BorreliaBase: a phylogeny-centered browser of Borrelia genomes.

Lia Di,Daniel Packer,Benjamin J Luft,Emmanuel F Mongodin,Pedro E Pagan,Girish Ramrattan,Steven E Schutzer,Sherwood R Casjens,Che L Martin,Claire M Fraser,Saymon Akther,Wei-Gang Qiu

doi:10.1186/1471-2105-15-233

Abstract

BackgroundThe bacterial genus Borrelia (phylum Spirochaetes) consists of two groups of pathogens represented respectively by B. burgdorferi, the agent of Lyme borreliosis, and B. hermsii, the agent of tick-borne relapsing fever. The number of publicly available Borrelia genomic sequences is growing rapidly with the discovery and sequencing of Borrelia strains worldwide. There is however a lack of dedicated online databases to facilitate comparative analyses of Borrelia genomes.DescriptionWe have developed BorreliaBase, an online database for comparative browsing of Borrelia genomes. The database is currently populated with sequences from 35 genomes of eight Lyme-borreliosis (LB) group Borrelia species and 7 Relapsing-fever (RF) group Borrelia species. Distinct from genome repositories and aggregator databases, BorreliaBase serves manually curated comparative-genomic data including genome-based phylogeny, genome synteny, and sequence alignments of orthologous genes and intergenic spacers.ConclusionsWith a genome phylogeny at its center, BorreliaBase allows online identification of hypervariable lipoprotein genes, potential regulatory elements, and recombination footprints by providing evolution-based expectations of sequence variability at each genomic locus. The phylo-centric design of BorreliaBase (http://borreliabase.org) is a novel model for interactive browsing and comparative analysis of bacterial genomes online.

Highlights

The bacterial genus Borrelia consists of two groups of pathogens represented respectively by B. burgdorferi, the agent of Lyme borreliosis, and B. hermsii, the agent of tick-borne relapsing fever
Spirochetes belonging to the genus Borrelia are obligate, tick- or louse-borne parasites of vertebrates and cause zoonotic infections in humans worldwide [1]
Phylogeny based on multiple genomic loci has confirmed the presence of two major Borrelia lineages, one represented by B. burgdorferi, the agent of Lyme borreliosis (LB), and the other by B. hermsii, the agent of tick-borne relapsing fever (RF) [2]

Summary

Conclusions

The phylogeny-centered design of BorreliaBase encourages comparing Borrelia genomes in the framework of their shared phylogenetic history. More than serving as a graphic guide for selecting and de-selecting strains, the genome phylogeny provides visual, evolution-based expectations on comparative genomic information such as an average level of sequence variability and the expected phylogenetic consistency of SNPs. When, and only when, an observed pattern deviates significantly from these evolutionary expectations should functional importance be conjectured. The observed high levels of sequence conservation of cis-regulatory elements deviate from the expected level of sequence variations between Borrelia species, consistent with gene-regulatory roles these IGS elements play (Figure 4). A phylogenetic expectation is especially valuable for identifying genomic footprints of recombination (Figure 5). Comparative features, including gene synteny and orthologs, are only available for the three universally present replicons. The source code of the website is publicly available at http://sourceforge.net/projects/phylobrowse/.

Background