Chromosome Evolution in theThermotogales: Large-Scale Inversions and Strain Diversification of CRISPR Sequences

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Abstract
In the present study, the chromosomes of two members of theThermotogaleswere compared. A whole-genome alignment ofThermotoga maritimaMSB8 andThermotoga neapolitanaNS-E has revealed numerous large-scale DNA rearrangements, most of which are associated with CRISPR DNA repeats and/or tRNA genes. These DNA rearrangements do not include the putative origin of DNA replication but move within the same replichore, i.e., the same replicating half of the chromosome (delimited by the replication origin and terminus). Based on cumulative GC skew analysis, both theT. maritimaandT. neapolitanalineages contain one or two major inverted DNA segments. Also, based on PCR amplification and sequence analysis of the DNA joints that are associated with the major rearrangements, the overall chromosome architecture was found to be conserved at most DNA joints for other strains ofT. neapolitana. Taken together, the results from this analysis suggest that the observed chromosomal rearrangements in theThermotogaleslikely occurred by successive inversions after their divergence from a common ancestor and before strain diversification. Finally, sequence analysis shows that size polymorphisms in the DNA joints associated with CRISPRs can be explained by expansion and possibly contraction of the DNA repeat and spacer unit, providing a tool for discerning the relatedness of strains from different geographic locations.