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

http://www.nescent.org/

http://www.slideshare.net/katehertweck

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


http://www.slideshare.net/katehertweck

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)


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


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


Overview

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




http://home.vicnet.net.au/~einstein/images/arabidopsis.jpg



http://ifw2irm2.irm1.r2.fws.gov/fishery/tx/SanMarcos/Rice.jpg



http://ifw2irm2.irm1.r2.fws.gov/fishery/tx/SanMarcos/Rice.jpg

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


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?


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)




● Annotation method:

● Motif searching

● Reference library: current RepBase, 3110 repeats, 98.7% are from grasses (RepeatMasker and CENSOR)


http://www.sequenceontology.org/

http://sourceforge.net/apps/mediawiki/cdao/index.php?title=Main_Page

Example: LTR from Hosta

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


REs in Core Asparagales


Very large genomes in Core Asparagales


Small genomes contain variation





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


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


Overview

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


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


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


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


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.


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!


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+ [email protected]


http://k8hert.blogspot.com/

http://twitter.com/k8hert

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