Comprehensive Genome Analysis of Bartonella

The whole genome sequences were trimmed, quality filtered, and quality assured using TrimGalore (v.0.5.0) [22 ]. The trimmed reads were submitted to the comprehensive genome analysis in the PATRIC database using UNICYCLER v.0.4.8 [23 (link)]. The resulting assembly was analyzed in PATRIC [24 ] and MiGa [25 ] to evaluate the genome features and completeness, contamination, and quality. The genomes were annotated by Bakta (v.1.6.1) [26 (link)], Prokka (v.3.2.1) [27 (link)], RASTtk (v1.073) [28 (link)], as well as PGAP (v.6.4) [29 (link)], and the PGAP was chosen as the reference annotation. A whole-genome-based phylogenetic tree was reconstructed using RAxML (v8.2.11) [30 (link)] implemented in PATRIC [31 (link)]. Whole-genome average nucleotide identity (ANI) was calculated between genomes of members of the genus Bartonella using the software Orthologous Average Nucleotide Identity Tool (OAT v.0.93.1) [18 (link),32 (link)]. Delimitation of species using OrthoANI results was based on Goris et al. [33 (link)] and Ciufo et al. [34 (link)], considering <95% values as novel species [19 (link)].