DOI: 10.5061/dryad.s7h44j13r
title: Transposable element landscape in Drosophila populations selected for longevity

description: Transposable elements (TEs) inflict numerous negative effects on health
 and fitness as they replicate by integrating into new regions of the host
 genome. Even though organisms employ powerful mechanisms to demobilize
 TEs, transposons gradually lose repression during aging. The rising TE
 activity causes genomic instability and was implicated in age-dependent
 neurodegenerative diseases, inflammation and the determination of
 lifespan. It is therefore conceivable that long-lived individuals have
 improved TE silencing mechanisms resulting in reduced TE expression
 relative to their shorter-lived counterparts and fewer genomic insertions.
 Here, we test this hypothesis by performing the first genome-wide analysis
 of TE insertions and expression in populations of Drosophila melanogaster
 selected for longevity through late-life reproduction for 50-170
 generations from four independent studies. Contrary to our expectation, TE
 families were generally more abundant in long-lived populations compared
 to non-selected controls. Although simulations showed that this was not
 expected under neutrality, we found little evidence for selection driving
 TE abundance differences. Additional RNA-seq analysis revealed a tendency
 for reducing TE expression in selected populations, which might be more
 important for lifespan than regulating genomic insertions. We further find
 limited evidence of parallel selection on genes related to TE regulation
 and transposition. However, telomeric TEs were genomically and
 transcriptionally more abundant in long-lived flies, suggesting improved
 telomere maintenance as a promising TE-mediated mechanism for prolonging
 lifespan. Our results provide a novel viewpoint indicating that
 reproduction at old age increases the opportunity of TEs to be passed on
 to the next generation with little impact on longevity.
description: Please see Materials and Methods section and Table S1.
description: Carnes_DeviaTE_raw.zip: Raw files for all
 transposable elements generated by DeviaTE.
 Carnes2015_MeanIns_SignificantRegimeApp1.pdf: Boxplots with
 jitter points for each population showing the number of insertions for TE
 families with significant regime differences according to approach
 #1. Carnes_all_pi_100kb.new: Nucleotide diversity pi
 calculated over non-overlapping 100kb windows using
 Popoolation. Carnes_all_theta_100kb.new:
 Watterson's theta calculated over non-overlapping 100kb windows using
 Popoolation. Fabian_DeviaTE_raw.zip: Raw files for
 all transposable elements generated by DeviaTE.
 Fabian2018_MeanIns_SignificantRegimeApp1.pdf: Boxplots with
 jitter points for each population showing the number of insertions for TE
 families with significant regime differences according to approach
 #1. Fabian_all_pi_100kb.new: Nucleotide diversity pi
 calculated over non-overlapping 100kb windows using
 Popoolation. Fabian_all_theta_100kb.new:
 Watterson's theta calculated over non-overlapping 100kb windows using
 Popoolation. Hoedjes_DeviaTE_raw.zip: Raw files for
 all transposable elements generated by DeviaTE.
 Hoedjes2019_MeanIns_SignificantRegimeApp1.pdf: Boxplots with
 jitter points for each population showing the number of insertions for TE
 families with significant regime differences according to approach
 #1. Hoedjes_all_pi_100kb.new: Nucleotide diversity pi
 calculated over non-overlapping 100kb windows using
 Popoolation. Hoedjes_all_theta_100kb.new:
 Watterson's theta calculated over non-overlapping 100kb windows using
 Popoolation.
 Remolina2012_Microarray_Stats_Age_Regime_AgeReg_PopAgeRandom_onReps_TissueSep.txt: Statistical analysis output for microarray analysis of Remolina2012. Remolina_DeviaTE_raw.zip: Raw files for all transposable elements generated by DeviaTE. Remolina2012_MeanIns_SignificantRegimeApp1.pdf: Boxplots with jitter points for each population showing the number of insertions for TE families with significant regime differences according to approach #1. Remolina_all_pi_100kb.new: Nucleotide diversity pi calculated over non-overlapping 100kb windows using Popoolation. Remolina_all_theta_100kb.new: Watterson's theta calculated over non-overlapping 100kb windows using Popoolation. carnes_all_TE_edited.txt: TE abundance file (edited from DeviaTE), used for analysis in R. fabian_all_TE_edited.txt: TE abundance file (edited from DeviaTE) used for analysis in R. hoedjes_all_TE_edited.txt: TE abundance file (edited from DeviaTE), used for analysis in R. remolina_all_TE_edited.txt: TE abundance file (edited from DeviaTE), used for analysis in R. hoedjes_all_Dmel_rawCov_edited.txt.zip: coverage of five single-copy genes implemented in DeviaTE used to normalize coverage of TE families. remolina_all_Dmel_rawCov_edited.txt.zip: coverage of five single-copy genes implemented in DeviaTE used to normalize coverage of TE families. carnes_all_Dmel_rawCov_edited.txt.zip: coverage of five single-copy genes implemented in DeviaTE used to normalize coverage of TE families. fabian_all_Dmel_rawCov_ediited.txt.zip: coverage of five single-copy genes implemented in DeviaTE used to normalize coverage of TE families. hoedjes_all_TE_edited_filtered.txt.zip: Output of TE familiy abundance from DeviaTE, edited and filtered for minimum normalized coverage. remolina_all_TE_edited_filtered.txt.zip: Output of TE familiy abundance from DeviaTE, edited and filtered for minimum normalized coverage. carnes_all_TE_edited_filtered.txt.zip: Output of TE familiy abundance from DeviaTE, edited and filtered for minimum normalized coverage. fabian_all_TE_edited_filtered.txt.zip: Output of TE familiy abundance from DeviaTE, edited and filtered for minimum normalized coverage. Genomic_TE_load.xlsx: Differences in total TE content. Average_Expression_per_Insertion.xlsx: Differences in average expression per TE insertion.