evolution of transposons, genomes, and organisms (hertweck fall 2014)

Evolution of transposons,genomes, and organisms

Kate L HertweckThe University of Texas at Tyler

Department of Biologyhttps://www.uttyler.edu/biology/

Research https://sites.google.com/site/k8hertweck Blog k8hert.blogspot.comTwitter @k8hert

https://sites.google.com/site/k8hertweck

http://k8hert.blogspot.com/

http://twitter.com/k8hert

http://creativecommons.org/licenses/by/4.0/

Today's goals

1. Overview: comparatve genomics

2. Drosophila, aging, and TE populaton genomics

3. TE proliferaton in Asparagales

4. Future research and conclusions

What's in a genome?

Sandwalk.blogspot.com

Regions between genes: Selfish, mystery, or junk DNA;dark matter

Wikimedia Commons

{{Gene

Intergenic region

Traditionally, genetics focused ongenes (functional sequence regions)

Overview Drosophila Asparagales Conclusions

Sequencing the “junk”

Intergenic (“non-coding”) regions are full ofrepetitive sequences: difficult to obtain sequence!

Telomeres, centromeres, ribosomal DNA, satelliteDNA, pseudogenes, transposable elements

Hertweck, unpublished data

ENCODE: “Google Maps for the human genome”

80% of the human genome is functional!

We're getting better at identifying portions of thegenome, reducing “dark matter”

Encodeproject.org


Transposable elements as a model system

● TEs, mobile genetic elements, or jumping genes

● Parasitic, self-replicating

● Similar to or derived from viruses

● Move independently in a genome

Class I: Retrotransposons(copy and paste)

LTRLINESINEERVSVA

Class II: DNA transposons(cut and paste)TIR (P elements)

MITECryptonHelitron

Maverick

Populations of TE sequences in a genome evolveAND

Surrounding genomic sequences evolve


TEs allow for evolutionary innovation

TEs are a special type of mutation

Interactions with genesDisrupting gene function

Regulatory changesExaptation

Genome-wide modificationsRates of insertion/deletionChromosomal restructuringChanges in genome size

Effects on the organismDisease

PhenotypeAdaptation


TEs allow for evolutionary innovation

Exaptaton of TEs into genes: Alu elements contributed to evoluton ofthree color vision (Dulai, 1999)

Genome size variaton: TEs account for ~70% of variaton in genome sizebetween Zea mays and Z. luxurians(Tenaillon et al., 2011)

TEs and disease: TE insertons in somatc cells are responsible for multplecancer pathways, (Lee et al., 2012); retrotranspositon in neurons contributes toschizophrenia (Bundo et al., 2014)


How do transposableelements affect genomic and

organismal evolution?

DataNext-generation sequencing

Genome annotationsLife history traits

MethodsBioinformaticsPhylogenetics

Comparative analysis

Research synthesisData integration

Methods developmentNovel applications


Collaborators:Mira Han (UNLV)Mark A. Phillips (UC Irvine)Lee F. Greer (UC Irvine)Michael R. Rose (UC Irvine)Joseph L. Graves (NC A&T, UNCG)





How and why to study aging?

Biological aging (senescence): accumulation of changes thatdisrupt metabolism

Complex phenotype not easily explained by genetics

Medical concerns drive our personal interest in aging

We study these questions using demographic and disease-relateddata

existanew.com


Aging as a phenotype

Aging as a biological phenomenon:what are evolutionaryimplications?

Model systems with much shorterlife span, ability to experimentallymanipulate

In Drosophila, we study the processof aging by examining time todevelopment, which is closelycorrelated with lifespan

Martinez, 1998


How do TEs affect aging?

Empirical data: it depends on model system, type of TE, and method ofmeasuring TE proliferation

● TIR DNA transposons: decrease or have no effect on lifespan(Drosophila: Nikitin and Woodruff 1995; C. elegans: Egilmez and Reis 1994)

● LTR retrotransposons decrease lifespan (Drosophila: Driver and McKechnie 1992)

● Alu SINEs reverse senescence (human cell lines: Wang et al. 2011)


Theory: accumulation of mutations (Kirkwood 1986, Murrey 1990)

More TEs lifespan

What is the relationship between TE insertions and aging?

ACO

CO

Rose laboratory Drosophila stocks

Long term experimental evolution systemEstablished 1980

A 9-day life cycleB 14-day life cycle (baseline)C 28-day life cycle

BO

NCO AO

B

O

Originalpopulation

A, B, C derived twice eachReversal of selectionTesting for convergence

All populations replicated five times


Phenotypes associated with selection

Physiological:

● Heart function● Flight duration● Stress resistance (starvation, dessication)

Developmental:

● Hatching rate● Time to pupation● Emergence from pupa

Phenotypes respond predictably to selective treatment


newswatch.nationalgeographic.com

http://newswatch.nationalgeographic.com/2014/04/10/insects-fruit-flies-science-flight-animals/

Experimental data

● How do frequencies of TE insertions respond to selectivepressures?

● Magnitude of variation?

● Which TEs?

● Where in the genome?


● Whole-genome resequencing (Illumina Hi-Seq)

120 females x six treatments x five replicates

● How do genomic features respond to selective treatment?

Pilot study (Burke et al., 2010)

● Our analysis:

● SNPs: Popoolation2 (Kofler et al., 2011)

● Structural variants: Delly (Rausch et al., 2012)

Analysis of known TE insertions

● T-lex (Fiston-Lavier et al. 2010): pipelinewith four modules

● 2947 known TE insertions annotated inDrosophila (Release 5)

● Resulting data: genome-widefrequencies (presence/absence) ofTE insertions from each population

● Comparing all populations:

no data, fixed, absent, variable


total0

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FBTIRLINELTRINE-1

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sert

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● 177 TE insertions vary in frequency

● Does variation matter?

total variable0

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● Fisher's Exact test● Cochran-Mantel-Haenszel (CMH) test

● 95 TE insertions vary significantly

● Does frequency of insertionsignificantly vary with selectivetreatment?

total variable significant0

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Which populations do we compare?


ACO

CO

BO

NCO AO

B

O

Originalpopulation

● Phenotype: time to development● Is there genomic convergence?

● Compare different treatments: short vs long

expect more more significantdifferentiation

Which populations do we compare?


ACO

CO

BO

NCO AO

B

O

Originalpopulation

● Phenotype: time to development● Is there genomic convergence?

● Compare same treatments:short vs shortlong vs longbaseline vs baseline

expect little significant differentiation

0

10

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# of

sig

nific

ant T

E in

sert

ion

sIs there convergence?

Comparedifferent treatments

Comparesame treatments

AC

O C

O

AO

NC

O

AC

O A

O

CO

NC

O

B B

O


● Much less differentiationwithin treatment than amongtreatment types

● Significant TEs aredistributed across thegenome

TEs which are known to existin the Drosophila genomeshow genomic convergence,similar to consistency ofmeasured phenotypes.

What about de novo TE insertions?


Hertweck, unpublished data

● TEs interact with a genome by movingindependently

● RelocaTE 1.0.4 (Robb et al. 2013): uses referencegenome and known TE sequences/motifs toidentify all TEs in genome

● Resulting data: total number and location ofTEs (LTR and IR) in genome● Compare number of TEs

What about de novo TE insertions?De novo TEs also show convergence

CO NCOACO AO BO B

**

Comparisons betweensome treatment typesshow significantdifferentiation

Short-lived populationshave more LTR-retrotransposons thanlong lived populations!


Continuing population genomics in Drosophila

● Continuing analysis of TEs:

Searching for unannotated (novel) insertions

Applying null models (Blumensteil et al., 2014)

● Integration of data types

Rearrangements and inversions?

Phenotypes with genotypes

Statistical testing to combine genotypic data


Conclusions: Drosophila

How do frequencies of TE insertions in experimentalpopulations respond to selective pressures?

TEs (both known and de novo) exhibit convergent patterns similarto phenotypes and other genomic data

All TE types change frequency in response to selection

Significant changes are seen across the genome

existanew.com


What does this mean across anevolutionary timescale?

Today's goals





Wikimedia Commons

Asparagales as a model system

ag.arizona.edu Naturehills.com

● ca. 26000 species, many edible and ornamental● Variation in life history traits: growth habit, habitat● Patterns of genomic evolution: size and chromosomes● Few genomic resources

Can we characterize TEs in huge genomes with very litle a priori informaton?


Next-gen sequencing in Asparagales

Steele, Hertweck, Mayfield, McKain,Leebens-Mack, and Pires, 2012 AJB

● Anonymous, low coverage,genome wide sequence data(genomic survey sequences,or GSS)

● Mined for phylogenetc markers● Used less than 90% of the data

collected!

Xeronemataceae

Asphodeloideae

Hemerocallidoideae

Xanthorrhoeoideae

Agapanthoideae

Allioideae

Amaryllidoideae

Lomandroideae

Asparagoideae

Nolinoideae

Aphyllanthoideae

Agavoideae

Scilloideae

Brodiaeoideae

Xan

thor

rhoe

aece

ae

Aga

pant

hace

aeA

spar

agac

eae


How can we use the leftover data?

Characterize repeats in eachgenomeInfer paterns of genome sizeevoluton with TE diversity andabundanceInterpret in a phylogenetccontext

Xeronemataceae

Asphodeloideae

Hemerocallidoideae

Xanthorrhoeoideae

Agapanthoideae

Allioideae

Amaryllidoideae

Lomandroideae

Asparagoideae

Nolinoideae

Aphyllanthoideae

Agavoideae

Scilloideae

Brodiaeoideae

Xan

thor

rhoe

aece

ae

Aga

pant

hace

aeA

spar

agac

eae

Hertweck, 2013, Genome


TE identification in non-model systems

Raw sequence data(fastq)

De novo genome assembly(MaSuRCA)

Filter out plastid and mtDNA sequences(BLAST to organellar genomes)

Estimate abundance of each TE type(Map raw reads back to scaffolds)

Identify results similar to known repeats(RepeatMasker, 3110 repeats in library, 98.7% are from grasses )

Categorize TEs by type(unknown and simple repeats removed, grouped by superfamily)

Scripts available on GitHub:AsparagalesTEscripts



https://github.com/k8hertweck/AsparagalesTEscripts.git

Genome size varies in sampled Asparagales

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0

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Gen

ome

size

(M

b/1C

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humans

Arabidopsis



Genome size varies in sampled Asparagales

Aph

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5000

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15000

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25000

Gen

ome

size

(M

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small

medium

large

Genome size



What proportion of the nuclear genome is from TEs?

Repeat content does not vary with genome size

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Unknown contigs

Known repeats

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ome

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(M

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Does genome size vary with phylogeny?


small

medium

large

Genome size

Phylogeny


LTR retrotransposon proportions vary independent of phylogeny

small

medium

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Genome size

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0.70%

0.80%

DNA TE superfamilies show some phylogenetic signal

small

medium

large

Genome size

EnSpm

MuDRPIF

hAT

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How can we improve these analyses?

● Need to improve TE characterization methods

LTR family analysis

Asparagales-specific repeat library

P-clouds and graph-based clustering methods (RepeatExplorer)

Protein domain searches (RT, INT, ENV, GAG)

RNA-Seq data● Increasing taxonomic sampling

Broader sampling across Asparagales

Targeted sampling in Agavoideae


Continuing work:TEs, genomes, and life history in Agavoideae

● Asparagaceae subfamily Agavoideae: 22 genera, 637 species● Rhizomatous, warm temperate herbs● Economically important: tequila, food starches, biofuels● Recent diversification correlated with ecological traits (Good-Avila, 2006)

● Emerging genomic/transcriptomic resources● Polyploidy, bimodality, changes in genome size

Collaborators:Michael McKain (Danforth Plant Science Center)Jim Leebens-Mack (U of Georgia)Alexandros Bousios (University of Sussex, UK)

gizmodo.comDarlington 1963, 1973


Conclusions: Asparagales

Can we characterize TEs in huge genomes with very little a prioriinformation?

Cross-validate TE abundance and diversity estimates with differentalgorithms

Union of TE, genomic, and organismal data requires fairly largetaxonomic sampling

Is transposon presence, abundance, and organization in Agaviodeaegenomes consistent with involvement in genomic evolution?

Do transposon proliferation and other genomic traits correlate with lifehistory traits in Agavoideae?

http://commons.wikimedia.org


Today's goals




4. Conclusions and synthesis

Transposable elements Genome Organism

A model of evolution

Transposable elements Genome Organism

Selection

Structural changes Ecological interactions(biotic and abiotic)

Genomic silencing machinery


TEs, genomes, and organisms

Working with messy data to answer broad questons

Quantitative analysis of relationships between genomic phenomenaand organismal evolution

Visualizing widespread genomic phenomena

MethodsMetagenomics

Gene predictionSimulations

Research synthesisData integration

Methods developmentNovel applications

DataDNA, RNA, environmental samples

Morphology, behaviorArtificial selection

YOUR QUESTION HERE


Acknowledgements

Collaborators

J. Chris Pires and lab (University of Missouri)

NESCent and Duke University

Community of scientists

Bioinformatics team

Mentors: A. Rodrigo, J. Graves

Research https://sites.google.com/site/k8hertweck

Blog:k8hert.blogspot.com

Twitter @k8hertGoogle+ [email protected]

https://sites.google.com/site/k8hertweck

http://k8hert.blogspot.com/

http://twitter.com/k8hert

https://plus.google.com/u/0/106530524024062442159/posts

evolution of transposons, genomes, and organisms (hertweck fall 2014)

Science

te proliferaton

genome sizeeffects

te insertons

te populaton genomics3

genome size variaton

tes account

genome sizebetween zea

alu elements