Comparative and Evolutionary genomics of Nucleocytoviricota

Viruses have been historically identified by their smaller sizes and simple genomic features compared to cellular life forms. Advances in virus cultivation and metagenomic analysis in recent years have shown that giant viruses, classified within the phylum Nucleocytoviricota, possess remarkably large genomes and complex structures, rivaling those of bacteria. Apart from their unusual genome and virion size, these nucleocytoviruses also encode Eukaryotic signature proteins (ESPs), including membrane trafficking proteins, cytoskeletal components, histones, ubiquitin signaling, and components of RNA and DNA processing proteins that are hallmarks of their eukaryotic hosts. Despite these intriguing findings, many groups of nucleocytoviruses remain underexplored. Similarly, their genomic complexity for example large genome size and encoded ESPs raise important questions about the role of nucleocytoviruses in the origins and evolution of eukaryotic hosts cells. In my work, I address this gap by performing comparative genomics and phylogenetic analysis to explore the genomics and evolutionary dynamics of giant viruses. In Chapter 1, I provide a literature review on giant viruses, their history, and their evolutionary links with eukaryotes. This chapter establishes the necessary background for the subsequent chapters. In Chapter 2, I perform comparative genomics, phylogenetics, and environmental distribution analysis to provide insights into the genomes and biogeography of the members of Asfarviridae family in the Nucleocytoviricota. In this chapter, I show that these viruses are widespread in the ocean, they have genes involved in different metabolic processes, and the members within this family have broad genomic diversity. In Chapter 3 and 4, I perform comprehensive phylogenetic analysis to uncover the co-evolutionary dynamics of nucleocytoviruses and eukaryotes. In Chapter 3, I focus on the vesicular trafficking and transport, ubiquitin system, and cytoskeleton system proteins to uncover complex patterns of gene exchange. My findings reveal that these proteins were acquired relatively recently by viruses, and in some cases multiple times independently suggesting that these genes might be important for countering the host changing environments and immune defenses. Similarly, in chapter 4, I focus on the replication and transcriptional machinery to study the ancient co-evolutionary dynamics of the virus and its host. My findings show that the DNA polymerase, especially the eukaryotic delta polymerase, a key processive polymerase required for genome replication in all eukaryotes, clusters adjacent to an ancient viral clade. The viral enzymes forming deep-branching clades adjacent to eukaryotic lineages, suggests their origin predates the Last Eukaryotic Common Ancestor (LECA). The replication and transcription machinery needed for viroplasm hints at an ancient virosphere with relics from extinct proto-eukaryotic lineages. Overall, these studies highlight the ancient as well as recent gene acquisition patterns between nucleocytoviruses and the hosts and provide valuable insight into the coevolutionary dynamics of these groups.