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Dissecting the sequential evolution of a selfish mitochondrial genome in Caenorhabditis elegans data

Cite this dataset

Dubie, Joseph; Katju, Vaishali; Bergthorsson, Ulfar (2024). Dissecting the sequential evolution of a selfish mitochondrial genome in Caenorhabditis elegans data [Dataset]. Dryad. https://doi.org/10.5061/dryad.1vhhmgr2z

Abstract

Mitochondrial genomes exist in a nested hierarchy of populations where mitochondrial variants are subject to genetic drift and selection at each level of organization, sometimes engendering conflict between different levels of selection, and between the nuclear and mitochondrial genomes. Deletion mutants in the Caenorhabditis elegans mitochondrial genome can reach high intracellular frequencies despite strongly detrimental effects on fitness. During a mutation accumulation (MA) experiment in C. elegans, a 499 bp deletion in ctb-1 rose to 90% frequency within cells while significantly reducing fitness. During the experiment, the deletion-bearing mtDNA acquired three additional mutations in nd5, namely two single insertion frameshift mutations in a homopolymeric run, and a base substitution. Despite an additional fitness cost of these secondary mutations, all deletion-bearing molecules contained the nd5 mutations at the termination of the MA experiment. The presence of mutant mtDNA was associated with increased mtDNA copy-number. Variation in mtDNA copy-number was greater in the MA lines than in a wildtype nuclear background, including a severe reduction in copy-number at one generational timepoint. Evolutionary replay experiments using different generations of the MA experiment as starting points suggests that two of the secondary mutations contribute to the proliferation of the original ctb-1 deletion by unknown mechanisms. 

README: Dissecting the Sequential Evolution of a Selfish Mitochondrial Genome in Caenorhabditis elegans Data

https://doi.org/10.5061/dryad.1vhhmgr2z

This data set contains four csv files

Fitness_data.xlsx contains raw measurements for four fitness traits measured in five populations of C. elegans.

Heteroplasmic_frequencies_Fig3.csv contains four tables of heteroplasmic frequencies of mitochondrial mutations from a mutation accumulation (MA) replay experiment

mtDNA_copynumber_backcrossed_lines_Fig4.csv contains a table of mitochondrial DNA copy numbers per nuclear genome in backcrossed lines normalized to the average of the wild-type N2 copy number

mtDNA_copynumber_MA_lines_Fig4.csv contains a table of mitochondrial DNA copy numbers per nuclear genome in MA lines normalized to the average of the wild-type N2 copy number

Description of the data and file structure

  • Fitness_data.xlsx
    • These lines were created by backcrossing the mitochondrial background of mutation accumulation (MA) lines into a wild-type nuclear background. * The 5 lines were derived from line MA line 1G, at generations 0 (preMA), 71, 96, 221, and 350
    • The four fitness traits measured were productivity, measured as the number of progeny produced by a single nematode; survivorship to adulthood, measured as the % of full sibling nematodes that survived to adulthood; longevity, measured as the number of days until the nematode died/was no longer respiring or responsive; and developmental time, measured as the number of hours an individual nematode took to reach adulthood. * Each sheet contains all the raw measurements for a given fitness trait in columns grouped by line. Mean, standard deviation, and n also provided.
  • Heteroplasmic_frequencies_Fig3.csv
    • Each table contains the heteroplasmic frequencies of a mitochondrial mutation of interest at generations 0, 5, and 10 of MA replay. * G71 contains the heteroplasmic frequencies of a ctb-1 deletion as determined by ddPCR (Bio-Rad)
    • G96 contains the heteroplasmic frequencies of an nd5 frameshift mutation determined by analyzing peak heights in sanger sequencing chromatograms via FIJI * G136 contains the heteroplasmic frequencies of an nd5 missense mutation determined by analyzing peak heights in sanger sequencing chromatograms via FIJI
    • G300 contains the heteroplasmic frequencies of a subsequent nd5 frameshift mutation determined by analyzing peak heights in sanger sequencing chromatograms via FIJI

cells with a value "n/a" are present in the data. These cells and represent samples lost due to single worm DNA extractions yielding too little or too degraded DNA for sequencing and ddPCR

  • mtDNA_copynumber_backcrossed_lines_Fig4.csv
    • Mitochondrial copy number was determined via ddPCR (Bio-Rad) * Relative mtDNA copy-number was calculated by dividing the copy number of each replicate by the mean copy number of wild-type N2 (WT in table)
    • Average was calculated by taking the average of each replicate for each line
  • mtDNA_copynumber_MA_lines_Fig4.csv
    • Mitochondrial copy number was determined via ddPCR (Bio-Rad) * Relative mtDNA copy-number was calculated by dividing the copy number of each replicate by the mean copy number of wild-type N2 (WT in table)
    • Average was calculated by taking the average of each replicate for each line

Funding

National Science Foundation, Award: MCB-1817762