High-throughput sequencing and analysis of the gill tissue transcriptome from the deep-sea hydrothermal vent mussel Bathymodiolus azoricus

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ID: 112480
2010
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Abstract
Bathymodiolus azoricus is a deep-sea hydrothermal vent mussel found in association with large faunal communities living in chemosynthetic environments at the bottom of the sea floor near the Azores Islands. Investigation of the exceptional physiological reactions that vent mussels have adopted in their habitat, including responses to environmental microbes, remains a difficult challenge for deep-sea biologists. In an attempt to reveal genes potentially involved in the deep-sea mussel innate immunity we carried out a high-throughput sequence analysis of freshly collected B. azoricus transcriptome using gills tissues as the primary source of immune transcripts given its strategic role in filtering the surrounding waterborne potentially infectious microorganisms. Additionally, a substantial EST data set was produced and from which a comprehensive collection of genes coding for putative proteins was organized in a dedicated database, "DeepSeaVent" the first deep-sea vent animal transcriptome database based on the 454 pyrosequencing technology. A normalized cDNA library from gills tissue was sequenced in a full 454 GS-FLX run, producing 778,996 sequencing reads. Assembly of the high quality reads resulted in 75,407 contigs of which 3,071 were singletons. A total of 39,425 transcripts were conceptually translated into amino-sequences of which 22,023 matched known proteins in the NCBI non-redundant protein database, 15,839 revealed conserved protein domains through InterPro functional classification and 9,584 were assigned with Gene Ontology terms. Queries conducted within the database enabled the identification of genes putatively involved in immune and inflammatory reactions which had not been previously evidenced in the vent mussel. Their physical counterpart was confirmed by semi-quantitative quantitative Reverse-Transcription-Polymerase Chain Reactions (RT-PCR) and their RNA transcription level by quantitative PCR (qPCR) experiments. We have established the first tissue transcriptional analysis of a deep-sea hydrothermal vent animal and generated a searchable catalog of genes that provides a direct method of identifying and retrieving vast numbers of novel coding sequences which can be applied in gene expression profiling experiments from a non-conventional model organism. This provides the most comprehensive sequence resource for identifying novel genes currently available for a deep-sea vent organism, in particular, genes putatively involved in immune and inflammatory reactions in vent mussels. The characterization of the B. azoricus transcriptome will facilitate research into biological processes underlying physiological adaptations to hydrothermal vent environments and will provide a basis for expanding our understanding of genes putatively involved in adaptations processes during post-capture long term acclimatization experiments, at "sea-level" conditions, using B. azoricus as a model organism.
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bettencourt2010bmchigh-throughput Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Raul Bettencourt;Miguel Pinheiro;Conceição Egas;Paula Gomes;Mafalda Afonso;Timothy Shank;Ricardo Serrão Santos;Raul Bettencourt;Miguel Pinheiro;Conceição Egas;Paula Gomes;Mafalda Afonso;Timothy Shank;Ricardo Serrão Santos;
Journal BMC genomics
Year 2010
DOI
doi:10.1186/1471-2164-11-559
URL
https://doi.org/10.1186%2F1471-2164-11-559
Keywords
Proteomics life sciences microarrays general animal genetics and genomics microbial genetics and genomics plant genetics and genomics databases Stress National Center for Biotechnology Information NCBI NLM MEDLINE genetic animals pubmed abstract nih national institutes of health national library of medicine research support non-u.s. gov't amino acid sequence Genes Sequence Analysis Expressed Sequence Tags DNA / methods* bacterial / genetics contig mapping gene expression profiling* oceans and seas inflammation / genetics reverse transcriptase polymerase chain reaction molecular sequence annotation inflammation / immunology pmid:20937131 pmc3091708 doi:10.1186/1471-2164-11-559 raul bettencourt miguel pinheiro ricardo serrão santos bivalvia / genetics* bivalvia / microbiology fresh water gills / metabolism* gills / microbiology high-throughput nucleotide sequencing / methods* hot springs* immunity / genetics physiological / genetics

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