Abstract
Mycobacterium species are the source of a variety of infectious diseases in a range of hosts. Genome based methods are used to understand the adaptation of each pathogenic species to its unique niche. In this work, we report the comparison of pathogenic and non-pathogenic Mycobacterium genomes. Phylogenetic trees were constructed using sequence of core orthologs, gene content and gene order. It is found that the genome based methods can better resolve the inter-species evolutionary distances compared to the conventional 16S based tree. Phylogeny based on gene order highlights distinct evolutionary characteristics as compared to the methods based on sequence, as illustrated by the shift in the relative position of M. abscessus. This difference in gene order among the Mycobacterium species is further investigated using a detailed synteny analysis. It is found that while rearrangements between some Mycobacterium genomes are local within synteny blocks, few possess global rearrangements across the genomes. The study illustrates how a combination of different genome based methods is essential to build a robust phylogenetic relationship between closely related organisms.
Highlights
Mycobacterium genus of pathogenic species causes a variety of infectious diseases in hosts ranging from humans to fish
M. ulcerans is responsible for skin ulcers in humans and M. avium leads to opportunistic infections, such as in immune HIV positive compromised patients [2]
For the comparative genomics study presented in this work, 6 pathogenic and 4 non-pathogenic species were selected from among the completely sequenced Mycobacterium genomes
Summary
Mycobacterium genus of pathogenic species causes a variety of infectious diseases in hosts ranging from humans to fish. While many genes contributing to pathogenesis have been identified [3,4], understanding the mechanisms of pathogenesis is an active area of research. In addition to these pathogenic species, the family consists of many non-pathogenic species such as M. smegmatis, M. gilvum and M. vanbaalenii. These non-pathogenic relatives, M. smegmatis have proved as useful hosts to express and study genes from pathogenic species. Comparative genomics of pathogenic and non-pathogenic species can help identify disease-related genes and vaccine candidates, and shed light on how each mycobacteria survives in its exclusive niche. A comparative study between various species provides insight into their evolutionary relationship
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