Chromosome-Level Assembly of the Asian Seabass Genome

Genome sequence information provides insights to understand the basis of euryhaline adaptation in Asian seabass, a tropical food fish species

 

Shubha Vij¹, Kathiresan Purushothaman¹, Jolly M Saju¹, Prakki Sai Rama Sridatta¹ László Orbán^1,2,3 and the Asian seabass genome sequencing consortium

 

1. Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
2. Department of Animal Sciences and Animal Husbandry, Georgikon Faculty, University of Pannonia, Keszthely, Hungary
3. Centre for Comparative Genomics, Murdoch University, Murdoch, 6150 Australia

Asian seabass (Lates calcarifer) is a popular food fish with a wide geographic distribution in the tropical Indo-West pacific region. An opportunistic predator, it is a catadromous, euryhaline marine teleost that belongs to the order Perciformes (the largest order within vertebrates).

We used a high coverage (90X) of long reads generated using Pacific Biosciences’ single molecule, real-time (SMRT) sequencing to produce a high-quality draft genome assembly. The genome was further scaffolded using the information from transcriptome, optical mapping, linkage map and synteny from closely related fish species. This resulted in a chromosomal-level genome assembly covering ~90% of the assembled sequence with a scaffold N50 of >25 Mb. Asian seabass genome has a repeat content of 18.6% and totally 22,184 genes were predicted. 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 with increased growth performance as well as disease resistance.

The availability of the genome provided a stepping stone to understand the biology of the Asian seabass. It is a migratory fish, spending most of its life in fresh water and going to the sea to breed. Its ability to tolerate changes in salinity makes it a good candidate fish for studying the versatility as well as pliability of salinity adaptation response. We compared the transcriptome of young juvenile Asian seabass grown in fresh water and sea water in two major osmoregulatory organs; i.e. gills and kidneys. In addition, we have the transcriptome information from fishes which were transferred first from sea water to fresh water and then to sea water again (to study the extent of the adaptability). This provided a global overview of changes in gene expression profiles under different salinity conditions and identified a distinct set of genes/pathways underlying this adaptation.