hertweck uva2012

Genome-wide effects of transposable element evolution

Kate L HertweckNational 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

● Today's goals

● What are most compelling questions? Interest in broad framework?

● Ask questions along way!

● 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

1. Transposable elements as a model system

2. Genomic contributions to life history evolution in Asparagales

3. TEs and aging in Drosophila

Overview

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

TEs Asparagales Drosophila

Class I: RetrotransposonsLTRLINESINEERVSVA

Class II: DNA transposonsTIRCryptonHelitronMaverick

www.virtualsciencefair.org

TEs directly affect organisms as they move throughout a genome

Kate Hertweck, Genomic effects of repetitive DNA

● 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

Kate Hertweck, NESCent, Genomic effects of junk DNATEs 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

Evolutionnews.org

● 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

TEs Asparagales Drosophila

Overview

Collaborators:J. Chris Pires and lab (U of Missouri)Patrick EdgerDustin Mayfield

1. Transposable elements as a model system

2. Genomic contributions to life history evolution in Asparagales

3. TEs and aging in Drosophila

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

Sidenote: improving the ontology for transposable elements (classification and annotation)Sequence Ontology (SO)Comparative Data Analysis Ontology (CDAO)

● 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

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

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

1. Transposable elements as a model system

2. Genomic contributions to life history evolution in Asparagales

3. TEs and aging in Drosophila

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

Kate Hertweck, Evolutionary effects of junk DNAKate Hertweck, TE ontology

NESCent (National Evolutionary Synthesis Center)Allen RoderigoKaren Cranston (and bioinformatics group!)

www.nescent.org

k8hert.blogspot.com

Find me:Twitter @k8hertGoogle+ k8hertweck@gmail.com