Comparative Genomics of Burkholderia and Allies

Complete, draft genomes, and raw reads of Burkholderia spp. including former Burkholderia genomes from the newly renamed genera Paraburkholderia and Caballeronia(Table S3) were analyzed using PhaME. Genomes from genera that have multiple available genomes were randomly selected to have a mixture of complete and draft genomes. Ralstonia solanacearum PSI07 was also included and used as an outgroup and PhaME picked B. mallei NCTC 10247 as the reference genome based on MinHash distances. Raw reads were first quality controlled using FaQCs v2.09^{81 (link)} and then added to PhaME analysis. Orthologous polymorphic positions were kept and used to build a maximum likelihood tree using RAxML (GTRGAMMAI) with 100 bootstrap supports.
Subsets of the genomes that belong to the Bcc or the B. pseudomallei groups were further analyzed using PhaME (Table S3). Genomes that belong to the corresponding clades were selected from the whole Burkholderia tree and the original alignments were used to recalculate the core genome and core SNPs, which were then used to reconstruct maximum likelihood tree using RAxML (GTRGAMMAI) with 100 bootstraps.