Long Read Sequencing of the Zebrafish Genome, BMC Genomics (2022)

Nanopore sequencing is a new way to read the information stored in our DNA. The sequences of DNA can be determined by passing DNA strands through tiny pores and measuring the changes in electrical current as each DNA base passes through the pore. Unlike older methods, nanopore sequencing can produce long and detailed readings of DNA, which help us explore parts of the genome that were previously difficult to study. 

Our paper focuses on nanopore sequencing of the zebrafish genome, which is important because zebrafish are often used as models to understand human diseases. However, a significant portion of the zebrafish genome is made up of repetitive and complex sections that traditional DNA sequencing methods struggle to analyze. We used nanopore sequencing to create a new and improved version of the zebrafish genome assembly. We identified 1697 new genetic changes, known as insertions and deletions. We also located and accurately placed 106 sections of DNA that were previously unpositioned in the reference genome. We also discovered new areas in the zebrafish genome where genetic elements called retrotransposons are active. These elements can move around the genome and contribute to its evolution. 

Our corrected zebrafish assembly will greatly benefit many studies that compare different species’ genetics and can help connect specific genetic events to disease traits. Ultimately, our work will enhance our understanding of human diseases and help us find better ways to diagnose and treat them.