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Genome-wide effects of
transposable element evolution
                  Kate L Hertweck
 National Evolutionary Synthesis Center (NESCent)




                              digthedirt.com
Overview
●
    Synthetic science: NESCent
    – I don't collect data.
    – Combining data/methods/results in new ways.
    – Big picture: patterns instead of “just so” stories
●
    Open science
    – Slideshare: my profile
    – Social networking
Overview
●
    Synthetic science: NESCent
    – I don't collect data.
    – Combining data/methods/results in new ways.
    – Big picture: patterns instead of “just so” stories
●
    Open science
    – Slideshare: my profile
    – Social networking
●
    Today's goals
    ●
        What are most compelling questions? Interest in broad
        framework?
    ●
        Ask questions along way!
Overview

1. Transposable elements as a model system
2. Genomic contributions to life history evolution in
   Asparagales
3. TEs and aging in Drosophila
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.org

TEs                                 Asparagales                             Drosophila
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/speciation




TEs
Kate Hertweck, Genomic effects of repetitive DNA DNA
               NESCent, Genomic effects of junk
                                       Asparagales              Drosophila
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
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.org

TEs                                   Asparagales               Drosophila
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.org

TEs                                       Asparagales               Drosophila
Overview

1. Transposable elements as a model system
2. Genomic contributions to life history evolution in
   Asparagales
3. TEs and aging in Drosophila

Collaborators:
     J. Chris Pires and lab (U of Missouri)
     Patrick Edger
     Dustin Mayfield
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.com

TEs                                 Asparagales                           Drosophila
TEs   Asparagales   Drosophila
TEs   Asparagales   Drosophila
TEs   Asparagales   Drosophila
TEs   Asparagales   Drosophila
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




TEs                                      Asparagales                  Drosophila
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
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
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
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
Example: LTR from Hosta




      ●
          Reads map across scaffold: assembly is reliable
      ●
          Some divergence in reads: measure of diversity?



TEs                                 Asparagales             Drosophila
REs in Core Asparagales




TEs          Asparagales        Drosophila
Very large genomes in Core Asparagales




TEs                 Asparagales        Drosophila
Small genomes contain variation




TEs              Asparagales        Drosophila
TEs   Asparagales   Drosophila
TEs   Asparagales   Drosophila
TEs   Asparagales   Drosophila
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 organisms




TEs                                    Asparagales                        Drosophila
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 organisms




TEs                                    Asparagales                        Drosophila
Overview

1. Transposable elements as a model system
2. Genomic contributions to life history evolution in
   Asparagales
3. TEs and aging in Drosophila


Collaborators:
     Joseph Graves (UNCG, NC A&T)
     Michael Rose (UC Irvine)
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 research




TEs                                 Asparagales                        Drosophila
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




TEs                                 Asparagales                         Drosophila
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
              sequence

TEs                                 Asparagales                         Drosophila
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 insertions




TEs                                Asparagales                        Drosophila
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
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
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.com




Kate Hertweck, TE ontology effects of junk DNA
               Evolutionary

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Hertweck uva2012

  • 1. Genome-wide effects of transposable element evolution Kate L Hertweck National Evolutionary Synthesis Center (NESCent) digthedirt.com
  • 2. Overview ● Synthetic science: NESCent – I don't 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 don't collect data. – Combining data/methods/results in new ways. – Big picture: patterns instead of “just so” stories ● Open science – Slideshare: my profile – Social networking ● Today's goals ● What are most compelling questions? Interest in broad framework? ● Ask questions along way!
  • 4. Overview 1. Transposable elements as a model system 2. Genomic contributions to life history evolution in Asparagales 3. 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.org TEs 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/speciation TEs Kate 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.org TEs 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.org TEs Asparagales Drosophila
  • 10. Overview 1. Transposable elements as a model system 2. Genomic contributions to life history evolution in Asparagales 3. TEs and aging in Drosophila Collaborators: 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.com TEs 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 repeats TEs 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 Asparagales TEs Asparagales Drosophila
  • 23. Very large genomes in Core Asparagales TEs Asparagales Drosophila
  • 24. Small genomes contain variation TEs 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 organisms TEs 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 organisms TEs Asparagales Drosophila
  • 30. Overview 1. Transposable elements as a model system 2. Genomic contributions to life history evolution in Asparagales 3. TEs and aging in Drosophila Collaborators: 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 research TEs 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 change TEs 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 sequence TEs 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 insertions TEs 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.com Kate Hertweck, TE ontology effects of junk DNA Evolutionary