Sequencing and characterization of striped venus transcriptome expand resources for clam fishery genetics
The striped venus Chamelea gallina clam fishery is among the oldest and the largest in the Mediterranean Sea, particularly in the inshore waters of northern Adriatic Sea. The high fishing pressure has lead to a strong stock abundance decline, enhanced by several irregular mortality events. The nearl...
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| Veröffentlicht in: | PloS one 2012-09, Vol.7 (9), p.e44185-e44185 |
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| creator | Coppe, Alessandro Bortoluzzi, Stefania Murari, Giulia Marino, Ilaria Anna Maria Zane, Lorenzo Papetti, Chiara |
| description | The striped venus Chamelea gallina clam fishery is among the oldest and the largest in the Mediterranean Sea, particularly in the inshore waters of northern Adriatic Sea. The high fishing pressure has lead to a strong stock abundance decline, enhanced by several irregular mortality events. The nearly complete lack of molecular characterization limits the available genetic resources for C. gallina. We achieved the first transcriptome of this species with the aim of identifying an informative set of expressed genes, potential markers to assess genetic structure of natural populations and molecular resources for pathogenic contamination detection.
The 454-pyrosequencing of a normalized cDNA library of a pool C. gallina adult individuals yielded 298,494 raw reads. Different steps of reads assembly and filtering produced 36,422 contigs of high quality, one half of which (18,196) were annotated by similarity. A total of 111 microsatellites and 20,377 putative SNPs were identified. A panel of 13 polymorphic transcript-linked microsatellites was developed and their variability assessed in 12 individuals. Remarkably, a scan to search for contamination sequences of infectious origin indicated the presence of several Vibrionales species reported to be among the most frequent clam pathogen's species. Results reported in this study were included in a dedicated database available at http://compgen.bio.unipd.it/chameleabase.
This study represents the first attempt to sequence and de novo annotate the transcriptome of the clam C. gallina. The availability of this transcriptome opens new perspectives in the study of biochemical and physiological role of gene products and their responses to large and small-scale environmental stress in C. gallina, with high throughput experiments such as custom microarray or targeted re-sequencing. Molecular markers, such as the already optimized EST-linked microsatellites and the discovered SNPs will be useful to estimate effects of demographic processes and to detect minute levels of population structuring. |
| doi_str_mv | 10.1371/journal.pone.0044185 |
| format | Article |
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The 454-pyrosequencing of a normalized cDNA library of a pool C. gallina adult individuals yielded 298,494 raw reads. Different steps of reads assembly and filtering produced 36,422 contigs of high quality, one half of which (18,196) were annotated by similarity. A total of 111 microsatellites and 20,377 putative SNPs were identified. A panel of 13 polymorphic transcript-linked microsatellites was developed and their variability assessed in 12 individuals. Remarkably, a scan to search for contamination sequences of infectious origin indicated the presence of several Vibrionales species reported to be among the most frequent clam pathogen's species. Results reported in this study were included in a dedicated database available at http://compgen.bio.unipd.it/chameleabase.
This study represents the first attempt to sequence and de novo annotate the transcriptome of the clam C. gallina. The availability of this transcriptome opens new perspectives in the study of biochemical and physiological role of gene products and their responses to large and small-scale environmental stress in C. gallina, with high throughput experiments such as custom microarray or targeted re-sequencing. Molecular markers, such as the already optimized EST-linked microsatellites and the discovered SNPs will be useful to estimate effects of demographic processes and to detect minute levels of population structuring.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0044185</identifier><identifier>PMID: 23028497</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Animals ; Automation ; Bioinformatics ; Biological diversity ; Biology ; Bivalvia ; Bivalvia - genetics ; Chamelea gallina ; Commercial fishing ; Computational Biology - methods ; Contamination ; Databases, Nucleic Acid ; Demographics ; Deoxyribonucleic acid ; DNA ; DNA microarrays ; DNA sequencing ; Ecology ; Ecosystem biology ; Ecosystems ; Environmental stress ; Filtration ; Fisheries ; Fisheries management ; Fishing ; Gene expression ; Gene Expression Profiling ; Genetic aspects ; Genetic resources ; Genetic structure ; Genetics ; Genomes ; Genomics ; High-Throughput Nucleotide Sequencing ; Internet ; Markers ; Microsatellite Repeats ; Microsatellites ; Molecular Sequence Annotation ; Molecular structure ; Mollusca ; Natural populations ; Nucleotide sequencing ; Physiological aspects ; Placopecten magellanicus ; Polymorphism, Single Nucleotide ; Population genetics ; Quality ; Single-nucleotide polymorphism ; Species ; Studies ; Transcription ; Transcriptome ; Venus ; Venus (planet) ; Veterinary Science</subject><ispartof>PloS one, 2012-09, Vol.7 (9), p.e44185-e44185</ispartof><rights>COPYRIGHT 2012 Public Library of Science</rights><rights>Coppe et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2012 Coppe et al 2012 Coppe et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-aa3a19f7b616438aa5a50be7f773bf831faa580ac3437b40ac81a83646c1ae9b3</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3445586/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3445586/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23847,27903,27904,53768,53770,79345,79346</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23028497$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Liu, Zhanjiang</contributor><creatorcontrib>Coppe, Alessandro</creatorcontrib><creatorcontrib>Bortoluzzi, Stefania</creatorcontrib><creatorcontrib>Murari, Giulia</creatorcontrib><creatorcontrib>Marino, Ilaria Anna Maria</creatorcontrib><creatorcontrib>Zane, Lorenzo</creatorcontrib><creatorcontrib>Papetti, Chiara</creatorcontrib><title>Sequencing and characterization of striped venus transcriptome expand resources for clam fishery genetics</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The striped venus Chamelea gallina clam fishery is among the oldest and the largest in the Mediterranean Sea, particularly in the inshore waters of northern Adriatic Sea. The high fishing pressure has lead to a strong stock abundance decline, enhanced by several irregular mortality events. The nearly complete lack of molecular characterization limits the available genetic resources for C. gallina. We achieved the first transcriptome of this species with the aim of identifying an informative set of expressed genes, potential markers to assess genetic structure of natural populations and molecular resources for pathogenic contamination detection.
The 454-pyrosequencing of a normalized cDNA library of a pool C. gallina adult individuals yielded 298,494 raw reads. Different steps of reads assembly and filtering produced 36,422 contigs of high quality, one half of which (18,196) were annotated by similarity. A total of 111 microsatellites and 20,377 putative SNPs were identified. A panel of 13 polymorphic transcript-linked microsatellites was developed and their variability assessed in 12 individuals. Remarkably, a scan to search for contamination sequences of infectious origin indicated the presence of several Vibrionales species reported to be among the most frequent clam pathogen's species. Results reported in this study were included in a dedicated database available at http://compgen.bio.unipd.it/chameleabase.
This study represents the first attempt to sequence and de novo annotate the transcriptome of the clam C. gallina. The availability of this transcriptome opens new perspectives in the study of biochemical and physiological role of gene products and their responses to large and small-scale environmental stress in C. gallina, with high throughput experiments such as custom microarray or targeted re-sequencing. Molecular markers, such as the already optimized EST-linked microsatellites and the discovered SNPs will be useful to estimate effects of demographic processes and to detect minute levels of population structuring.</description><subject>Animals</subject><subject>Automation</subject><subject>Bioinformatics</subject><subject>Biological diversity</subject><subject>Biology</subject><subject>Bivalvia</subject><subject>Bivalvia - genetics</subject><subject>Chamelea gallina</subject><subject>Commercial fishing</subject><subject>Computational Biology - methods</subject><subject>Contamination</subject><subject>Databases, Nucleic Acid</subject><subject>Demographics</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA microarrays</subject><subject>DNA sequencing</subject><subject>Ecology</subject><subject>Ecosystem biology</subject><subject>Ecosystems</subject><subject>Environmental stress</subject><subject>Filtration</subject><subject>Fisheries</subject><subject>Fisheries management</subject><subject>Fishing</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Genetic aspects</subject><subject>Genetic resources</subject><subject>Genetic structure</subject><subject>Genetics</subject><subject>Genomes</subject><subject>Genomics</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Internet</subject><subject>Markers</subject><subject>Microsatellite Repeats</subject><subject>Microsatellites</subject><subject>Molecular Sequence Annotation</subject><subject>Molecular structure</subject><subject>Mollusca</subject><subject>Natural populations</subject><subject>Nucleotide sequencing</subject><subject>Physiological aspects</subject><subject>Placopecten magellanicus</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Population genetics</subject><subject>Quality</subject><subject>Single-nucleotide polymorphism</subject><subject>Species</subject><subject>Studies</subject><subject>Transcription</subject><subject>Transcriptome</subject><subject>Venus</subject><subject>Venus (planet)</subject><subject>Veterinary 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and characterization of striped venus transcriptome expand resources for clam fishery genetics</title><author>Coppe, Alessandro ; Bortoluzzi, Stefania ; Murari, Giulia ; Marino, Ilaria Anna Maria ; Zane, Lorenzo ; Papetti, Chiara</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-aa3a19f7b616438aa5a50be7f773bf831faa580ac3437b40ac81a83646c1ae9b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Animals</topic><topic>Automation</topic><topic>Bioinformatics</topic><topic>Biological diversity</topic><topic>Biology</topic><topic>Bivalvia</topic><topic>Bivalvia - genetics</topic><topic>Chamelea gallina</topic><topic>Commercial fishing</topic><topic>Computational Biology - methods</topic><topic>Contamination</topic><topic>Databases, Nucleic Acid</topic><topic>Demographics</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA microarrays</topic><topic>DNA sequencing</topic><topic>Ecology</topic><topic>Ecosystem biology</topic><topic>Ecosystems</topic><topic>Environmental stress</topic><topic>Filtration</topic><topic>Fisheries</topic><topic>Fisheries management</topic><topic>Fishing</topic><topic>Gene expression</topic><topic>Gene Expression Profiling</topic><topic>Genetic aspects</topic><topic>Genetic resources</topic><topic>Genetic structure</topic><topic>Genetics</topic><topic>Genomes</topic><topic>Genomics</topic><topic>High-Throughput Nucleotide Sequencing</topic><topic>Internet</topic><topic>Markers</topic><topic>Microsatellite Repeats</topic><topic>Microsatellites</topic><topic>Molecular Sequence Annotation</topic><topic>Molecular structure</topic><topic>Mollusca</topic><topic>Natural populations</topic><topic>Nucleotide sequencing</topic><topic>Physiological aspects</topic><topic>Placopecten magellanicus</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Population genetics</topic><topic>Quality</topic><topic>Single-nucleotide polymorphism</topic><topic>Species</topic><topic>Studies</topic><topic>Transcription</topic><topic>Transcriptome</topic><topic>Venus</topic><topic>Venus (planet)</topic><topic>Veterinary Science</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Coppe, Alessandro</creatorcontrib><creatorcontrib>Bortoluzzi, Stefania</creatorcontrib><creatorcontrib>Murari, Giulia</creatorcontrib><creatorcontrib>Marino, Ilaria Anna Maria</creatorcontrib><creatorcontrib>Zane, Lorenzo</creatorcontrib><creatorcontrib>Papetti, Chiara</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: Opposing Viewpoints</collection><collection>Gale In Context: Science</collection><collection>ProQuest 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One</addtitle><date>2012-09-18</date><risdate>2012</risdate><volume>7</volume><issue>9</issue><spage>e44185</spage><epage>e44185</epage><pages>e44185-e44185</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>The striped venus Chamelea gallina clam fishery is among the oldest and the largest in the Mediterranean Sea, particularly in the inshore waters of northern Adriatic Sea. The high fishing pressure has lead to a strong stock abundance decline, enhanced by several irregular mortality events. The nearly complete lack of molecular characterization limits the available genetic resources for C. gallina. We achieved the first transcriptome of this species with the aim of identifying an informative set of expressed genes, potential markers to assess genetic structure of natural populations and molecular resources for pathogenic contamination detection.
The 454-pyrosequencing of a normalized cDNA library of a pool C. gallina adult individuals yielded 298,494 raw reads. Different steps of reads assembly and filtering produced 36,422 contigs of high quality, one half of which (18,196) were annotated by similarity. A total of 111 microsatellites and 20,377 putative SNPs were identified. A panel of 13 polymorphic transcript-linked microsatellites was developed and their variability assessed in 12 individuals. Remarkably, a scan to search for contamination sequences of infectious origin indicated the presence of several Vibrionales species reported to be among the most frequent clam pathogen's species. Results reported in this study were included in a dedicated database available at http://compgen.bio.unipd.it/chameleabase.
This study represents the first attempt to sequence and de novo annotate the transcriptome of the clam C. gallina. The availability of this transcriptome opens new perspectives in the study of biochemical and physiological role of gene products and their responses to large and small-scale environmental stress in C. gallina, with high throughput experiments such as custom microarray or targeted re-sequencing. Molecular markers, such as the already optimized EST-linked microsatellites and the discovered SNPs will be useful to estimate effects of demographic processes and to detect minute levels of population structuring.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>23028497</pmid><doi>10.1371/journal.pone.0044185</doi><tpages>e44185</tpages><oa>free_for_read</oa></addata></record> |
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| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2012-09, Vol.7 (9), p.e44185-e44185 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1344508703 |
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| subjects | Animals Automation Bioinformatics Biological diversity Biology Bivalvia Bivalvia - genetics Chamelea gallina Commercial fishing Computational Biology - methods Contamination Databases, Nucleic Acid Demographics Deoxyribonucleic acid DNA DNA microarrays DNA sequencing Ecology Ecosystem biology Ecosystems Environmental stress Filtration Fisheries Fisheries management Fishing Gene expression Gene Expression Profiling Genetic aspects Genetic resources Genetic structure Genetics Genomes Genomics High-Throughput Nucleotide Sequencing Internet Markers Microsatellite Repeats Microsatellites Molecular Sequence Annotation Molecular structure Mollusca Natural populations Nucleotide sequencing Physiological aspects Placopecten magellanicus Polymorphism, Single Nucleotide Population genetics Quality Single-nucleotide polymorphism Species Studies Transcription Transcriptome Venus Venus (planet) Veterinary Science |
| title | Sequencing and characterization of striped venus transcriptome expand resources for clam fishery genetics |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-28T09%3A28%3A38IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Sequencing%20and%20characterization%20of%20striped%20venus%20transcriptome%20expand%20resources%20for%20clam%20fishery%20genetics&rft.jtitle=PloS%20one&rft.au=Coppe,%20Alessandro&rft.date=2012-09-18&rft.volume=7&rft.issue=9&rft.spage=e44185&rft.epage=e44185&rft.pages=e44185-e44185&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0044185&rft_dat=%3Cgale_plos_%3EA498262350%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1344508703&rft_id=info:pmid/23028497&rft_galeid=A498262350&rft_doaj_id=oai_doaj_org_article_af34eb47360040f2bec116707bb4b27e&rfr_iscdi=true |