc.). Similarly, 2,241 sequences were related to the immune system and several novel key immune genes were identified ( BCL , TRAF , NCK , CD28 and TOLLIP, among others). The number of genes of many relevant reproduction- and immune-related pathways present in the database was 50–90% of the total gene count of each pathway. In addition, 1,237 microsatellites and 7,362 single nucleotide polymorphisms (SNPs) were also compiled. Further, 2,976 putative natural antisense transcripts (NATs) including microRNAs were also identified. Conclusions The combined sequencing strategies employed here significantly increased the turbot genomic resources available, including 34,400 novel sequences. The generated database contains a . |
format |
Article in Journal/Newspaper |
author |
Ribas, Laia Pardo, Belén G Fernández, Carlos Álvarez-Diós, José Gómez-Tato, Antonio Quiroga, María Planas, Josep V Sitjà-Bobadilla, Ariadna Martínez, Paulino Piferrer, Francesc |
author_facet |
Ribas, Laia Pardo, Belén G Fernández, Carlos Álvarez-Diós, José Gómez-Tato, Antonio Quiroga, María Planas, Josep V Sitjà-Bobadilla, Ariadna Martínez, Paulino Piferrer, Francesc |
author_sort |
Ribas, Laia |
title |
A combined strategy involving Sanger and 454 pyrosequencing increases genomic resources to aid in the management of reproduction, disease control and genetic selection in the turbot (Scophthalmus maximus) |
title_short |
A combined strategy involving Sanger and 454 pyrosequencing increases genomic resources to aid in the management of reproduction, disease control and genetic selection in the turbot (Scophthalmus maximus) |
title_full |
A combined strategy involving Sanger and 454 pyrosequencing increases genomic resources to aid in the management of reproduction, disease control and genetic selection in the turbot (Scophthalmus maximus) |
title_fullStr |
A combined strategy involving Sanger and 454 pyrosequencing increases genomic resources to aid in the management of reproduction, disease control and genetic selection in the turbot (Scophthalmus maximus) |
title_full_unstemmed |
A combined strategy involving Sanger and 454 pyrosequencing increases genomic resources to aid in the management of reproduction, disease control and genetic selection in the turbot (Scophthalmus maximus) |
title_sort |
combined strategy involving sanger and 454 pyrosequencing increases genomic resources to aid in the management of reproduction, disease control and genetic selection in the turbot (scophthalmus maximus) |
publisher |
BioMed Central Ltd. |
publishDate |
2013 |
url |
http://www.biomedcentral.com/1471-2164/14/180 |
genre |
Scophthalmus maximus Turbot |
genre_facet |
Scophthalmus maximus Turbot |
op_relation |
http://www.biomedcentral.com/1471-2164/14/180 |
op_rights |
Copyright 2013 Ribas et al.; licensee BioMed Central Ltd. |
_version_ |
1766189146369425408 |