Status Report on the Asian Seabass Genome Project

Lates calcarifer (Asian seabass/barramundi) is an important food fish species belonging to the order Perciformes. The Asian seabass has a wide geographic distribution stretching from Northern Australia to at least the Western part of India. A comprehensive analysis of the identity of Asian seabass is, however, lacking.  Therefore, in order to ascertain species identity, we barcoded individuals from across various regions representing its native range using mitochondrial markers.

The Asian seabass has an estimated genome size of ~700Mb and a poorly represented transcriptome in GenBank. We embarked on this project with the main aim of employing next generation sequencing (NGS) platforms to produce an “improved high-quality draft of the genome”. A backcrossed individual with decreased genomic polymorphism was chosen to serve as a resource for the Asian seabass genome project.

Sequencing was done using the Illumina HiSeq platform (80X coverage). Two BAC libraries (73,728 clones) were constructed with an average insert size of ~115 kb. Also, 5,760 BAC clones were sequenced from both ends using Sanger’s sequencing to get 1X coverage. In addition, sequencing was done using Pacific Biosciences, single-molecule, real-time sequencing system in three rounds representing >80X coverage of the genome. The first draft of the genome would thus be assembled using the above three mentioned sequence datasets.

We aim to use the genome sequence information for genetic/genomic selection assisted by ‘state of the art’ large-scale platform technologies to enable the development of elite Asian seabass varieties in terms of growth as well as disease resistance.