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)
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-through...
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| Veröffentlicht in: | BMC genomics 2013-03, Vol.14 (1), p.180-180, Article 180 |
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| creator | Ribas, Laia Pardo, Belén G Fernández, Carlos Alvarez-Diós, José Antonio Gómez-Tato, Antonio Quiroga, María Isabel Planas, Josep V Sitjà-Bobadilla, Ariadna Martínez, Paulino Piferrer, Francesc |
| description | 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.
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, ZPGs, 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.
The combined sequencing strategies employed here significantly increased the turbot genomic resources available, including 34,400 novel sequences. The generated database contains a larger number of genes relevant for reproduction- and immune-associated studies, with an excellent coverage of most genes present in many relevant physiological pathways. This database also allowed |
| doi_str_mv | 10.1186/1471-2164-14-180 |
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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, ZPGs, 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.
The combined sequencing strategies employed here significantly increased the turbot genomic resources available, including 34,400 novel sequences. The generated database contains a larger number of genes relevant for reproduction- and immune-associated studies, with an excellent coverage of most genes present in many relevant physiological pathways. This database also allowed the identification of many microsatellites and SNP markers that will be very useful for population and genome screening and a valuable aid in marker assisted selection programs.</description><identifier>ISSN: 1471-2164</identifier><identifier>EISSN: 1471-2164</identifier><identifier>DOI: 10.1186/1471-2164-14-180</identifier><identifier>PMID: 23497389</identifier><language>eng</language><publisher>England: BioMed Central Ltd</publisher><subject>Animals ; Aquaculture ; Breeding ; Breeding - methods ; Chromosomes ; Databases, Genetic ; DNA sequencing ; Fish Diseases - prevention & control ; Fish-culture ; Fishes ; Flatfishes ; Flatfishes - genetics ; Flatfishes - immunology ; Flatfishes - physiology ; Genetic aspects ; Genetic markers ; Genetic Markers - genetics ; Genomics ; Humans ; Instrument industry ; Methods ; Millora de les espècies ; Molecular Sequence Annotation ; Nucleotide sequencing ; Oligonucleotide Array Sequence Analysis ; Peixos ; Physiological aspects ; Polymorphism, Single Nucleotide ; Reproduction - genetics ; RNA, Antisense - genetics ; RNA, Messenger - genetics ; Scophthalmus maximus ; Sequence Analysis, RNA ; Single nucleotide polymorphisms</subject><ispartof>BMC genomics, 2013-03, Vol.14 (1), p.180-180, Article 180</ispartof><rights>COPYRIGHT 2013 BioMed Central Ltd.</rights><rights>cc-by (c) Ribas et al., 2013 info:eu-repo/semantics/openAccess <a href="http://creativecommons.org/licenses/by/3.0/es">http://creativecommons.org/licenses/by/3.0/es</a></rights><rights>Copyright © 2013 Ribas et al.; licensee BioMed Central Ltd. 2013 Ribas et al.; licensee BioMed Central Ltd.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-b632t-dcea18267ca940694e53528b9a04237870808b6f3c98a1273c6c3cd22bb73beb3</citedby><cites>FETCH-LOGICAL-b632t-dcea18267ca940694e53528b9a04237870808b6f3c98a1273c6c3cd22bb73beb3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3700835/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3700835/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,26951,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23497389$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Ribas, Laia</creatorcontrib><creatorcontrib>Pardo, Belén G</creatorcontrib><creatorcontrib>Fernández, Carlos</creatorcontrib><creatorcontrib>Alvarez-Diós, José Antonio</creatorcontrib><creatorcontrib>Gómez-Tato, Antonio</creatorcontrib><creatorcontrib>Quiroga, María Isabel</creatorcontrib><creatorcontrib>Planas, Josep V</creatorcontrib><creatorcontrib>Sitjà-Bobadilla, Ariadna</creatorcontrib><creatorcontrib>Martínez, Paulino</creatorcontrib><creatorcontrib>Piferrer, Francesc</creatorcontrib><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><title>BMC genomics</title><addtitle>BMC Genomics</addtitle><description>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.
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, ZPGs, 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.
The combined sequencing strategies employed here significantly increased the turbot genomic resources available, including 34,400 novel sequences. The generated database contains a larger number of genes relevant for reproduction- and immune-associated studies, with an excellent coverage of most genes present in many relevant physiological pathways. This database also allowed the identification of many microsatellites and SNP markers that will be very useful for population and genome screening and a valuable aid in marker assisted selection programs.</description><subject>Animals</subject><subject>Aquaculture</subject><subject>Breeding</subject><subject>Breeding - methods</subject><subject>Chromosomes</subject><subject>Databases, Genetic</subject><subject>DNA sequencing</subject><subject>Fish Diseases - prevention & control</subject><subject>Fish-culture</subject><subject>Fishes</subject><subject>Flatfishes</subject><subject>Flatfishes - genetics</subject><subject>Flatfishes - immunology</subject><subject>Flatfishes - physiology</subject><subject>Genetic aspects</subject><subject>Genetic markers</subject><subject>Genetic Markers - genetics</subject><subject>Genomics</subject><subject>Humans</subject><subject>Instrument industry</subject><subject>Methods</subject><subject>Millora de les espècies</subject><subject>Molecular Sequence Annotation</subject><subject>Nucleotide sequencing</subject><subject>Oligonucleotide Array Sequence Analysis</subject><subject>Peixos</subject><subject>Physiological aspects</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Reproduction - genetics</subject><subject>RNA, Antisense - genetics</subject><subject>RNA, Messenger - genetics</subject><subject>Scophthalmus maximus</subject><subject>Sequence Analysis, RNA</subject><subject>Single nucleotide polymorphisms</subject><issn>1471-2164</issn><issn>1471-2164</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>XX2</sourceid><recordid>eNqFU01r3DAQNaWlSdPeeyqCXhLopvqwLfkSWEI_AoFC056FLM96VWxpK8kh-Y_9UR1nkyULKcU2kmfeexpmnoriLaOnjKn6IyslW3BWlwuGr6LPisNd6Pmj_UHxKqVflDKpePWyOOCibKRQzWHxZ0lsGFvnoSMpR5OhvyXOX4fh2vmeXBnfQyTGd6SsSrK5jSHB7wm8nbPO2wgmQSI9-DA6SyKkMEWLkRyIcR1CSF4DGY03PYzgMwkrRG1i6CabXfAfSOfSLIJ1-BzDcHcY6kFGvQQD3MEehPIU25DJ8ZUNm3Vem2GcEqrfOFxPXhcvVmZI8OZ-PSp-fv704_zr4vLbl4vz5eWirQXPi86CYYrX0pqmpHVTQiUqrtrG0JILqSRVVLX1SthGGcalsLUVtuO8baVooRVHxdlWdzO1I6AcFm4GvYluNPFWB-P0fsa7te7DtRaSUiUqFGBbAZsmqyNYiNbkO-LuZ_44lVzzWjSyQc75ltO68I9D9zM4Vz07QM8OwJ1Gg6DK8X3pMeAcU9ajSxaGwXgIU0IY4xXaRKr_Q0WjSiHqaq7t_RbamwG086uAFdgZrpeVQOc0gklEnT6BwqcD9E7wsHIY3yOc7BFmh8BN7s2Ukr64-r6PpfctRYumCKtdZxjV82V5qhfvHo9xR3i4HeIvs6sSaw</recordid><startdate>20130315</startdate><enddate>20130315</enddate><creator>Ribas, Laia</creator><creator>Pardo, Belén G</creator><creator>Fernández, Carlos</creator><creator>Alvarez-Diós, José Antonio</creator><creator>Gómez-Tato, Antonio</creator><creator>Quiroga, María Isabel</creator><creator>Planas, Josep V</creator><creator>Sitjà-Bobadilla, Ariadna</creator><creator>Martínez, Paulino</creator><creator>Piferrer, Francesc</creator><general>BioMed Central Ltd</general><general>BioMed Central</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>ISR</scope><scope>7X8</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>XX2</scope><scope>5PM</scope></search><sort><creationdate>20130315</creationdate><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><author>Ribas, Laia ; Pardo, Belén G ; Fernández, Carlos ; Alvarez-Diós, José Antonio ; Gómez-Tato, Antonio ; Quiroga, María Isabel ; Planas, Josep V ; Sitjà-Bobadilla, Ariadna ; Martínez, Paulino ; Piferrer, Francesc</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-b632t-dcea18267ca940694e53528b9a04237870808b6f3c98a1273c6c3cd22bb73beb3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Animals</topic><topic>Aquaculture</topic><topic>Breeding</topic><topic>Breeding - methods</topic><topic>Chromosomes</topic><topic>Databases, Genetic</topic><topic>DNA sequencing</topic><topic>Fish Diseases - prevention & control</topic><topic>Fish-culture</topic><topic>Fishes</topic><topic>Flatfishes</topic><topic>Flatfishes - genetics</topic><topic>Flatfishes - immunology</topic><topic>Flatfishes - physiology</topic><topic>Genetic aspects</topic><topic>Genetic markers</topic><topic>Genetic Markers - genetics</topic><topic>Genomics</topic><topic>Humans</topic><topic>Instrument industry</topic><topic>Methods</topic><topic>Millora de les espècies</topic><topic>Molecular Sequence Annotation</topic><topic>Nucleotide sequencing</topic><topic>Oligonucleotide Array Sequence Analysis</topic><topic>Peixos</topic><topic>Physiological aspects</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Reproduction - genetics</topic><topic>RNA, Antisense - genetics</topic><topic>RNA, Messenger - genetics</topic><topic>Scophthalmus maximus</topic><topic>Sequence Analysis, RNA</topic><topic>Single nucleotide polymorphisms</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ribas, Laia</creatorcontrib><creatorcontrib>Pardo, Belén G</creatorcontrib><creatorcontrib>Fernández, Carlos</creatorcontrib><creatorcontrib>Alvarez-Diós, José Antonio</creatorcontrib><creatorcontrib>Gómez-Tato, Antonio</creatorcontrib><creatorcontrib>Quiroga, María Isabel</creatorcontrib><creatorcontrib>Planas, Josep V</creatorcontrib><creatorcontrib>Sitjà-Bobadilla, Ariadna</creatorcontrib><creatorcontrib>Martínez, Paulino</creatorcontrib><creatorcontrib>Piferrer, Francesc</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Science</collection><collection>MEDLINE - Academic</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>Recercat</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>BMC genomics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ribas, Laia</au><au>Pardo, Belén G</au><au>Fernández, Carlos</au><au>Alvarez-Diós, José Antonio</au><au>Gómez-Tato, Antonio</au><au>Quiroga, María Isabel</au><au>Planas, Josep V</au><au>Sitjà-Bobadilla, Ariadna</au><au>Martínez, Paulino</au><au>Piferrer, Francesc</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>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)</atitle><jtitle>BMC genomics</jtitle><addtitle>BMC Genomics</addtitle><date>2013-03-15</date><risdate>2013</risdate><volume>14</volume><issue>1</issue><spage>180</spage><epage>180</epage><pages>180-180</pages><artnum>180</artnum><issn>1471-2164</issn><eissn>1471-2164</eissn><abstract>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.
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, ZPGs, 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.
The combined sequencing strategies employed here significantly increased the turbot genomic resources available, including 34,400 novel sequences. The generated database contains a larger number of genes relevant for reproduction- and immune-associated studies, with an excellent coverage of most genes present in many relevant physiological pathways. This database also allowed the identification of many microsatellites and SNP markers that will be very useful for population and genome screening and a valuable aid in marker assisted selection programs.</abstract><cop>England</cop><pub>BioMed Central Ltd</pub><pmid>23497389</pmid><doi>10.1186/1471-2164-14-180</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; Springer Nature - Complete Springer Journals; DOAJ Directory of Open Access Journals; Recercat; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; PubMed Central Open Access; Springer Nature OA Free Journals |
| subjects | Animals Aquaculture Breeding Breeding - methods Chromosomes Databases, Genetic DNA sequencing Fish Diseases - prevention & control Fish-culture Fishes Flatfishes Flatfishes - genetics Flatfishes - immunology Flatfishes - physiology Genetic aspects Genetic markers Genetic Markers - genetics Genomics Humans Instrument industry Methods Millora de les espècies Molecular Sequence Annotation Nucleotide sequencing Oligonucleotide Array Sequence Analysis Peixos Physiological aspects Polymorphism, Single Nucleotide Reproduction - genetics RNA, Antisense - genetics RNA, Messenger - genetics Scophthalmus maximus Sequence Analysis, RNA Single nucleotide polymorphisms |
| 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) |
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