Sequencing and de novo Assembly of the Mozambique Tilapia Transcriptome

Tilapias are an important aquaculture species with commercial production leaping from ~100,000 tons in 1980 to ~4 million tons in 2011 (FAO). Large scale culture of this freshwater species will definitely be affected by the declining freshwater sources. Therefore, a salt-tolerant tilapia species that is suitable for culture in brackish water or seawater is desirable. The Mozambique tilapia (Oreochromis mossambicus) is a suitable candidate as it is known to have higher salt tolerance than other tilapia species [1]. However, it has slower growth rate compared to the Nile tilapia. In 2011, we started a project to develop a Mozambique tilapia strain that is commercially viable (high salt tolerance and fast growth) for marine culture.

Here, we report the sequencing and assembly of the Mozambique tilapia transcriptome, which is an essential foundation for the development of tools for gene expression analysis and genome annotation. We built the transcriptome by sequencing pooled samples from various organs of multiple individuals, which yielded ~122 million pairs of reads. De novo assembly generated a total of 154,022 representative contigs with average length of 714 bp. Using the Nile tilapia protein dataset (NCBI RefSeq Protein) as reference for annotation, we found that 73,630 (~48%) of our contigs matched to 21,282 (~80%) of the Nile tilapia proteins. Among the mapped Nile tilapia proteins, our contigs covered the full coding sequences of 9,071 Nile tilapia’s proteins while the rest had partial coverage. Using contigs that mapped to 19,613 Nile tilapia proteins, an expression oligo microarray was designed (Agilent 8x60k platform). The microarray contains three probes per gene and targets regions that align to the 3’ end of the Nile tilapia genes. This microarray will be a useful molecular tool for future experiments relating to heat and salt tolerance.

Reference

1.         Uchida K, Kaneko T, Miyazaki H et al. (2000). Excellent salinity tolerance of Mozambique tilapia (Oreochromis mossambicus): Elevated chloride cell activity in the branchial and opercular epithelia of the fish adapted to concentrated seawater. Zool Sci 17:149.