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Data from: Thoracic underreplication in Drosophila species estimates a minimum genome size and the dynamics of added DNA

Citation

Hjelmen, Carl E. et al. (2020), Data from: Thoracic underreplication in Drosophila species estimates a minimum genome size and the dynamics of added DNA, Dryad, Dataset, https://doi.org/10.5061/dryad.sqv9s4n1m

Abstract

Many cells in the thorax of Drosophila were found to stall during replication, a phenomenon known as underreplication. Unlike underreplication in nuclei of salivary and follicle cells, this stall occurs with less than one complete round of replication. This stall point allows precise estimations of early-replicating euchromatin and late-replicating heterochromatin regions, providing a powerful tool to investigate the dynamics of structural change across the genome. We measure underreplication in 132 species across the Drosophila genus and leverage this data to propose a model for estimating the rate at which additional DNA is accumulated as heterochromatin and euchromatin and also predict the minimum genome size for Drosophila. According to comparative phylogenetic approaches, the rates of change of heterochromatin differ strikingly between Drosophila subgenera. While these subgenera differ in karyotype, there were no differences by chromosome number, suggesting other structural changes may influence accumulation of heterochromatin. Measurements were taken for both sexes, allowing the visualization of genome size and heterochromatin changes for the hypothetical path of XY sex chromosome differentiation. Additionally, the model presented here estimates a minimum genome size in Sophophora remarkably close to the smallest insect genome measured to date, in a species over 200 million years diverged from Drosophila.

Methods

Levels of thoracic underreplication were measured using flow cytometry in 132 species across the Drosophila genus.  These measurements were used to estimated the proportion of the genome which is euchromatic versus heterochromatic.  These data were then used to estimate the rate of change of euchromatin and heterochromatin in the genus and its subgenera.  Additionally, a phylogeny was constructed for this group for comparative analyses using MrBayes.  The files here include a csv of values for all species of interest, which includes genome size, chromosome number, underreplication value, amount of replicated DNA, amount of Unreplicated DNA, sex differences in genome size, sex differences in replicated DNA,and sex differences in unreplicated DNA.  A consensus tree is uploaded which contains 152 species. The four tree files used to construct the consensus tree are also included.  A tree file which has been adjusted to representevolutionary time for analyses is also included.  Separate tree files trimmed for male and female data are also included.

Usage Notes

These data include the phylogenies used for the analyses, as well as a csv file which includes values measured for each species.