DOI: 10.5061/dryad.b2rbnzstx
title: Data from: Meiotic double strand DNA breaks and spontaneous mutation in <em>Drosophila melanogaster</em>

description: 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.
description: # Data from: Meiotic double strand DNA breaks and spontaneous mutation in
 *Drosophila melanogaster* Dataset DOI:
 [10.5061/dryad.b2rbnzstx](https://doi.org/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).