Hertweck Evolution 2014
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Transcript of Hertweck Evolution 2014
Jumping genes and aging: de novo transposable element insertions respond
to selection for time to developmentKate L. HertweckMira 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 @k8hertGoogle+ [email protected]
Blog: k8hert.blogspot.comwww.slideshare.net/katehertweck
Wikicommons
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)
LTRLINESINEERVSVA
Class II: DNA transposons(cut and paste)TIR (P elements)
MITECryptonHelitronMaverick
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?
K. Hertweck (@k8hert), NESCent, de novo TEs and time to development
Rose laboratory Drosophila stocks
Long term experimental evolution systemEstablished 1980
A 9-day life cycleB 14-day life cycle (baseline)C 28-day life cycle
ACO
CO
BO
NCO AO
B
O
Original population
A, B, C derived twice eachReversal of selectionTesting for convergence
All populations replicated five times
Joe Graves, “Genome-wide convergence with repeated evolution in Drosophila melanogaster, Monday 10:30 305B (Experimental Evolution)
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?
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)
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)
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?
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?
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
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
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?
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.comwww.slideshare.net/katehertweck
Twitter @k8hertGoogle+ [email protected]