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.
Highlights
IntroductionThe Asian seabass (or barramundi; Lates calcarifer) is a marine teleost from the Latidae family
The assembly using combined 454 and SOLiD data generated 53,862 contigs, which were merged with 22,322 NCBI EST sequences and 81,479 sequences from a 454-based Asian seabass intestine assembly published earlier [9], resulting in 157,457 contigs
Making use of the individual organ assemblies from HiSeq Round 2 (HR2) (Figure 1), we identified protein-coding sequences that were common to all organs as well as those that are unique to specific organs based on the BLASTX results against Nile tilapia protein reference sequences
Summary
The Asian seabass (or barramundi; Lates calcarifer) is a marine teleost from the Latidae family. For more than a decade, our group has been involved in the breeding and selection program for the Asian seabass. The genome of the Asian seabass is estimated to be ~700 Mb and is currently being assembled and annotated [5], while the mitochondrial genome has previously been completely sequenced [6]. Transcriptome information for the Asian seabass to date is mainly represented by ~22,000 EST sequences in GenBank along with a limited number of organ-specific transcriptome studies and repetitive sequence analyses [7,8,9]
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