Sequential discovery - from small RNA to genomes, and investigation of the hyperthermophilic genus Pyrobaculum.

摘要

The archaeal domain is comprised of organisms of prokaryotic morphology and intracellular organization, while using molecular systems that are drawn from both bacterial and eukaryal domains. In spite of their organizational simplicity and molecular breadth, archaeal members are relatively underexplored. They may represent 20% of the biomass on earth, inhabiting the most extreme environments this planet has to offer. I will focus on a neutrophilic clade within the kingdom Crenarchaeota; the genus Pyrobaculum , where we now have five completed genomes, making this genus a model for study of hyperthermophilic life.;This study makes use of both small RNA sequencing and genomic DNA sequencing to discover examples of novel molecules, mechanisms, genomes and a novel organism. As such, this work has asked many more questions than it answers. I provide new examples of antisense RNA associated with core metabolic genes, a classification of CRISPR arrays and their associated expression pattern, and a new molecular form for pseudouridylation guide RNA.;I have also sequenced the genome of Pyrobaculum oguniense revealing both the consensus sequence, its varied forms and a novel parasite---the Pyrobaculum Icosahedral Virus (PIV). I show evidence of the promiscuous host integration of PIV as well as a model for its attachment. Each of these investigations were made possible by using, adapting and extending high-throughput next-generation sequencing techniques.;I also provide a method of using paired-end sequencing for final assembly of a genome as well as a method for evaluating variation in its inversions. This material has been previously presented in a short-seminar series in December 2009.