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Hertweck uva2012

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

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

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  • 1. Genome-wide effects oftransposable element evolution Kate L Hertweck National Evolutionary Synthesis Center (NESCent) digthedirt.com
  • 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. 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. Overview1. Transposable elements as a model system2. Genomic contributions to life history evolution in Asparagales3. TEs and aging in Drosophila
  • 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. 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. 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. 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. 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. 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. 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. TEs Asparagales Drosophila
  • 13. TEs Asparagales Drosophila
  • 14. TEs Asparagales Drosophila
  • 15. TEs Asparagales Drosophila
  • 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. 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. 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. 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. 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. Example: LTR from Hosta ● Reads map across scaffold: assembly is reliable ● Some divergence in reads: measure of diversity?TEs Asparagales Drosophila
  • 22. REs in Core AsparagalesTEs Asparagales Drosophila
  • 23. Very large genomes in Core AsparagalesTEs Asparagales Drosophila
  • 24. Small genomes contain variationTEs Asparagales Drosophila
  • 25. TEs Asparagales Drosophila
  • 26. TEs Asparagales Drosophila
  • 27. TEs Asparagales Drosophila
  • 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. 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. 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. 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. 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. 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. 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. 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. 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. 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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