UC Santa Cruz

All the processes of life are controlled by the complex and carefully regulated usage of the genome. Thus, the understanding of an organism's genomic DNA sequence and regions of the genome that are transcribed into complementary RNA transcripts is critical to the study of life and biomedical research. Our understanding of the DNA and RNA composition of a cell has been heavily based on the high throughput short-read sequencing by synthesis technology. However, DNA and RNA molecules, polymers consisting of long chains of molecular subunits, stretch on for lengths far beyond these methods capabilities such that it requires their fragmentation prior to sequencing followed by computational assembly of the short fragments to estimate their arrangement in the much larger original molecule. Thus, I have developed and optimized methods utilizing nanopore based long-read sequencing to improve the accuracy and completeness of genome assemblies and genomic annotations (transcriptome). These methods include a hybrid genome sequencing and assembly workflow that works with minimal amounts of DNA to generate chromosome-scale assemblies, the conversion of short-read libraries for highly accurate nanopore sequencing that makes DNA sequencing more accessible and, an approach for the deep sequencing of full length transcript isoforms to improve genomic annotations for model organisms. Together, this work improves our ability to understand how living things operate on the molecular level.