Next Generation Sequencing in Aquatic Models

The most valuable application of next generation sequencing (NGS) technology is genome sequencing. Genomes of several aquatic models had been sequenced in the past few years due to their importance in genomics, development biology, toxicology, pathology, and cancer research. NGS technology is greatly advanced in sequencing length and accuracy, which facilitate the sequencing process, but sequence assembly, especially for the species with complicated genomes, is still the biggest challenge for bench-top scientists. This chapter will focus on the application of NGS in aquatic genome and transcrip‐ tome assemblies. However, the associated techniques, problems, concerns, and solutions can also be applied to genome sequencing of other eukaryotic systems. Using our Xiphophorus genome and transcriptome sequencing as examples, this chapter will cover the technical details of NGS, data processing, genome assembly, and different methods of transcriptome assembly, as well as genome/transcriptome annotation. Additionally, the problems that were confronted in genome sequencing of several fish models and alternative approaches to assemble these genomes will be discussed. Lastly, the problems that remain to be the bottleneck of genome sequencing will be discussed, and a plan of what needs to be fulfilled is proposed.