**9. Future perspective**

fish species to have their genomes sequenced and characterized, but they have attracted the highest research in genomic studies among teleost species. Their genomes have been widely used for comparative analyses as model species [235, 237–239]. Sequence analyses of the Atlantic cod genome in 2011 using the whole genome shotgun 454 pyrosequencing technol‐ ogy showed that this fish species lacks the major histocompatibility (MHC) II genes, which are compensated with expansion of the MHC‐I and specific adaption of toll‐like receptor genes demonstrating that whole genome sequencing can be used to elucidate evolutionary differences in the vertebrate taxa [240]. As shown in **Table 4**, there has been a spontane‐ ous increase in the number of fish species whose genomes have characterized since the dis‐ covery of HTS technologies in recent years. Sequencing of other aquatic organism genomes is going on and it is anticipated that as HTS becomes cheaper, more sequences of aquatic organisms will become readily available for more advanced functional genomics research

190 Applications of RNA-Seq and Omics Strategies - From Microorganisms to Human Health

**Common name Scientific name Year Published Reference** Atlantic salmon *Salmon salar* L. 2016 [264] Atlantic cod *Gadus morhua* 2011 [240] Asian arowana *Scleropages formosus* 2015 [8] Medaka *Oryzias latipes* 2007 [236] Nile tilapia *Oreochromis niloticus* 2015 [7]

Platyfish *Xiphophorus maculatus* 2013 [265, 266] Puffer fish *Takifugu rubripes* 2002 [234] Puffer fish *Tetraodon nigroviridis* 2004 [267] Three‐spined stickleback *Gasterosteus aculeatus* 2012 [268] Rainbow trout *Oncorhynchus mykiss* 2014/2016 [269, 270] Killifish *Nothobranchius furzeri* 2015 [271, 272] Pearl oyster *Pinctada fucata* 2012 [273]

In this chapter, we have shown that HTS has contributed to the rapid discovery of novel patho‐ gens in aquaculture using metagenomics, which has significantly contributed in enhancing our ability to develop rationale disease control strategies unlike in the past when it took long from the first report of a clinical disease to identification of a novel pathogen. Moreover, metagenom‐ ics enable us to identify and monitor microbial communities found in different ecosystems

in aquaculture.

**8. Conclusions**

**Table 4.** Whole genome sequencing of aquatic organisms.

As HTS technologies become cheaper, it is anticipated that more genomes for different aquatic organisms will characterized and that this shall pave to a better understanding of the genome duplication seen in some fish species. The use of HTS technologies in pathogen discovery and microbiota inhabiting mucosal surfaces of different aquatic organisms is expected to pave way into timely design of rational disease control strategies. Hence, in future generations, we shall not only sequence whole genomes of all aquatic organisms, but we expect to provide a better understanding of the evolutionary aspects of the vertebrate taxa as well as providing new insight into host‐pathogen interaction mechanisms at protein‐protein level. It is our per‐ ception that current HTS studies are building a strong foundation for more advanced func‐ tional genomics developments in the future.
