Abstract
We announce the draft genome sequence of Borrelia garinii strain NMJW1, isolated from Ixodes persulcatus in northeastern China. The 902,789-bp linear chromosome (28.4% GC content) contains 813 open reading frames, 33 tRNAs, and 4 complete rRNAs.
GENOME ANNOUNCEMENT
Borrelia burgdorferi sensu lato is known to include 15 genospecies, of which B. burgdorferi sensu stricto, B. afzelii, B. garinii, B. spielmanii, and B. valaisiana are associated with human Lyme disease (3, 10–14). To date, whole-genome sequences of B. burgdorferi from China have not been reported. Here, we report the complete linear chromosome of Borrelia garinii strain NMJW1, isolated from Ixodes persulcatus in the Inner Mongolia Autonomous Region in northeastern China. B. garinii NMJW1, grown in Barbour-Stoenner-Kelly H medium (Sigma, St. Louis, MO) supplemented with 6% rabbit serum at 30°C (2, 15), was sequenced with a combined strategy involving the Roche 454 GS FLX sequencer and Solexa. Using strain B. garinii PBi as a reference, an average 157.52-fold genomic coverage was obtained over 383,310 reads, which were assembled using the Newbler 2.6 assembler (Roche), generating 36 interscaffold and intrascaffold gaps. We resequenced by Solexa sequencing technology to close these gaps and then used SOAPdenovo, version 1.05 (7), to assemble the 9,906,046 pair-end Illumina sequencing reads (3-kb and 500-bp inserts) with 1,097.27-fold genome coverage which were generated by using the Illumina HiSeq2000 system (9). Based on this assembly, the interscaffold and intrascaffold gaps were closed by local assembly. Gene prediction was performed using Glimmer1 (4). The tRNA genes were searched for with tRNAScan-SE2 (8). The rRNA genes were searched for with RNAmmer3 (6). Protein BLAST4 was run, using the translated coding sequences as a query against the reference sequence (1).
The linear B. garinii NMJW1 chromosome includes 902,789 bp in total (28.4% GC content) and carries 33 tRNAs, 4 complete rRNAs, and 813 open reading frames (ORFs), of which 75% do not code for a hypothetical protein. This strain is highly similar to the B. garinii Bgvir strain (isolated from Russian) and the B. garinii PBi strain (isolated from Germany). The core-gene analysis between B. garinii NMJW1 and B. garinii Bgvir (832 genes) (5) showed that 796 ORFs are conserved, and strain NMJW1 was 97.91% similar to strain Bgvir. In-depth comparative analysis among different species will be the focus of our work.
Comparative analysis of B. garinii NMJW1 with the different Borrelia species and in-depth study of strain NMJW1 can provide major insights into the evolution of Borrelia and explain its taxonomic relationships in China, and new knowledge will be gained from analyzing the genome which will help identify new surface proteins to possibly help prevent, diagnose, and treat Lyme disease.
Nucleotide sequence accession number.
The complete genome sequence of B. garinii NMJW1 was deposited in GenBank under the accession number CP003866.
ACKNOWLEDGMENTS
This study is supported by the Funds for International Cooperation and Exchange of the National Natural Science Foundation of China (grant 2011DFB30370) and the Natural Science Foundation of China (grant 81130086).
REFERENCES
- 1. Altschul SF, et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389–3402 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2. Callister SM, et al. 1990. Effects of bovine serum albumin on the ability of Barbour-Stoenner-Kelly medium to detect Borrelia burgdorferi. J. Clin. Microbiol. 28:363–365 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3. Chu CY, et al. 2008. Novel genospecies of Borrelia burgdorferi sensu lato from rodents and ticks in southwestern China. J. Clin. Microbiol. 46:3130–3133 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4. Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673–679 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5. Glockner G, et al. 2004. Comparative analysis of the Borrelia garinii genome. Nucleic Acids Res. 32:6038–6046 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6. Lagesen K, et al. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35:3100–3108 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7. Li R, et al. 2010. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20:265–272 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955–964 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9. Margulies M, et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10. Masuzawa T, et al. 2001. Borrelia sinica sp. nov., a Lyme disease-related Borrelia species isolated in China. Int. J. Syst. Evol. Microbiol. 51(Pt 5):1817–1824 [DOI] [PubMed] [Google Scholar]
- 11. Postic D, Garnier M, Baranton G. 2007. Multilocus sequence analysis of atypical Borrelia burgdorferi sensu lato isolates—description of Borrelia californiensis sp. nov., and genomospecies 1 and 2. Int. J. Med. Microbiol. 297:263–271 [DOI] [PubMed] [Google Scholar]
- 12. Richter D, et al. 2006. Delineation of Borrelia burgdorferi sensu lato species by multilocus sequence analysis and confirmation of the delineation of Borrelia spielmanii sp. nov. Int. J. Syst. Evol. Microbiol. 56(Pt 4):873–881 [DOI] [PubMed] [Google Scholar]
- 13. Rudenko N, Golovchenko M, Grubhoffer L, Oliver JH., Jr2009. Borrelia carolinensis sp. nov., a new (14th) member of the Borrelia burgdorferi sensu lato complex from the southeastern region of the United States. J. Clin. Microbiol. 47:134–141 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14. Rudenko N, et al. 2009. Delineation of a new species of the Borrelia burgdorferi sensu lato complex, Borrelia americana sp. nov. J. Clin. Microbiol. 47:3875–3880 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 15. Wang G, et al. 2004. Variations in Barbour-Stoenner-Kelly culture medium modulate infectivity and pathogenicity of Borrelia burgdorferi clinical isolates. Infect. Immun. 72:6702–6706 [DOI] [PMC free article] [PubMed] [Google Scholar]