Files
Abstract
Cryptosporidium parvum is a medically important eukaryotic pathogen in the phylum Apicomplexa. This protist parasite can cause diarrheal disease in both humans and animals. Despite recent advances in molecular genetics, genomics, and culturing, there are still major gaps in knowledge regarding gene regulation. Complete telomere-to-telomere (T2T) genome assembly and accurate, evidence-based genome annotation are crucial in teasing apart complex gene regulation in C. parvum. In addition, identification of gene structures, such as promoters, cis-regulatory elements (CRE), untranslated regions (UTR), transcript isoforms, and poly-A tails, all contribute to our understanding of gene regulation. Limited by traditional short-read-based sequencing, as well as insufficient sequence data, much of the parasite’s genome sequence and gene structures remain poorly characterized. Through a comprehensive multi-omics study, this work generates the first complete telomere-to-telomere (T2T) genome assembly for C. parvum IOWA, improves its gene annotation, identifies cis-regulatory elements, and reveals novel RNA biology. Chapter 1 dives into the assembly and annotation of a T2T C. parvum genome sequence with 3rd generation single-molecule long-read DNA / RNA sequencing technologies. Chapter 2 covers the exciting discovery of polycistronic transcription, as well as the validation / characterization of the polycistrons. Chapter 3 focuses on the UTRs and CREs for non-polycistronic protein-encoding genes. Conclusions and future directions are discussed in Chapter 4.