Analysis of a deep transcriptome from the mantle tissue of Patella vulgata Linnaeus (Mollusca: Gastropoda: Patellidae) reveals candidate biomineralising genes
The gastropod Patella vulgata is abundant on rocky shores in Northern Europe and a significant grazer of intertidal algae. Here we report the application of Illumina sequencing to develop a transcriptome from the adult mantle tissue of P. vulgata. We obtained 47,237,104 paired-end reads of 51 bp, tr...
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| Veröffentlicht in: | Marine biotechnology (New York, N.Y.) N.Y.), 2013-04, Vol.15 (2), p.230-243 |
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| creator | Werner, Gijsbert D. A Gemmell, Patrick Grosser, Stefanie Hamer, Rebecca Shimeld, Sebastian M |
| description | The gastropod Patella vulgata is abundant on rocky shores in Northern Europe and a significant grazer of intertidal algae. Here we report the application of Illumina sequencing to develop a transcriptome from the adult mantle tissue of P. vulgata. We obtained 47,237,104 paired-end reads of 51 bp, trialled de novo assembly methods and settled on the additive multiple K method followed by redundancy removal as resulting in the most comprehensive assembly. This yielded 29,489 contigs of at least 500 bp in length. We then used three methods to search for candidate genes relevant to biomineralisation: searches via BLAST and Hidden Markov Models for homologues of biomineralising genes from other molluscs, searches for predicted proteins containing tandem repeats and searches for secreted proteins that lacked a transmembrane domain. From the results of these searches we selected 15 contigs for verification by RT-PCR, of which 14 were successfully amplified and cloned. These included homologues of Pif-177/BSMP, Perlustrin, SPARC, AP24, Follistatin-like and Carbonic anhydrase, as well as three containing extensive G-X-Y repeats as found in nacrein. We selected two for further verification by in situ hybridisation, demonstrating expression in the larval shell field. We conclude that de novo assembly of Illumina data offers a cheap and rapid route to a predicted transcriptome that can be used as a resource for further biological study. |
| doi_str_mv | 10.1007/s10126-012-9481-0 |
| format | Article |
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We then used three methods to search for candidate genes relevant to biomineralisation: searches via BLAST and Hidden Markov Models for homologues of biomineralising genes from other molluscs, searches for predicted proteins containing tandem repeats and searches for secreted proteins that lacked a transmembrane domain. From the results of these searches we selected 15 contigs for verification by RT-PCR, of which 14 were successfully amplified and cloned. These included homologues of Pif-177/BSMP, Perlustrin, SPARC, AP24, Follistatin-like and Carbonic anhydrase, as well as three containing extensive G-X-Y repeats as found in nacrein. We selected two for further verification by in situ hybridisation, demonstrating expression in the larval shell field. 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A</creatorcontrib><creatorcontrib>Gemmell, Patrick</creatorcontrib><creatorcontrib>Grosser, Stefanie</creatorcontrib><creatorcontrib>Hamer, Rebecca</creatorcontrib><creatorcontrib>Shimeld, Sebastian M</creatorcontrib><title>Analysis of a deep transcriptome from the mantle tissue of Patella vulgata Linnaeus (Mollusca: Gastropoda: Patellidae) reveals candidate biomineralising genes</title><title>Marine biotechnology (New York, N.Y.)</title><addtitle>Mar Biotechnol</addtitle><addtitle>Mar Biotechnol (NY)</addtitle><description>The gastropod Patella vulgata is abundant on rocky shores in Northern Europe and a significant grazer of intertidal algae. Here we report the application of Illumina sequencing to develop a transcriptome from the adult mantle tissue of P. vulgata. We obtained 47,237,104 paired-end reads of 51 bp, trialled de novo assembly methods and settled on the additive multiple K method followed by redundancy removal as resulting in the most comprehensive assembly. 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A</au><au>Gemmell, Patrick</au><au>Grosser, Stefanie</au><au>Hamer, Rebecca</au><au>Shimeld, Sebastian M</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Analysis of a deep transcriptome from the mantle tissue of Patella vulgata Linnaeus (Mollusca: Gastropoda: Patellidae) reveals candidate biomineralising genes</atitle><jtitle>Marine biotechnology (New York, N.Y.)</jtitle><stitle>Mar Biotechnol</stitle><addtitle>Mar Biotechnol (NY)</addtitle><date>2013-04-01</date><risdate>2013</risdate><volume>15</volume><issue>2</issue><spage>230</spage><epage>243</epage><pages>230-243</pages><issn>1436-2228</issn><eissn>1436-2236</eissn><abstract>The gastropod Patella vulgata is abundant on rocky shores in Northern Europe and a significant grazer of intertidal algae. Here we report the application of Illumina sequencing to develop a transcriptome from the adult mantle tissue of P. vulgata. 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| subjects | Algae Animal Shells - anatomy & histology Animal Shells - metabolism Animals Base Sequence Biomedical and Life Sciences carbonate dehydratase Cloning Computational Biology DNA Primers - genetics Engineering England Freshwater & Marine Ecology Gastropoda Gastropoda - genetics Gastropoda - metabolism Gene Expression Profiling - methods genes Genetic Association Studies In Situ Hybridization International Life Sciences Marine Marine biology Markov chains Microbiology Minerals - metabolism Models, Genetic Molecular Sequence Data Mollusca molluscs Mollusks Neurosciences Original Article Patella vulgata Patellidae Proteins Reverse Transcriptase Polymerase Chain Reaction RNA, Messenger - genetics Sequence Analysis, RNA Shells Studies tandem repeat sequences Tandem Repeat Sequences - genetics transcriptome Transcriptome - genetics Zoology |
| title | Analysis of a deep transcriptome from the mantle tissue of Patella vulgata Linnaeus (Mollusca: Gastropoda: Patellidae) reveals candidate biomineralising genes |
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