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De Novo Characterisation of the Greenlip Abalone Transcriptome (Haliotis laevigata) with a Focus on the Heat Shock Protein 70 (HSP70) Family

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Abstract

Abalone (Haliotis) are economically important molluscs for fisheries and aquaculture industries worldwide. Despite this, genomic resources for abalone and molluscs are still limited. Here we present a description and functional annotation of the greenlip abalone (Haliotis laevigata) transcriptome. We present a focused analysis on the heat shock protein 70 (HSP70) family of genes with putative functions affecting temperature stress and immunity. A total of ~38 million paired end Illumina reads were obtained, resulting in a Trinity assembly of 222,172 contigs with minimum length of 200 base pairs and maximum length of 33 kilobases. The 20,702 contigs were annotated with gene descriptions by BLAST. We created a program to maximise the number of functionally annotated genes, and over 10,000 contigs were assigned Gene ontologies (GO terms). By using CateGOrizer, immunity related GO terms for stressors such as heat, hypoxia, oxidative stress and wounding received the highest counts. Twenty-six contigs with homology to the HSP70 family of genes were identified. Ninety-one putative single-nucleotide polymorphisms were observed in the abalone HSP70 contigs. Eleven of these were considered non-synonymous. The annotated transcriptome described in this study will be a useful basis for future work investigating the genetic response of abalone to stress.

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Abbreviations

HSP:

Heat shock protein

GO:

Gene ontology

SNP:

Single-nucleotide polymorphism

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Acknowledgements

This work was funded by Australian Research Council (ARC) Discovery Project DP110100592 awarded to Jan Strugnell. Thanks to the Australian Bight Abalone group for supplying abalone for this study. Thanks to the Life Science Computation Centre for summer internship (BPS).

Conflict of Interest

The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. Department of Genetics, La Trobe Institute for Molecular Science, La Trobe University, Kingsbury Drive, Melbourne, VIC, 3086, Australia

    Brett P. Shiel, Nathan E. Hall & Jan M. Strugnell

  2. Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Kingsbury Drive, Melbourne, VIC, 3086, Australia

    Ira R. Cooke

  3. Life Sciences Computation Centre, VLSCI, Parkville, VIC, Australia

    Nathan E. Hall & Ira R. Cooke

  4. Nofima, P.O. Box 210, 1431, Ås, Norway

    Nicholas A. Robinson

  5. Flinders University, Sturt Road, Bedford Park, S.A., 5042, Australia

    Nicholas A. Robinson

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  1. Brett P. Shiel
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Correspondence to Brett P. Shiel.

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Shiel, B.P., Hall, N.E., Cooke, I.R. et al. De Novo Characterisation of the Greenlip Abalone Transcriptome (Haliotis laevigata) with a Focus on the Heat Shock Protein 70 (HSP70) Family. Mar Biotechnol 17, 23–32 (2015). https://doi.org/10.1007/s10126-014-9591-y

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