Non-X-alignments

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This tracks examples of bacteria and archaea syntenic dotplots which do not show the classical x-alignment pattern of inversions. One possible methodological reason for these non-x-alignments is mis-assembly.

Genome-wide random orientation

Syntenic dotplot generated by SynMap between two species of Methanocaldococcus: Methanocaldococcus fervens strain AG86 (x-axis); Methanocaldococcus sp. strain FS406-22 (y-axis). Results can be regenerated at: http://genomevolution.org/r/oro
Syntenic dotplot generated by SynMap between two species of Thermococcus: gammatolerans strain DSM 15229; EJ3 (x-axis); onnurineus strain NA1 (y-axis). Results can be regenerated at: http://genomevolution.org/r/os7

Local region of syntenic instability

These are interesting. Lots of inversions at the same local sub-regions, but not around a single point in the genome. Multiple events appear to be independent by comparison to different genomes. Perhaps there is some factor contributing to a local region of syntenic instability?

Syntenic dotplot generated by SynMap between two strains of Sulfolobus islandicus: M.14.25 (x-axis); Y.G.57.14 (y-axis). Results can be regenerated at: http://genomevolution.org/r/osn
Syntenic dotplot generated by SynMap between two strains of Sulfolobus islandicus: L.D.8.5 (x-axis); Y.G.57.14 (y-axis). Results can be regenerated at: http://genomevolution.org/r/oso
Syntenic dotplot generated by SynMap between two strains of Sulfolobus islandicus: strain L.S.2.15 (x-axis); strain Y.G.57.14 (y-axis). Results can be regenerated at: http://genomevolution.org/r/osp
Syntenic dotplot generated by SynMap between two species of Sulfolobus: solfataricus strain P2 (x-axis); islandicus strain Y.G.57.14 (y-axis). Results can be regenerated at: http://genomevolution.org/r/osg