Data from: Meiotic double strand DNA breaks and spontaneous mutation in Drosophila melanogaster
Data files
Nov 07, 2025 version files 456.23 MB
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README.md
2.64 KB
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RECMA_SCRIPT_V8.R
176.77 KB
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RECMA_WORKSPACEV8.RData
454.02 MB
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Supplemental_tables.xlsx
2.03 MB
Jan 16, 2026 version files 457.37 MB
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mcclintock_results.RData
1.11 MB
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README.md
3.33 KB
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RECMA_process_mcclintock_results.r
16.63 KB
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RECMA_SCRIPT_V9.R
191.52 KB
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RECMA_WORKSPACEV9.RData
454.02 MB
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Supplemental_tables.xlsx
2.03 MB
Abstract
The exchange of genetic material during meiosis requires the formation and repair of DNA double-strand breaks (DSBs), which may not be repaired with perfect fidelity. If meiotic exchange is mutagenic, this would add to the costs of sexual reproduction and affect patterns of genome evolution, but much of the evidence for this is indirect. In the fruit fly Drosophila melanogaster, it is possible to completely suppress endogenous DSBs while retaining normal fertility. We took advantage of this system to generate fly strains with and without a mutant allele of mei-P22, a gene that is essential for meiotic DSB formation, on a common genetic background. This allowed us to investigate the relationship between DSBs and genome-wide mutation patterns, using a mutation accumulation design to allow un-selected spontaneous mutations to be observed. Following 30 generations of mutation accumulation, we identified over 1800 mutations by whole-genome sequencing. The presence of meiotic DSBs had little effect on the rate and spectrum of point mutations. We found that mutations were more likely to occur in areas of the genome with higher rates of crossover recombination, regardless of whether meiotic DSBs were occurring. We also found that the rate of transposable element insertions across multiple TE families was substantially elevated in the group lacking meiotic DSBs, suggesting that host suppression of mobile genetic elements is closely associated with meiotic recombination mechanisms.
Dataset DOI: 10.5061/dryad.b2rbnzstx
Description of the data and file structure
This data supplements the manuscript titled Meiotic double strand DNA breaks and spontaneous mutation in Drosophila melanogaster. Here we use experimental lines of Drosophila melanogaster that either did or did not have meiotic double strand DNA breaks in an effort to understand how meiotic DSBs impact genome wide patterns of mutation. We find that meiotic DSBs have no significant effect on the rate, spectrum, or genomic distribution of point mutations (SNVs, INDELs, MNV, COMPLEXs) and that the presence of meiotic DSBs is associated with reduced levels of transposable element insertions. This effect was observed across numerous TE families and was not exclusive to any specific genomic contexts.
Files and variables
File: RECMA_SCRIPT_V9.R
Description: This R script processes the data and shows our statistical testing and figure creation methods. We ran this script with R version 4.3.2. While steps 1-7 of this script appear to require input files, you can bypass those by using the provided workspace and skipping to step 8 of the script.
File: Supplemental_tables.xlsx
Description: This table contains the point mutation callset, the TE callset, the structural variant callset, and the genomic window information used in our analysis.
Variables
- Described in detail in the readme page of the excel file.
File: RECMA_WORKSPACEV9.RData
Description: This R workspace goes alongside the R script RECMA_SCRIPT_V9.r. This workspace is what is produced after running sections 1-7 of the script. To use this workspace you should download the file and then edit section #8 in the script to fit wherever this workspace file is located on your local machine.
File: RECMA_process_mcclintock_results.r
Description: This R script processes the outputs of the McClintock metapipeline to identify de novo TE insertion. We ran this script with R version 4.5.0. We provide a precomputed R datastructure with mcclintock results for the analysis, which can be loaded by providing the path to the file location on your local machine.
File: mcclintock_results.RData
Description: This R workspace contains raw McClintock outputs used for processing in RECMA_process_mcclintock_results.r. It can be used by providing the the path to the file location on your local machine. in the R script.
File: RECMA_Supplementary_Information_Figs_r1.docx
Description: This file contains the supplemental figures alongside their figure legends.
Code/software
To work with the provided files we used RStudio v4.3.2. The workspace will get you to step 8 after which you will need to run the remaining code in the script.
Access information
Other publicly accessible locations of the data:
- The raw short reads are available at the SRA under bioproject accession number PRJNA1346113
Data was derived from the following sources:
- This data was derived from Illumina Novaseq X Plus short reads obtained through the University of Wisconsin Biotechnology Center DNA Sequencing Core Facility (RRID:SCR_017759).
Changes after Nov 7, 2025:
After receiving peer reviews we have updated the R script with some small additional statistical tests and some additional supplemental figures. Alongside those changes we have an updated supplemental information file and a new workspace file. There is also an additional R script that we have included for better transparency with how our TE callset was curated (RECMA_process_mcclintock_results.r) along with its corresponding R datafile (mcclintock_results.RData).
