Computational analysis of transposable element evolution...

Casey M. Bergman

Faculty of Life SciencesUniversity of Manchester

[email protected]://bioinf.manchester.ac.uk/bergman

Computational analysis of transposable element evolution in Drosophila genomes.

Overview of Talk

• Demographic history of TEs in D. melanogaster

• TE population genomics using 454 sequencing

• Discovery and detection of TEs in genomes

• Abundance and distribution of TEs in Drosophila genomes

• Noncoding DNA (ncDNA) & transposable elements (TEs)

Higher organisms have ahigher proportion of ncDNA

Bacteria15 %

Yeast30 %

Higher organisms have ahigher proportion of ncDNA

Bacteria15 %

Yeast30 %

Human98 %

Fly75 %

The function of most noncoding DNA is unknown & unannotated

= Exon

Mef2

Mef2

Mef2

Mef2

Mef2

CG15863

CG12130

CG1418

CG12133

Adam

CG12134

CG12134

eve

TER94

TER94

Pka-R2

Pka-R2

Pka-R2

CG12128

BS 1360

(A)n

Mef2

Mef2

Mef2

Mef2

Mef2

CG15863

CG12130

CG1418

CG12133

Adam

CG12134

CG12134

eve

TER94

TER94

Pka-R2

Pka-R2

Pka-R2

CG12128

BS 1360

Enhancers

AR3/72

APRCQ4/6

mes

15RP2

Transposable elements

Goal: comprehensive functional annotation of noncoding sequences in Drososphila

(A)n

DNA transposons (cut+paste)

RNA retrotransposons (copy+paste)

3 major types of transposable element (TE)

Terminal Inverted Repeat (TIR)

LINE-like (non-LTR)

Long Terminal Repeat (LTR)(A)n

Why is the discovery and detection of TE sequences in genomes important?

• Genome alignment

• Genome evolution

• Population genomics

• Genome organization

• Genome assembly

Discovery of new TE families

• Homology to TE proteins (e.g. transposase) => HMMer, tBLASTx

gagPBS

3’TSD 5’LTR 3’LTR 3’TSD

PPTpol env

Dmin ! (b3 – b5) ! Dmax

Lmin ! (e5 – b5), (e3 – b3) ! Lmax

b5 e5 b3 e5

• structural motifs (e.g. LTRs)=> LTRstruc, LTRharvest

• comparative genomics=> compTE

• dispersed repeats (all-by-all, k-mers)=> RECON, PILER, RepeatScout, ReAS

Reviewed in: Bergman & Quesneville (2007) Brief Bioinf. 8:382-92

hmmall-by-allRECON

BLASTER

RepeatMasker

TBLASTX

RMBLR

Release 3

Release 4

Quesneville, Bergman et al. (2005) PLoS Comp. Biol. 1:e22

Detection of individual TE copies

Genomic TE distribution in D. melanogaster

~3% ~20%

genome-wideaverage ~5.5%

10

20

30

40

50

5 10 15 20

X# TEs per 50kb

~ centromere~ high-low rec.

Bergman, Quesneville et al. (2006) Genome Biology 7:R112

Drosophila 12 genomes project

Clark, Eisen, Smith, Bergman, et al (2007) Nature 450:203-18

0

0.05

0.1

0.15

0.2

0.25

0.3

0.35

D.mel D.sim D.sec D.yak D.ere D.ana D.pse D.per D.wil D.vir D.moj D.gri

Proport

ion T

E/R

epea

t in

Sca

ffold

s >

200 K

bBLASTER-tx+Repbase-NoDros

BLASTER-tx+BDGP

BLASTER-tx+PILER

RepeatMasker+ReAS

RepeatRunner+PILER

CompTE

TE abundance in 12 Drosophila genomes


5.3%

2.7% 3.7%

12.0

%

24.9

%

6.9%

15.6

%

2.8%2.7%

8.5%

13.9

%

8.9%

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

D.mel D.sim D.sec D.yak D.ere D.ana D.pse D.per D.wil D.vir D.moj D.gri

Proport

ion T

E C

lass

in S

caff

old

s >

200 K

b

LTR

LINE

TIR

OTHER

Abundance of major TE types is conserved across genus Drosophila

non-LTR

LTR

TIR


Is the genomic distribution of TEs in D. melanogaster affected by historical activity?

A brief introduction to transposable element (TE) evolution: the current paradigm

• TEs are mobile DNA sequences, intra-genomic parasites

• Transposition rates >> excision rates

• Equilibrium maintained by transposition-selection balance

• Mode of natural selection is debated

- deleterious effects of transposition

- deleterious effects of TE insertion

- deleterious effects of TE-mediated ectopic recombination

✴ TE insertions observed at low frequency in nature

Estimating the age of ‘pseudogene-like’ retrotransposons

Petrov & Hartl (1998) Mol. Biol. Evol. 15:293-302

Alignment of paralogous TEs

Petrov & Hartl (1998) Mol. Biol. Evol. 15:293-302

Estimating the age of ‘pseudogene-like’ retrotransposons

# families

# elements

Total bp Surveyed 1st 2nd 3rd Total Point

Sub. P (Ho) Ψ

All non-LTR 19 377 836,819 1,515 1,424 1,917 4,884 3.56E-24 N

Ψ non-LTR 10 158 336,748 791 746 781 2,341 0.192 Y

All LTR 27 385 1,973,013 677 603 1,120 2,420 2.18E-44 N

Ψ LTR 17 279 1,491,867 272 267 307 851 0.159 Y

Grand Total 46 762 2,809,832 2,192 2,027 3,037 7,304 5.18E-61 N

Total Ψ 27 437 1,828,615 1,063 1,013 1,088 3,192 0.06 Y

59% of retrotransposon families exhibit a pseudogene-like mode of evolution on terminal branches

Most retrotransposon families exhibit a ‘pseudogene-like’ mode of sequence evolution

D. mel - D. sim speciation

Bergman & Bensasson (2007) PNAS 104:11340-5

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iverg

ence (

sub/s

ite)

0

1.80

3.60

5.41

7.21

9.01

10.81

Age (

Mya)

Retrotransposon demographics in D. melanogaster

Intra-element LTR-LTR comparisons support age estimates based on terminal branch length

5’ LTR ACGTAGCTAGGCTGACGTGGACTGTAC ||||||||||| ||||||| |||||||3’ LTR ACGTAGCTAGGGTGACGTGCACTGTAC

T = D/(2*r)

T - absolute timeD - 5’ vs. 3’ LTR divergence

r - neutral substitution rate (0.0111/my)

see also Bowen and McDonald (2001) Genome Res 11:1527-1540

a_

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(su

b/s

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0

1.80

3.60

5.41

7.21

9.01

10.81

Ag

e (

Mya

)

Intra-element LTR-LTR age estimates correlate with terminal branch age estimates

sqrt(branch length)

sqrt

(LTR

-LTR

div

erge

nce)

Spearman’s Rank Correlation Test:

p= 0.006531

Recent demographic history of D. melanogaster

Li & Stephan (2006) PLoS Genet. 2:e166

15,800 ya60,000 ya

Current paradigm is based on LTR families

Maside et al. (2000) Genet. Res 75:275-284

******?

****

Current paradigm assumes transposition-selection equilibrium

Carr et al. (2002) Chromosoma 110:511-518

Current paradigm interprets low TE frequency as evidence for purifying selection

Aquadro et al. (1986) Genetics 114:1165-1190

Summary of retrotransposon demographicsinferred from intra-genomic comparisons

• LTR elements systematically younger than non-LTR elements

=> Low frequency of LTR insertions may not be due to selection

• non-LTR families inserted in waves since speciation

• most LTR families inserted since colonization of non-African habitats

=> LTR insertions not at transposition-selection equilibrium

• LTR elements evolve under pseudogene-like mode like non-LTR elements

From evolutionary statics to dynamics: population genomics of TEs using 454 sequencing

Population genomics of TEs using 454 sequencing

Hybrid TE-unique reads“Unique Flank Tags”

Strain X

454 Reads

TEs


Hybrid TE-unique reads“Unique Flank Tags”

Strain X

454 Reads

TEs

KNOWN ✓ReferenceNEW !


TEs in reference sequence


TEs in reference sequence

Known INE-1 insertion present in NC and AF strains

Novel jockey insertion present in >1 strain

Preliminary findings using 454 sequencing

• 10 strains of D. melanogaster: 6 USA, 4 Malawi

• ~1/3 of INE-1 found in nature, so estimate ~3900 annotated TEs present in >=1 wild strain

• ~24% of annotated TEs found in >=1 wild strain (1300/5400)

• ~72% found in nature in low recomb. regions (950/1300)

• DNA transposons (~30%) found in nature more often than LTR/non-LTR retrotransposons (~10%)

• consistent with all TEs fixed in low recomb. regions plus few hundred segregating in high recomb. regions

Summary

• Mature methods exist for analysis of TEs in genomeshttp://www.bioinf.manchester.ac.uk/bergman/te-tools.html

• Structural classes of TEs have different genome dynamics

• Recent LTR insertion has implications for transposition-selection balance paradigm

• Population genomics using next generation sequencing will help resolve forces controlling TE evolution

Hadi QuesnevilleRuqiang Li

Douda Bensasson

Post-doctoral & PhD positions open

Andy Clark

University of Sheffield•15-17 July 2009

RES Symposium on insect infection and immunity: Evolution, Ecology and MechanismsRES Annual National Meeting

ento’09

Specialist topics to include: • Immunity • Comparative genomics • Reproduction • Range expansion/climate change • Insect Evo-devo • General Entomology • Insect chemoreceptionSpeakers include: Professor Fotis Kafatos, Imperial College, London, UK; Professor Paul Schmid-Hempel, ETH Zurich, Switzerland;Professor Shelley Adamo, Dalhousie University, Canada; Professor Bruno Lemaitre, EPF Lausanne, Switzerland

SYMPOSIUM CONVENORS:Professor Stuart Reynolds, University of Bath, [email protected]. Jens Rolff, University of Sheffield, [email protected]

NATIONAL MEETING CONVENORS:Professor Roger Butlin, University of Sheffield, [email protected] Mike Siva-Jothy, University of Sheffield, [email protected]. Klaus Reinhardt, University of Sheffield, [email protected]

Further information, registration, abstract and accommodation booking forms available on www.royensoc.co.uk

Tel: +44 (0)1727 899387 Fax: +44 (0)1727 894797E-mail: [email protected]

PHOTO CREDITS: PAUL DEAN, STAINED CELL SHOTS; RICHARD NAYLOR, BED BUG.

Computational analysis of transposable element evolution...

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