Borrelia burgdorferi, the agent of Lyme disease, differentially expresses numerous genes and proteins as it cycles between mammalian hosts and tick vectors. Insights on regulatory mechanisms have been provided by earlier studies that examined B. burgdorferi gene expression patterns during cultivation. However, prior studies examined bacteria at only a single time point of cultivation, providing only a snapshot of what is likely a dynamic transcriptional program driving B. burgdorferi adaptations to changes during culture growth phases. To address that concern, we performed RNA sequencing (RNA-Seq) analysis of B. burgdorferi cultures at early-exponential, mid-exponential, and early-stationary phases of growth. We found that expression of nearly 18% of annotated B. burgdorferi genes changed significantly during culture maturation. Moreover, genome-wide mapping of the B. burgdorferi transcriptome in different growth phases enabled insight on transcript boundaries, operon structures, and identified numerous putative non-coding RNAs. These RNA-Seq data are discussed and presented as a resource for the community of researchers seeking to better understand B. burgdorferi biology and pathogenesis.

Document Type


Publication Date


Notes/Citation Information

Published in PLOS ONE, v. 11, no. 10, e0164165, p. 1-22.

© 2016 Arnold et al.

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Digital Object Identifier (DOI)


Funding Information

This work was supported by National Institutes of Health grants R03-AI113648 to B. Stevenson, J. Seshu, and J. Livny, and R21-AI120602 to B. Stevenson.

journal.pone.0164165.s001.EPS (41430 kB)
S1 Fig. Correlation between replicates.

journal.pone.0164165.s002.XLSX (59 kB)
S1 Table. PCR oligonucleotide primers used in these studies.

journal.pone.0164165.s003.XLSX (210 kB)
S2 Table. Relative gene expression of annotated genes.

journal.pone.0164165.s004.XLSX (165 kB)
S3 Table. Annotated ORFs that were not readily transcribed in any culture.

journal.pone.0164165.s005.XLSX (36 kB)
S4 Table. Transcripts with significantly different abundance in mid-exponential compared to early-exponential.

journal.pone.0164165.s006.XLSX (44 kB)
S5 Table. Transcripts with significantly different abundance in stationary phase compared to mid-exponential.

journal.pone.0164165.s007.XLSX (67 kB)
S6 Table. Transcripts with significantly differen abundance in stationary phase compared to early-exponential.

journal.pone.0164165.s008.XLSX (137 kB)
S7 Table. Putative transcript 5’ ends.

journal.pone.0164165.s009.XLSX (21 kB)
S8 Table. Bioinformatically predicted intrinsic termination sites.

journal.pone.0164165.s010.XLSX (63 kB)
S9 Table. Identified non-coding RNAs.