Abstract
Helicobacter pylori strains have quite diverse genome sequences likely because of high mutation and recombination rates, and they may be a useful model to study genetics and evolution. Here, I discuss some features of their evolution that have emerged from comparative analyses of complete H. pylori genomes and methylomes. Emphasis will be placed on the roles of various modes of recombination.
The evolution of their chromosome synteny was reconstructed by analyzing inversions via four mechanisms: recombination events involving long or short sequence similarities, inversions adjacent to the insertion of a mobile element, and DNA duplications associated with inversions, a novel process of DNA duplication.
Phylogenetic trees of individual genes are often different from that of the core genome in size and topology, partly due to homologous recombination between lineages. The fine population structure of the species was inferred from an analysis of homologous recombination using a method called chromosome painting. Gene sequences often diverge between European strains and East Asian strains. The evolution of Western-type CagA to East Asian-type CagA can be explained by illegitimate recombination events, with the Amerindian type as an intermediate. Massive decay of molybdenum-related genes was found in East Asian strains.
Whole methylome decoding at single-nucleotide resolution revealed that the H. pylori methylome is highly variable because its many methyltransferases often change sequence specificity. Their target recognition domains may move between different genes, sometimes beyond species barriers, and they may even move within a gene (domain movement). These extremely variable methylomes, as opposed to variable genomes, might provide targets for natural selection in adaptive evolution—a hypothesis that may be called epigenetics-driven adaptive evolution.
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Kobayashi, I. (2016). Genome Evolution: Helicobacter pylori as an Extreme Model. In: Backert, S., Yamaoka, Y. (eds) Helicobacter pylori Research. Springer, Tokyo. https://doi.org/10.1007/978-4-431-55936-8_9
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DOI: https://doi.org/10.1007/978-4-431-55936-8_9
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