De novo characterisation of the greenlip abalone transcriptome (Haliotis laevigata) with a focus on the heat shock protein 70 (HSP70) family

Shiel, Brett P., Hall, Nathan E., Cooke, Ira R., Robinson, Nicholas A, and Strugnell, Jan M. (2015) De novo characterisation of the greenlip abalone transcriptome (Haliotis laevigata) with a focus on the heat shock protein 70 (HSP70) family. Marine Biotechnology, 17. pp. 23-32.

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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.

Item ID: 43953
Item Type: Article (Research - C1)
ISSN: 1436-2236
Keywords: abalone; transcriptome; stress; heat shock protein; HSP70; HSPA
Funders: Australian Research Council (ARC)
Projects and Grants: ARC DP110100592
Date Deposited: 16 May 2016 02:16
FoR Codes: 06 BIOLOGICAL SCIENCES > 0601 Biochemistry and Cell Biology > 060102 Bioinformatics @ 50%
06 BIOLOGICAL SCIENCES > 0604 Genetics > 060408 Genomics @ 50%
SEO Codes: 83 ANIMAL PRODUCTION AND ANIMAL PRIMARY PRODUCTS > 8301 Fisheries - Aquaculture > 830103 Aquaculture Molluscs (excl. Oysters) @ 100%
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