Hertweck Evolution 2014

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Presented at Evolution 2014 in Raleigh, NC (http://evolution2014.org)
Jumping genes and life history: De novo transposable element insertions respond to selection for accelerated and delayed development times

Kate L Hertweck, NESCent, k8hertweck@gmail.com
Mira Han, UNLV, mira.han@unlv.edu
Lee F Greer, University of California, Irvine, lgreer@uci.edu
Mark A Phillips, UC Irvine, mphillips6789@gmail.com
Michael R Rose, University of California, Irvine, mrrose@uci.edu
Joseph L Graves, JSNN, North Carolina A&T State University, gravesjl@ncat.edu

A wealth of scientific literature has speculated on the response of both the genome and organism to proliferation of transposable elements (TEs, or jumping genes). In particular, the relationship between TEs and aging has been addressed by both theory and empirical studies. Theory suggests TEs may contribute to life history features such as aging, by introducing detrimental somatic mutation. However, a comparison TEs between organisms indicate the number of copies may increase, decrease, or have no effect on lifespan, depending on the model system and type of TE investigated. Long-term studies in experimental evolution allow explicit testing of such hypothesis using replicated populations. Our data represent pooled population genome-wide resequencing from Drosophila selected for both delayed and accelerated reproduction times and development. Our previous results indicate that insertion frequencies of ancestral TEs (i.e., annotated in the fully sequenced reference genome) respond fairly consistently to selection. For the present study, we use two independent approaches (PoPoolation TE and RelocaTE) to identify de novo TE insertions. We find that the magnitude of TE proliferation varies among multiple families of LTRs, LINEs, and DNA transposons. We present methodological considerations for interpreting such results.

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Hertweck Evolution 2014

  1. 1. Jumping genes and aging: de novo transposable element insertions respond to selection for time to development Kate L. Hertweck Mira Han (NESCent) Lee F. Greer (UC Irvine) Mark A. Phillips (UC Irvine) Joseph L. Graves, Jr. (NC A&T, UNC Greensboro) Michael R. Rose (UC Irvine) Twitter @k8hert Google+ k8hertweck@gmail.com Blog: k8hert.blogspot.com www.slideshare.net/katehertweck Wikicommons
  2. 2. Transposable elements as a model system K. Hertweck (@k8hert), NESCent, de novo TEs and time to development ● TEs, mobile genetic elements, or jumping genes ● Parasitic, self-replicating ● Similar to or derived from viruses ● Move independently in a genome Class I: Retrotransposons (copy and paste) LTR LINE SINE ERV SVA Class II: DNA transposons (cut and paste) TIR (P elements) MITE Crypton Helitron Maverick
  3. 3. Genome-wide TE insertions and lifespan Kate Hertweck, Genomic effects of repetitive DNAKate Hertweck, NESCent, Genomic effects of junk DNAK. Hertweck (@k8hert), NESCent, de novo TEs and time to development Empirical data: it depends! ● TIR DNA transposons: decrease or have no effect on lifespan (Drosophila: Nikitin and Woodruff 1995; C. elegans: Egilmez and Reis 1994) ● LTR retrotransposons decrease lifespan (Drosophila: Driver and McKechnie 1992) ● Alu SINEs reverse senescence (human cell lines: Wang et al. 2011) ● TEs linked with epigenetic changes (Wilkins 2010, Baillie et al. 2011) Theory: TE proliferation will decrease lifespan, accumulation of mutations (Kirkwood 1986, Murrey 1990) What is the relationship between TE insertions and lifespan?
  4. 4. K. Hertweck (@k8hert), NESCent, de novo TEs and time to development Rose laboratory Drosophila stocks Long term experimental evolution system Established 1980 A 9-day life cycle B 14-day life cycle (baseline) C 28-day life cycle ACO CO BO NCO AO B O Original population A, B, C derived twice each Reversal of selection Testing for convergence All populations replicated five times Joe Graves, “Genome-wide convergence with repeated evolution in Drosophila melanogaster, Monday 10:30 305B (Experimental Evolution)
  5. 5. Experimental data K. Hertweck (@k8hert), NESCent, de novo TEs and time to development ● Whole-genome resequencing (Illumina Hi-Seq) 120 females x six treatments x five replicates ● Are there areas of significant differentiation in the genome? Where? Hard vs. soft sweeps (Burke et al., 2010)? SNP analysis: Popoolation2 (Kofler et al., 2011) Known (ancestral) TE detection: Tlex (Fiston-Lavier et al. 2010) Structural variant analysis: Delly (Rausch et al., 2012) How do frequencies of known TE insertions respond to selective pressures? How does total TE load respond to selective pressures?
  6. 6. Bioinformatics approach K. Hertweck (@k8hert), NESCent, de novo TEs and time to development ● RelocaTE 1.0.4 (Robb et al. 2013) ● Uses TSD sequence motifs (LTR and TIR) and reference genome ● 82 canonical sequences (Bergman, v.9.43) and Dmel v5 ● Filtered for read count >10 (custom) ● PoPoolationTE 1.02 (Kofler et al. 2012) ● Uses known insertions, reference genome, TE hierarchy ● 5200 insertions from annotation 5.55 ● Filtered for read count >10 ● Summarizing data ● Total TE insertions identified (by order) ● Total TE families (by order)
  7. 7. RelocaTE: total TE insertions K. Hertweck (@k8hert), NESCent, de novo TEs and time to development CO NCOACO AO BO B * * Populations of flies with short v long lifespan have significantly different numbers of total TEs (all C v all A: p=0.028*) This difference appears to be driven by retrotransposons (shorter lifespan, more LTRs)
  8. 8. RelocaTE: total TE families K. Hertweck (@k8hert), NESCent, de novo TEs and time to development CO NCOACO AO BO B No significant differences between treatments for number of TE families What about other types of TEs?
  9. 9. PoPoolationTE: total TE insertions K. Hertweck (@k8hert), NESCent, de novo TEs and time to development CO NCOACO AO BO B No significant differences between groups What's the deal with replicate 5?
  10. 10. PoPoolationTE: total TE families K. Hertweck (@k8hert), NESCent, de novo TEs and time to development CO NCOACO AO BO B PoPoolationTE more consistently IDs TE families ACO CO BO NCO AO B O Original population
  11. 11. Conclusions ● RelocaTE is more conservative than PoPoolationTE in estimates of de novo TE insertions, but appears to miss some families ● Some evidence for more TEs associated with shorter lifespan, most variation in LTRs ● One population replicate presents a much different profile in overall TE load: ● Not apparent with all algorithms ● Multiple types of genomic responses to same selection? K. Hertweck (@k8hert), NESCent, de novo TEs and time to development
  12. 12. Continuing work K. Hertweck (@k8hert), NESCent, de novo TEs and time to development ● Additional filtering and screening to determine exact specificity of de novo TE calls between algorithms ● Overlap between TE calls from different programs ● Genome-wide tests for significance of different genomic events (SNPs, structural variation, TEs) ● Testing for repeatability of evolution? What is up with replicate 5?
  13. 13. Acknowledgements ● Fellow NESCent scientists (for abiding my gluttonous shared computer cluster appetite) ● Casey Bergman and Michael Nelson (U Manchester) ● Joe Graves, “Genome-wide convergence with repeated evolution in Drosophila melanogaster, Monday 10:30 305B (Experimental Evolution) Blog: k8hert.blogspot.com www.slideshare.net/katehertweck Twitter @k8hert Google+ k8hertweck@gmail.com
  14. 14. Variation in replicate 5 from sequencing coverage? K. Hertweck (@k8hert), NESCent, de novo TEs and time to development

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