Extended Data Fig. 1: Pipeline for identifying rearrangement events in Y. pestis phylogroups.
From: Insights into Yersinia pestis evolution through rearrangement analysis of 242 complete genomes
a, Synteny block construction without a reference genome using SibellaZ and maf2synteny tools. The adjacency marks synteny block neighbors, with ‘h’ for the head and ‘t’ for the tail of blocks. For instance, ‘2h-3t’ illustrates that the head of block no. 2 is adjacent to the tail of block no. 3. b, Pairwise rearrangement detection based on reference genomes with SyRI software. SYN denotes syntenic regions, INV for inversions, TRANS for translocations, INVTR for inverted translocations, and DUP for duplications. Our focus of genomic rearrangements was on INV, TRANS, and INVTR. c, Synteny block analysis combined with pairwise rearrangement identification. d, Determining rearrangement events in the last common ancestor (LCA) of phylogroups. e, Detecting rearrangement events within specific phylogroups.
