2.5. Assembly and Polishing

Multiple assembly and polishing software processes were run on the contigs (Table 1) and the resulting consensus was annotated using RASTtk v2.0 for preliminary annotation without backfilling gaps or frameshift correction [23]. The multiple annotated genomes were then aligned to the GenBank files of currently available NCBI depositions using Mauve v2.4.0 to assess the LCB alignment of the scaffolds before submission [24]. The chosen assembly and polishing pipeline varied across genomes but was determined by manually finding the assembly conditions that resulted in a circularized contig of each bacterial species of interest. The recommended polishing pipeline based on the assembler software used was then performed for each assembly. All assembler versions and software used in assembly and polishing are listed in Table 1. Data were stored and analyzed via bioinformatic software modules installed on the University of Florida HiPerGator Research Computing cluster.

Assembly statistics comparing the NCBI PGAP annotations of this publication to the closest strains deposited to NCBI sharing the highest nucleotide similarity. From left to right for NCBI strains: Ca. L. asiaticus str. ishi, Wolbachia KPSwDI05P40, Ca. P. armatura str. DC, Ca. C. ruddii str. DC. The size reported in parentheses for Ca. P. armatura reflects the length of the plasmid.