| Summary: | In addition to the main chromosome, many bacterial genomes have a second element, often called a "second chromosome" or "megaplasmid". It has become clear that, while they carry some essential genes, these replicons do not have the properties normally expected of chromosomes. In this thesis a systematic analysis of all publicly available sequenced bacterial genomes demonstrates that these large secondary replicons represent a single class of elements with a distinct and consistent set of properties. The term 'chromid' is proposed to distinguish them from both chromosomes and plasmids. Chapter Two utilises compositional measures to demonstrate that chromids are present in approximately one in ten sequenced genomes, and found in many bacteria of medical, agricultural' and environmental importance. Moreover, the nucleotide composition and codon usage of chromids is very similar to that of the chromosomes they are associated with, despite possessing plasmid replication and partitioning systems. Chapter Three determines that chromids possess a number of orthologous genes held on chromosomes in other species, as well as being particularly rich in genus-specific genes. This, combined with chromids of different genera having unrelated replication and maintenance systems, suggests that the creation of a new chromid may be associated with the origin of a genus. Chapter Four demonstrates that only genes held on the chromosome maintain high levels of phylogenetic consistency, and Chapter Five highlights the complexity of the interaction between gene composition, expression and function, investigating differences between the three classes of replicon. No large-scale study incorporating all published data has previously been conducted. Yet the identification and characterisation of this component provides an important framework for understanding the evolution and organisation of bacterial genomes. By proposing a clear definition, this thesis seeks to encourage consistent annotation and discussion of the evolution and functional biology of this distinct and common type of replicon.
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