Hertweck uva2012

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Presentation to EEBio at University of Virginia, Charlottesville, VA, 6 Nov 2012.

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Hertweck uva2012

  1. 1. Genome-wide effects oftransposable element evolution Kate L Hertweck National Evolutionary Synthesis Center (NESCent) digthedirt.com
  2. 2. Overview● Synthetic science: NESCent – I dont collect data. – Combining data/methods/results in new ways. – Big picture: patterns instead of “just so” stories● Open science – Slideshare: my profile – Social networking
  3. 3. Overview● Synthetic science: NESCent – I dont collect data. – Combining data/methods/results in new ways. – Big picture: patterns instead of “just so” stories● Open science – Slideshare: my profile – Social networking● Todays goals ● What are most compelling questions? Interest in broad framework? ● Ask questions along way!
  4. 4. Overview1. Transposable elements as a model system2. Genomic contributions to life history evolution in Asparagales3. TEs and aging in Drosophila
  5. 5. What is in a genome? ● The first step in analyzing genomes is usually to mask or filter repetitive sequences, which often comprise a large portion of the nuclear genome ● Repetitive sequences include satellites, telomeres, and other “junk” DNA elements ● “Selfish” DNA is a category of repetitive sequences representing transposable elements ● Growing evidence (including ENCODE) supports that “junk” DNA contains essential function and provides material for evolutionary innovation Class I: Retrotransposons Class II: DNA transposons LTR TIR LINE Crypton SINE Helitron ERV Maverick SVA www.virtualsciencefair.orgTEs Asparagales Drosophila
  6. 6. TEs directly affect organisms as they move throughout a genome ● TEs interact with genes ● TE insertion within a gene disrupts function ● Exaptation of TEs into genes: Alu elements contributed to evolution of three color vision (Dulai, 1999) ● Gene expression and regulatory changes ● TEs affect molecular evolution ● Indels ● increased recombination (chromosomal restructuring) ● Links between TEs and adaptation/speciationTEsKate Hertweck, Genomic effects of repetitive DNA DNA NESCent, Genomic effects of junk Asparagales Drosophila
  7. 7. TEs indirectly affect organisms through changes in genome size Changes in overall genome size Physical-mechanical effects of nuclear size and mass Many historical hypotheses about relationships between genome size and life history (complexity, mean generation time, ecology, growth form)TEs Asparagales Drosophila
  8. 8. Research questions and goals ● What are patterns of genome expansion and contraction throughout the evolutionary history of organisms? ● Patterns in genome size change ● Proliferation of TEs within lineages Evolutionnews.orgTEs Asparagales Drosophila
  9. 9. Research questions and goals ● What are patterns of genome expansion and contraction throughout the evolutionary history of organisms? ● Patterns in genome size change ● Proliferation of TEs within lineages ● Do genomic patterns correlate with changes in life history? ● Improving methods for comparative genomics across broad taxonomic levels ● Application of phylogenetic comparative methods to genomic data Evolutionnews.orgTEs Asparagales Drosophila
  10. 10. Overview1. Transposable elements as a model system2. Genomic contributions to life history evolution in Asparagales3. TEs and aging in DrosophilaCollaborators: J. Chris Pires and lab (U of Missouri) Patrick Edger Dustin Mayfield
  11. 11. Genomic evolution in Asparagales ● Many edible species (onion, asparagus, agave) and ornamentals (orchid, amaryllis, yucca) ● Lots of variation in life history traits: physiology, growth habit, habitat ● Interesting patterns of genomic evolution ● Wide variation genome size ● Bimodal karyotypes ● Despite possessing some of the largest angiosperm genomes, we know little about the TEs in Asparagales ● Possibility to test hypotheses of correlations between genomic changes and life history traits ag.arizona.edu Naturehills.comTEs Asparagales Drosophila
  12. 12. TEs Asparagales Drosophila
  13. 13. TEs Asparagales Drosophila
  14. 14. TEs Asparagales Drosophila
  15. 15. TEs Asparagales Drosophila
  16. 16. Our data ● Illumina (80-120 bp single end), 6 taxa per lane ● GSS (Genome Survey Sequences): total genomic DNA! ● Data originally collected for systematics ● Assembled plastomes, mtDNA genes, and nrDNA genes from less than 10% of data (Steele et al 2012) ● Poaceae (family of grasses, model system) ● Medium-sized genomes ● Well-annotated library of repeats ● Asparagales (order of petaloid monocots, non-model system) ● Very large genomes ● Discovery of novel repeatsTEs Asparagales Drosophila
  17. 17. Our data ● Illumina (80-120 bp single end), 6 taxa per lane ● GSS (Genome Survey Sequences): total genomic DNA! ● Data originally collected for systematics ● Assembled plastomes, mtDNA genes, and nrDNA genes from less than 10% of data (Steele et al 2012) ● Poaceae (family of grasses, model system) ● Medium-sized genomes ● Well-annotated library of repeats ● Asparagales (order of petaloid monocots, non-model system) ● Very large genomes ● Discovery of novel repeats ● Is there a way to characterize repeats when the genome is a big black box?TEs Asparagales Drosophila
  18. 18. Bioinformatics approach ● Sequence assembly: ● Ab initio repeat construction: use raw sequence reads to build pseudomolecules or ancestral sequences ● De novo sequence assembly: standard genome assembly methods, screen resulting contigs (MSR-CA)TEs Asparagales Drosophila
  19. 19. Bioinformatics approach ● Sequence assembly: ● Ab initio repeat construction: use raw sequence reads to build pseudomolecules or ancestral sequences ● De novo sequence assembly: standard genome assembly methods, screen resulting contigs (MSR-CA) ● Annotation method: ● Motif searching ● Reference library: current RepBase, 3110 repeats, 98.7% are from grasses (RepeatMasker and CENSOR)TEs Asparagales Drosophila
  20. 20. Bioinformatics approach ● Sequence assembly: ● Ab initio repeat construction: use raw sequence reads to build pseudomolecules or ancestral sequences ● De novo sequence assembly: standard genome assembly methods, screen resulting contigs (MSR-CA) ● Annotation method: ● Motif searching ● Reference library: current RepBase, 3110 repeats, 98.7% are from grasses (RepeatMasker and CENSOR) Sidenote: improving the ontology for transposable elements (classification and annotation) Sequence Ontology (SO) Comparative Data Analysis Ontology (CDAO)TEs Asparagales Drosophila
  21. 21. Example: LTR from Hosta ● Reads map across scaffold: assembly is reliable ● Some divergence in reads: measure of diversity?TEs Asparagales Drosophila
  22. 22. REs in Core AsparagalesTEs Asparagales Drosophila
  23. 23. Very large genomes in Core AsparagalesTEs Asparagales Drosophila
  24. 24. Small genomes contain variationTEs Asparagales Drosophila
  25. 25. TEs Asparagales Drosophila
  26. 26. TEs Asparagales Drosophila
  27. 27. TEs Asparagales Drosophila
  28. 28. So what? ● Plant genomes tolerate more plasticity than animal genomes • Polyploidy, chromosomal restructuring more common in plants • Repetitive compliment comprises a higher proportion of plant genomes • Differences in gene silencing ● Look for dramatic patterns in plants to identify potentially subtle effects in other organismsTEs Asparagales Drosophila
  29. 29. So what? ● Plant genomes tolerate more plasticity than animal genomes • Polyploidy, chromosomal restructuring more common in plants • Repetitive compliment comprises a higher proportion of plant genomes • Differences in gene silencing ● Look for dramatic patterns in plants to identify potentially subtle effects in other organismsTEs Asparagales Drosophila
  30. 30. Overview1. Transposable elements as a model system2. Genomic contributions to life history evolution in Asparagales3. TEs and aging in DrosophilaCollaborators: Joseph Graves (UNCG, NC A&T) Michael Rose (UC Irvine)
  31. 31. Genomics of aging ● Aging as “detuning” of adaptation ● Age-related genes and expression patterns ● Does the movement of TEs throughout a genome correspond to how long an organism lives? ● Previously discussed life history traits only involve TE proliferation in gametic tissue ● Questions about aging involve changes in organisms throughout lifespan, especially if results can be transferred to human researchTEs Asparagales Drosophila
  32. 32. Experimental approach ● Replicate populations of fruit flies selected for both short and long life spans (Burke et al 2010) ● Next-gen sequencing of pooled populations ● SNP analysis indicates allele frequency changes at many loci, but little evidence for selective sweeps ● Extensive gene expression changeTEs Asparagales Drosophila
  33. 33. Experimental approach ● Replicate populations of fruit flies selected for both short and long life spans (Burke et al 2010) – Next-gen sequencing of pooled populations ● SNP analysis indicates allele frequency changes at many loci, but little evidence for selective sweeps ● Extensive gene expression change ● Comparisons of selected populations and control populations using next- gen sequencing ● Are the same TEs present, in the same frequencies? ● Are there unique TE insertions related to longer life spans? ● T-lex: perl script for identifying presence and absence of annotated transposable elements ● 5425 transposable elements from publicly available genome sequenceTEs Asparagales Drosophila
  34. 34. Preliminary results ● Ten populations: five selected for shorter lifespan with their respective controls ● ~30 elements with noticeable changes in TE frequency between populations ● All classes of TEs (DNA transposons, SINEs, LINEs) ● Sometimes frequencies move to fixation ● Other populations involve different selective treatments ● T-lex de novo: searching for unannotated insertionsTEs Asparagales Drosophila
  35. 35. Conclusions ● What are general patterns of TE evolution? ● Different TEs contribute to genome size obesity. ● We still need better methods to compare genomes. ● Are there common patterns between TEs and life history trait evolution? ● Yes, very specific insertions, at least in Drosophila. ● How can comparative methods be appropriated for genomic characeristics? ● Does TE proliferation contribute to diversification or shifts in rates of molecular evolution? ● We are getting closer to possessing enough data to answer these questions.TEs Asparagales Drosophila
  36. 36. Conclusions ● There are many interesting questions to be investigated using other folks genomic trash! ● A little sequencing data can tell you a lot about a genome. ● Many markers for systematic purposes ● You can characterize major groups of repeats even in the absence of a robust reference library for the species. ● Informatics tools and resources abound!TEs Asparagales Drosophila
  37. 37. Acknowledgements NESCent (National Evolutionary Synthesis Center) Allen Roderigo Karen Cranston (and bioinformatics group!) www.nescent.org k8hert.blogspot.com Find me: Twitter @k8hert Google+ k8hertweck@gmail.comKate Hertweck, TE ontology effects of junk DNA Evolutionary

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