ArticleMarine biotechnology (New York, N.Y.)2013
Analysis of a deep transcriptome from the mantle tissue of Patella vulgata Linnaeus (Mollusca: Gastropoda: Patellidae) reveals candidate biomineralising genes.
Article in Marine biotechnology (New York, N.Y.), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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27 citing papers in PubMed, 59 citations in OpenAlex.
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- Immunity-related genes and signaling pathways under hypoxic stresses in Haliotis diversicolor: a transcriptome analysis.Scientific reports · 2019Article
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- Proteomics Studies on the three Larval Stages of Development and Metamorphosis of Babylonia areolata.Scientific reports · 2018Article
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- Functional Involvement of Carbonic Anhydrase in the Lysosomal Response to Cadmium Exposure inFrontiers in physiology · 2018Article
- Co-Option and De Novo Gene Evolution Underlie Molluscan Shell Diversity.Molecular biology and evolution · 2017Article
- De novo assembly, characterization and annotation for the transcriptome of Sarcocheilichthys sinensis.PloS one · 2017Article
- Comparative transcriptomics enlarges the toolkit of known developmental genes in mollusks.BMC genomics · 2016Article
- Transcriptome sequencing and de novo characterization of Korean endemic land snail, Koreanohadra kurodana for functional transcripts and SSR markers.Molecular genetics and genomics : MGG · 2016Article
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Authors and funding
5 authors at 1 institution in 2 countries.
Funding
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. 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.
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