Orientia tsutsugamushi (Ot) is an obligate intracellular bacteria, a species under the order Rickettsiales within the family Rickettsiaceae. It infects both mites and mammals and is the causative agent of scrub typhus in humans.
Ot has the most fragmented and repetitive genome of all bacteria. Its 2.0Mb - 2.7Mb genome is made up of about 70% degraded/complete version of a integrative and conjugative element called rickettsial amplified genetic element (RAGE).
This project investigates the genome dynamics of Ot using 25 genomes (17 complete and 8 incomplete).
I used Pangraph to visualise the relative order of alignment blocks among 17 complete genomes. For Pangraph documentation, see https://docs.pangraph.org
The genomes were ordered according to relatedness given by Panaroo 70% core gene alignment (among 90%, 80% and 70% core, 70% gave the best bootstrap score, therefore is the most reliable).