Data Sharing
Borrelia (Borreliella) burgdorferi B31 Genome Annotation
Genomic coordinate predictions for the boundaries of ORFs, 5′ UTRs, 3′ UTRs, rRNAs, tRNAs, and sRNAs for B. burgdorferi grown to logarithmic phase in BSKII culture media, at 35°C.
Download the table:
Tabular Format (CSV 319 KB)
Gene Transfer Format (GTF 1.6 MB)
To suggest an update to these gene annotations please contact Philip Adams (philip.adams@nih.gov)
Interactive B. burgdorferi Genome Browsers
To navigate the UCSC genome browsers:
- search for any gene of interest by either typing the gene name or gene ID into the search tool and pressing “go” (example formats: “ospC”, “BB_B19” or “bb_b19”); note that the search feature is case-sensitive
- search for any genomic region by typing the replicon and nucleotide coordinates into the search tool and pressing “go” (example format: “cp26:16,904-17,535”)
- data tracks are organized by experimental replicate and DNA strand separated
- read counts (indicated at the top left of each track) will auto-scale per sample group
RNA 5' and 3' end mapping (logarithmic phase cells):
5'RNA-seq, total RNA-seq, and 3'RNA-seq was performed using total RNA isolated from logarithmic grown spirochetes (3-5x107 cells/ml), in BSKII culture media, at 35°C. Transcription start sites (TSSs) are indicated for each DNA strand and were determined based on a 2-fold enrichment of a 5' end in the TAP+ tracks (RNA samples incubated with pyrophosphatase) compared to the TAP- tracks. 3'ends were determined by identifying peaks using a statistically-informed method and multiple replicates. Browser assembled by C. Esnault.
- Adams PP, Flores Avile C, Popitsch N, Bilusic I, Schroeder R, Lybecker M, Jewett MW. 2017. In Vivo Expression Technology and 5′ End Mapping of the Borrelia burgdorferi Transcriptome Identify Novel RNAs Expressed During Mammalian Infection
. Nucleic Acids Research 45(2):775‐792. doi:10.1093/nar/gkw1180 - Petroni E and Esnault C, Tetreault D, Dale RK, Storz G, Adams PP. 2023. Extensive Diversity in RNA Termination and Regulation Revealed by Transcriptome Mapping for the Lyme Pathogen Borrelia burgdorferi . Nature Communications 14, 3931. doi:10.1038/s41467-023-39576-1
RNA 3' end mapping (logarithmic and TS-stationary phase cells):
3'RNA-seq was performed using total RNA isolated from either logarithmic grown spirochetes (3-5x107 cells/ml) at 35°C or temperature-shifted (TS) stationary phase spirochetes in BSKII culture media. Temperature-shifted stationary cultures were grown to mid-logarithmic phase (3-5x107 cells/ml) at 35°C, temperature shifted to the bench (~23°C) for 48 hours, and then temperature shifted back to 35°C for 48 hours resulting in a stationary culture (2-3x108 cells/ml). 3' ends were determined by identifying peaks using a statistically-informed method and multiple replicates. Browser assembled by C. Esnault.
- Petroni E and Esnault C, Tetreault D, Dale RK, Storz G, Adams PP. 2023. Extensive Diversity in RNA Termination and Regulation Revealed by Transcriptome Mapping for the Lyme Pathogen Borrelia burgdorferi . Nature Communications 14, 3931. doi:10.1038/s41467-023-39576-1
B. burgdorferi Rho-dependent 3' ends (logarithmic phase cells):
Total RNA-seq was performed using total RNA isolated from logarithmic grown spirochetes (3-5x107 cells/ml) in the presence or absence of bicyclomycin (BCM) – the selective inhibitor of Rho. Rho regions were determined by calculating the degree of transcriptional readthrough when Rho-activity is inhibited, for each biological replicate.
- Petroni E and Esnault C, Tetreault D, Dale RK, Storz G, Adams PP. 2023. Extensive Diversity in RNA Termination and Regulation Revealed by Transcriptome Mapping for the Lyme Pathogen Borrelia burgdorferi . Nature Communications 14, 3931. doi:10.1038/s41467-023-39576-1
B. burgdorferi ±spermidine total RNA-seq (stationary phase cells):
Total RNA-seq was performed using total RNA isolated from stationary phase spirochetes (1-2x108 cells/ml) in the presence or absence of 10 mM spermidine.
- Petroni E and Esnault C, Tetreault D, Dale RK, Storz G, Adams PP. 2023. Extensive Diversity in RNA Termination and Regulation Revealed by Transcriptome Mapping for the Lyme Pathogen Borrelia burgdorferi . Nature Communications 14, 3931. doi:10.1038/s41467-023-39576-1
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