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Transcriptome survey of a marine food fish: Asian seabass (Lates calcarifer)

Thevasagayam, N., Sridatta, P., Jiang, J., Tong, A., Saju, J., Kathiresan, P., Kwan, H., Ngoh, S., Liew, W., Kuznetsova, I., Shen, X., Lok, S., Vij, S. and Orbán, L. (2015) Transcriptome survey of a marine food fish: Asian seabass (Lates calcarifer). Journal of Marine Science and Engineering, 3 (2). pp. 382-400.

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Abstract

The Asian seabass (or barramundi; Lates calcarifer) is a marine teleost and a popular food fish in Southeast Asia and Australia. To date, comprehensive genome and transcriptome sequence information has not been available for this species in public repositories. Here, we report a comprehensive de novo transcriptome assembly of the Asian seabass. These data will be useful for the development of molecular tools for use in aquaculture of Asian seabass as well as a resource for genome annotation. The transcriptome was obtained from sequences generated from organs of multiple individuals using three different next-generation sequencing platforms (454-FLX Titanium, SOLiD 3+, and paired-end Illumina HiSeq 2000). The assembled transcriptome contains >80% of the expected protein-coding loci, with 58% of these represented by a predicted full-length cDNA sequence when compared to the available Nile tilapia RefSeq dataset. Detailed descriptions of the various steps involved in sequencing and assembling a transcriptome are provided to serve as a helpful guide for transcriptome projects involving de novo assembly of short sequence reads for non-model teleosts or any species of interest.

Publication Type: Journal Article
Murdoch Affiliation: Centre for Comparative Genomics
Publisher: MDPI
Copyright: © 2015 MDPI AG
URI: http://researchrepository.murdoch.edu.au/id/eprint/38471
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