Hertweck uva2012
-
Upload
kate-hertweck -
Category
Documents
-
view
157 -
download
0
description
Transcript of Hertweck uva2012
![Page 1: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/1.jpg)
Genome-wide effects of transposable element evolution
Kate L HertweckNational Evolutionary Synthesis Center (NESCent)
digthedirt.com
![Page 2: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/2.jpg)
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
![Page 3: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/3.jpg)
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
![Page 4: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/4.jpg)
1. Transposable elements as a model system
2. Genomic contributions to life history evolution in Asparagales
3. TEs and aging in Drosophila
Overview
![Page 5: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/5.jpg)
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
![Page 6: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/6.jpg)
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
![Page 7: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/7.jpg)
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
![Page 8: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/8.jpg)
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
![Page 9: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/9.jpg)
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
![Page 10: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/10.jpg)
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
![Page 11: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/11.jpg)
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
![Page 12: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/12.jpg)
TEs Asparagales Drosophila
![Page 14: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/14.jpg)
TEs Asparagales Drosophila
![Page 15: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/15.jpg)
TEs Asparagales Drosophila
![Page 16: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/16.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
TEs Asparagales Drosophila
![Page 17: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/17.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
● Is there a way to characterize repeats when the genome
is a big black box?
TEs Asparagales Drosophila
![Page 18: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/18.jpg)
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
![Page 19: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/19.jpg)
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
![Page 20: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/20.jpg)
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
![Page 21: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/21.jpg)
Example: LTR from Hosta
● Reads map across scaffold: assembly is reliable● Some divergence in reads: measure of diversity?
TEs Asparagales Drosophila
![Page 22: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/22.jpg)
REs in Core Asparagales
TEs Asparagales Drosophila
![Page 23: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/23.jpg)
Very large genomes in Core Asparagales
TEs Asparagales Drosophila
![Page 24: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/24.jpg)
Small genomes contain variation
TEs Asparagales Drosophila
![Page 25: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/25.jpg)
TEs Asparagales Drosophila
![Page 26: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/26.jpg)
TEs Asparagales Drosophila
![Page 27: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/27.jpg)
TEs Asparagales Drosophila
![Page 28: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/28.jpg)
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
![Page 29: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/29.jpg)
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
![Page 30: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/30.jpg)
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
![Page 31: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/31.jpg)
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
![Page 32: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/32.jpg)
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
![Page 33: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/33.jpg)
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
![Page 34: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/34.jpg)
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
![Page 35: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/35.jpg)
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
![Page 36: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/36.jpg)
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
![Page 37: Hertweck uva2012](https://reader035.fdocuments.in/reader035/viewer/2022062418/554ea50eb4c905fb7c8b491b/html5/thumbnails/37.jpg)
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]