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J. Mar. Sci. Eng. 2015, 3(2), 382-400; doi:10.3390/jmse3020382

Transcriptome Survey of a Marine Food Fish: Asian Seabass (Lates calcarifer)

1
Reproductive Genomics Group, Strategic Research Program, Temasek Life Sciences Laboratory, Singapore 117604, Singapore
2
Agri-Food and Veterinary Authority of Singapore, Singapore 608550, Singapore
3
Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
4
The Centre for Applied Genomics, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada
5
Centre for Comparative Genomics, Murdoch University, Murdoch 6150, Australia
6
Department of Animal Sciences and Animal Husbandry, Georgikon Faculty, University of Pannonia, Keszthely H-8360, Hungary
These authors contributed equally to this work.
*
Authors to whom correspondence should be addressed.
Academic Editor: Dean Jerry
Received: 12 May 2015 / Accepted: 22 May 2015 / Published: 2 June 2015
(This article belongs to the Special Issue Genetic Breeding Technology and Its Application in Marine Aquaculture)
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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. View Full-Text
Keywords: Asian seabass; barramundi; transcriptome sequencing; transcriptome assembly; NGS; RNA-Seq Asian seabass; barramundi; transcriptome sequencing; transcriptome assembly; NGS; RNA-Seq
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MDPI and ACS Style

Thevasagayam, N.M.; Sridatta, P.S.; Jiang, J.; Tong, A.; Saju, J.M.; Kathiresan, P.; Kwan, H.Y.; Ngoh, S.Y.; Liew, W.C.; Kuznetsova, I.S.; Shen, X.; Lok, S.; Vij, S.; Orbán, L. Transcriptome Survey of a Marine Food Fish: Asian Seabass (Lates calcarifer). J. Mar. Sci. Eng. 2015, 3, 382-400.

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