Table 2 Main features of BorreliaBase
From: BorreliaBase: a phylogeny-centered browser of Borrelia genomes
Comparative feature | Contents | Utility |
|---|---|---|
Genome phylogeny | • Based on 266 sets of single-copy orthologs present in all Borrelia | • Select or de-select genomes |
• Used as a navigation guide and a framework for genome comparison | • Generate phylogenetic expectations | |
Plasmid composition | • Length and identity of 489 contigs, inferred based on sequences of plasmid partition genes | • Identify presence and absence of plasmids |
Genome synteny | • Gene co-linearity of lp54, cp26, and the main chromosome | • Identify gene gains and losses (Figure 2) |
• Across 35 genomes from 8 species of LB-group Borrelia and 7 species of RF-group Borrelia | ||
Orthologous IGSs | • 541, 29, and 17 orthologous IGS families from main chromosome, lp54, and cp26, respectively | • Identify conserved regulatory sequences through phylogenetic footprinting (Figure 3) |
• Start and end positions manually curated according to consensus start-codon positions of flanking orthologous ORFs | ||
Orthologous ORFs | • 750, 61, and 26 orthologous ORF families from main chromosome, lp54, and cp26, respectively | • Visualize synonymous and nonsynonymous variations (Figure 4) |
• 5’ end sequences of each ORF manually curated according to the consensus start-codon position of each ortholog ORF family | • Identify recombination through homoplasy (phylogenetic inconsistency) (Figure 5) |