Application of next generation sequencing (NGS) technologies to explore problems with or improve aquaculture have been increasing in recent years due to the continued lowering of costs associated with these methods. NGS is used to quickly and efficiently determine the order of nucleotides in entire genomes or targeted regions of DNA or RNA. Using these technologies allows for the exploration of normal biological processes as well as how those processes change in a diseased or otherwise altered states (stressed by pollutants, environmental changes, etc..).
DNA-based NGS technologies can provide information regarding an organism’s potential suite of genetic functions and a look into its potential molecular mechanisms. Having an organism’s annotated genome through whole genome sequencing provides a database of genes with known or predicted functions to compare to. This could include using genotyping by sequencing to find single nucleotide polymorphisms or biomarkers associated with production relevant traits such as growth or disease resistance. Individual fish can then be tested for these positive traits and used for in selective breeding.
Finfish microbiomes (internal and external) are important to the normal functioning of an organism’s metabolism, growth, development, and immunity. When an organism’s normal microbial community is disturbed, this leads to disruption of these normal physiological processes. Amplicon metagenomic sequencing focuses on a specific region of DNA associated with particular types of organisms such as bacteria/archaea (16S) or eukaryotes (18S) to gain taxonomic information. Shotgun metagenomic sequencing is untargeted allowing for sequencing of any of the DNA within a sample providing information regarding both taxonomy and function for any type of organism present in the community. The tradeoff for more information is that it is more expensive and computationally intensive than amplicon sequencing. Understanding how the whole or partial microbiome changes in an altered state allows for discovery of differentially abundant organisms. These could become targets for disease diagnosis or biomarker detection on the organism or in its surrounding environment to respond to potential issues before they lead to physiologically changes in the fish. Potential probiotics can also be identified with these methods by comparing organism with low and high positive traits such as growth.
Transcriptomics aka RNA-seq allows for exploration of gene expression at a specific point in time. Whereas an organism’s genome is static, the transcriptome is constantly changing to respond to environmental and biological cues. Similar to metagenomics, comparing the transcriptome of normal and altered states can help discover differentially expressed genes between states. This allows for detection of molecular markers of growth, immunity, stress, and toxicology. NGS technologies can help to make significant advances in our ability to improve warm water finfish aquaculture by unlocking the potential of DNA and RNA.