Detecting rare structural variation in evolving microbial populations from new sequence junctions using breseq
Open accessAbstract
New mutations leading to structural variation (SV) in genomes-in the form of mobile element insertions, large deletions, gene duplications, and other chromosomal rearrangements-can play a key role in microbial evolution. Yet, SV is considerably more difficult to predict from short-read genome resequencing data than single-nucleotide substitutions and indels (SN), so it is not yet routinely identified in studies that profile population-level genetic diversity over time in evolution experiments. We implemented an algorithm for detecting polymorphic SV as part of the breseq computational pipeline. This procedure examines split-read alignments, in which the two ends of a single sequencing read match disjoint locations in the reference genome, in order to detect structural variants and estimate their frequencies within a sample. We tested our algorithm using simulated Escherichia coli data and then applied it to 500- and 1000-generation population samples from the Lenski E. coli long-term evolution experiment (LTEE). Knowledge of genes that are targets of selection in the LTEE and mutations present in previously analyzed clonal isolates allowed us to evaluate the accuracy of our procedure. Overall, SV accounted for ~25% of the genetic diversity found in these samples. By profiling rare SV, we were able to identify many cases where alternative mutations in key genes transiently competed within a single population. We also found, unexpectedly, that mutations in two genes that rose to prominence at these early time points always went extinct in the long term. Because it is not limited by the base-calling error rate of the sequencing technology, our approach for identifying rare SV in whole-population samples may have a lower detection limit than similar predictions of SNs in these data sets. We anticipate that this functionality of breseq will be useful for providing a more complete picture of genome dynamics during evolution experiments with haploid microorganisms.
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Plotting RNAseq reads on the wild type genome revealed two novel DNA-junctions in the promoter region of LP_RS05225.
“However, plotting RNAseq reads on the wild type genome revealed two novel DNA-junctions in the promoter region of LP_RS05225, that apparently could only be detected with the high read numbers produced in RNAseq experiments and the dedicated breseq software with a low detection limit for identification of variations in the genome [55].”
From Bistable auto-aggregation phenotype in Lactiplantibacillus plantarum emerges after cultivation in in vitro colonic microbiota (2021) · cites this paper as [55]
The Methods section (page unavailable) describes breseq detecting new structural-variant junctions from sequencing reads, and the Results section says greater read-depth coverage is the primary consideration for detecting rare junctions. The paper does not report RNA-seq analysis or two junctions in the promoter of LP_RS05225, so it does not support that specific observation. (LLM, conf=0.85)
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- Authors
- Deatherage, D. E., Traverse, C. C., Wolf, L. N., & Barrick, J. E.
- Affiliations
- The University of Texas at Austin (US)
- Corresponding author
- Barrick, Jeffrey E.
- Venue
- Frontiers in Genetics
- Publisher
- Frontiers Media SA
- Published
- 2015-01-21
- Volume
- 5
- Pages
- 468-468
- ISSN
- 1664-8021 (ISSN-L)
- PMC
- PMC4301190
- OpenAlex
- W2013647724
- Cited by
- 93
- References
- 52
- Citations by year
- 2026: 4 · 2025: 7 · 2024: 11 · 2023: 9 · 2022: 12 · 2021: 11 · 2020: 10 · 2019: 13 · 2018: 4 · 2017: 6 · 2016: 2 · 2015: 4
- FWCI
- 2.32
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Frontiers in Genetics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Science Foundation (0939454)
- Cancer Prevention and Research Institute of Texas (RP130124)
- National Institutes of Health (DBI-0939454)
- National Institute of General Medical Sciences (R00GM087550)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- structural variants, rare variants, Escherichia coli, long-term evolution experiment, population genetic variation, mobile element insertions, gene duplication, chromosomal rearrangements
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