**7. Whole genome sequencing of aquatic organisms**

Although teleost fish are the largest known vertebrate group with more than 27,000 species [8], they account for a small proportion of vertebrate species whose whole genomes have been fully sequenced and characterized. The pufferfish genome is one of the earliest fish genome to be sequenced and characterized by 2002 [234], which raised interests to sequence the genomes of other fish species. The zebrafish (*Danio rerio*) whole genome sequencing proj‐ ect was started by Welcome Trust Sanger Institute in 2001 [235] while the Medaka genome was sequenced in 2007 [236]. Thus, Zebrafish and medaka are not only among the earliest 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 in aquaculture.

used in aquaculture. It has also proved to be an important tool able to map mucosal micro‐ biota of different aquatic organisms. In vaccine production, genomics studies are being used to identify cross‐neutralizing antigens able to confer protection across variant strains of the same pathogens. In genetics and epigenetics, several genomics traits have been identified that cur‐ rently contributing to the improvement of production in aquaculture. Nutrigenomics have not only enhanced our understanding of the genetic markers for enteropathy and other nutritional diseases, but they have also highlighted our ability to formulate diets able to maintain stable GALT homeostasis in the gut. And as shown from the example of the Atlantic salmon produc‐ tion cycle in **Figure 2**, it is evident that functional genomics are used at different production stages of aquatic organisms to improve the overall production in aquaculture. Hence, genomics studies are not only useful at elucidating host‐pathogen interactions [13‐15], but they also serve

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as optimization tools for improving the quality and quantity of aquaculture products.

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‐

**9. Future perspective**

**Author details**

valsveien, Oslo, Norway

1990;**62**(13):1202‐1214

**References**

tional genomics developments in the future.

Hetron M. Munang'andu\* and Øystein Evensen

\*Address all correspondence to: hetroney.mweemba.munangandu@nmbu.no

Department of Basic Sciences and Aquatic Medicine, Section of Aquatic Medicine and Nutrition, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, Ulle‐

[1] Gibbs RA. DNA amplification by the polymerase chain reaction. Analytical Chemistry.


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

#### **8. Conclusions**

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 used in aquaculture. It has also proved to be an important tool able to map mucosal micro‐ biota of different aquatic organisms. In vaccine production, genomics studies are being used to identify cross‐neutralizing antigens able to confer protection across variant strains of the same pathogens. In genetics and epigenetics, several genomics traits have been identified that cur‐ rently contributing to the improvement of production in aquaculture. Nutrigenomics have not only enhanced our understanding of the genetic markers for enteropathy and other nutritional diseases, but they have also highlighted our ability to formulate diets able to maintain stable GALT homeostasis in the gut. And as shown from the example of the Atlantic salmon produc‐ tion cycle in **Figure 2**, it is evident that functional genomics are used at different production stages of aquatic organisms to improve the overall production in aquaculture. Hence, genomics studies are not only useful at elucidating host‐pathogen interactions [13‐15], but they also serve as optimization tools for improving the quality and quantity of aquaculture products.
