Abstract
Marine shrimp form part of one of the most important species groups for aquaculture worldwide with production reaching over 3 million tonnes in 2010. Fenneropenaeus merguiensis is one of the most commercially significant shrimp species in South East Asia, India and Australia with over 86,000 tonnes being produced in 2007. However, only minimal genetic information is available for this species. Improvement in our basic knowledge of genomics and genetics of these shrimp could greatly benefit the development of this industry. The development of next generation sequencing technologies has greatly expanded the capacity for gene discovery in non-model species. Here we carried out high-throughput RNA sequencing of farmed F.merguiensis. Messenger RNA was isolated from eight tissue types including eye stalk, nervous system, hepatopancreas, stomach, muscle, gonads and androgenic gland. Individual cDNA libraries were produced from the mRNA from each tissue and sequenced at the AGRF using 454 FLX Titanium chemistry generating a combined set of 822,076 high quality reads. These reads were assembled de novo into 50,257 unique transcripts representing approximately 32Mb of transcriptome sequence. Average length was 650 and N50 was 698. Putative genes involved in growth and reproduction were predicted using BLAST sequence homology searches against publicly available databases. Transcriptomic data generated in this study provides a resource for further gene discovery and can be exploited for the development of functional markers. This information can lead to a better understanding of shrimp biology and contribute to improvements in aquaculture of this species.