Interactive Genomics of Spirochetes (IGS) Database

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

B. burgdorferi Transcriptome Mapping

• 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; manuscript citations: Adams et al., 2017 and Petroni and Esnault et al., 2023.
• 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; manuscript citations: Adams et al., 2017 and Petroni and Esnault et al., 2023.
• 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. Browser assembled by C. Esnault; manuscript citation: Petroni and Esnault et al., 2023.

B. burgdorferi Differential RNA-seq Datasets

• 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. Browser assembled by C. Esnault; manuscript citation: Petroni and Esnault et al., 2023.

The following downloadable files are lists of predicted gene annotations and gene descriptions that can be used for differential RNA-seq analysis:

• Tabular Format
• Gene Transfer Format

Gerardo Perez, Galt P Barber, Anna Benet-Pages, Jonathan Casper, Hiram Clawson, Mark Diekhans, Clay Fischer, Jairo Navarro Gonzalez, Angie S Hinrichs, Christopher M Lee, Luis R Nassar, Brian J Raney, Matthew L Speir, Marijke J van Baren, Charles J Vaske, David Haussler, W James Kent, Maximilian Haeussler. 2025. The UCSC Genome Browser database: 2025 update. Nucleic Acids Research 53(D1):D1243-D1249.

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.

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.

• Available for public use