Complete Genome Sequence of Borrelia crocidurae

Abstract

We announce the draft genome sequence of Borrelia crocidurae (strain Achema). The 1,557,560-bp genome (27% GC content) comprises one 919,477-bp linear chromosome and 638,083-bp plasmids that together carry 1,472 open reading frames, 32 tRNAs, and three complete rRNAs, with almost complete colinearity between B. crocidurae and Borrelia duttonii chromosomes.

GENOME ANNOUNCEMENT

Borrelia crocidurae is a spirochete responsible for tick-borne zoonotic relapsing fever in West Africa, where the soft tick Ornithodoros sonrai is the vector (2, 12). Relapsing fever mimics malaria, with which relapsing fever is often confused in the absence of laboratory confirmation (7). B. crocidurae remains a neglected organism that is rarely investigated using nonspecific laboratory tools.

The B. crocidurae Achema strain (11), grown in Barbour-Stoenner-Kelly H medium (Sigma, Saint-Quentin-Fallavier, France) supplemented with 6% rabbit serum (Eurobio, Courtaboeuf, France) at 33°C, was sequenced using pyrosequencing technology on a Roche 454 GS FLX sequencer (Roche, Boulogne-Billancourt, France). An average 24-fold genomic coverage was obtained over 22,610 paired-end reads, which were assembled using the Newbler 2.3 assembler (Roche), generating 41 scaffolds. Ordering, using the Borrelia duttonii genome (5) as a reference, left 39 plasmid scaffolds in draft status, whereas 2 chromosome scaffolds were closed by PCR sequencing. An in-house pipeline based on the Prodigal program was used to annotate the DNA sequences (3). tRNAs were predicted using the Aragorn program (4), and rRNAs were predicted using RNAmmer. The functional annotation of predicted genes was performed using RPS-BLAST (6) against Pfam (9) and the Cluster of Orthologous Groups (COG) database (10). We performed BLASTP analysis of B. duttonii open reading frames (ORFs) versus the B. crocidurae chromosome (1), and codon usage was determined using the E-CAI server (8).

The 1,557,560-bp linear B. crocidurae genome (27% GC content) carries 1,472 ORFs, 32 tRNAs, and three complete rRNAs. The 919,477-bp chromosome carries 865 ORFs, of which 79% are proteins listed in the COG database. The S200-like transposase and transposase IS605 OrfB in B. crocidurae disrupt the almost complete colinearity between B. crocidurae, B. duttonii, and B. recurrentis chromosomes. Seven copies of these elements are found in the B. duttonii plasmid complement, and six copies are found in the Borrelia recurrentis plasmid complement. Additionally, a 5-kbp B. duttonii duplication encoding an RNA pseudouridylate synthase family protein, MurC, and the hypothetical proteins BDU_828 and BDU_830 is absent from the B. crocidurae chromosome. Comparing B. crocidurae with B. duttonii revealed 771 orthologs with an average pairwise amino acid sequence identity of 95 to 100% and identical codon usage. Unlike B. recurrentis, B. crocidurae has intact recA, mutS, and smf genes (5). The exact number of plasmids remained undetermined due to repeat sequences and size overlap, but 607 ORFs, including a telomerase resolvase, are conserved among the three species. The B. duttonii pI165 and pI11 plasmids are merged as one pI173 plasmid in B. crocidurae. In addition, the B. crocidurae genome has a counterpart for B. recurrentis plasmid PI6, which is absent in B. duttonii.

Availability of the B. crocidurae genome sequence provides major insights into the evolution of borreliae and explains the taxonomic relationship between recurrent fever groups in Africa. This sequence will also facilitate the development of molecular tools to improve the diagnosis and characterization of relapsing fever pathogens.

Nucleotide sequence accession numbers.

The complete genome sequence of the B. crocidurae Achema strain was deposited in GenBank under the accession numbers CP003426 (chromosome) and CP003427 to CP003465 (plasmids).