Casey M. Bergman

Faculty of Life SciencesUniversity of Manchester

casey.bergman@manchester.ac.ukhttp://bioinf.manchester.ac.uk/bergman

Population and comparative genomics of Drosophila transposable elements.

http://scienceblogs.com/pharyngula/2007/11/30/white_drosophila.jpg

Transposable elements cause most spontaneous visible mutations in Drosophila

(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

Lessons from “the” D. melanogaster genome

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

02468

10

genome normal rec. low rec.

0

20

40

60

80

genome normal rec. low rec.

# TE

s / M

b%

TE

Abundance of major TE types in D. melanogaster

non-LTR

LTR

TIR

Estimating the age of ‘pseudogene-like’ retrotransposons

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

Alignment of paralogous TEs

D. mel - D. sim speciation

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

a_

inva

de

r2_

6

b_

mic

rop

ia_

4

c_

Ta

bo

r_3

d_

17

.6_

11

e_

Sta

lke

r_4

f_ro

ve

r_3

g_

fle

a_

16

h_

co

pia

_2

8

i_m

dg

3_

10

j_ro

o_

86

k_

Tra

nsp

ac_

4

l_o

pu

s_

16

m_

blo

od

_2

2

n_

41

2_

24

o_

Bu

rdo

ck_

13

p_

div

er_

9

q_

Tira

nt_

20

r_jo

cke

y2

_7

s_

He

len

a_

7

t_C

r1a

_3

6

u_

ba

gg

ins_

6

v_

G4

_1

0

w_

Do

c3

_7

x_

G5

_8

y_

BS

_1

5

z_

Ju

an

_9

zz_

Do

c_

53

0.00

0.02

0.04

0.06

0.08

0.10

0.12

Div

erg

en

ce

(su

b/s

ite

)

0

1.80

3.60

5.41

7.21

9.01

10.81

Ag

e (

Mya

)

Retrotransposon demographics in D. melanogaster

Lessons from 12 Drosophila genomes

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

b

BLASTER-tx+Repbase-NoDros

BLASTER-tx+BDGP

BLASTER-tx+PILER

RepeatMasker+ReAS

RepeatRunner+PILER

CompTE

TE abundance in 12 Drosophila genomes

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

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

caffold

s >

200 K

b

LTR

LINE

TIR

OTHER

Abundance of major TE types is conserved across genus Drosophila

non-LTR

LTR

TIR

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

Lessons from 10 D. melanogaster genomes

Population genomics of TEs using 454 sequencing

Hybrid TE-unique reads“Unique Flank Tags”

Strain X

454 Reads

TEs

Population genomics of TEs using 454 sequencing

Hybrid TE-unique reads“Unique Flank Tags”

Strain X

454 Reads

TEs

KNOWN ✓ReferenceNEW !

Population genomics of TEs using 454 sequencing

TEs in reference sequence

Population genomics of TEs using 454 sequencing

TEs in reference sequence

Known INE-1 insertion present in NC and AF strains

Novel jockey insertion present in >1 strain

chr3L: 5000000 10000000 15000000 20000000Release 5 TEs

NC301 overlap UFT

NC303 overlap UFT

NC306 overlap UFT

NC358 overlap UFT

NC375 overlap UFT

NC732 overlap UFT

AF28-5 overlap UFT

AF56-4 overlap UFT

AF63-5 overlap UFT

Population genomics of TEs in 9 strains of D. melanogaster based on ~1X 454 shotgun data

Sackton, Kulathinal, Bergman, et al (2009) submitted

• 9 strains of D. melanogaster: 6 USA, 3 Malawi

• ~22% of annotated TEs found in >=1 wild strain

• ~72% found in nature in low recomb. regions

• DNA transposon insertions (~30%) found more often than non-LTR (~15%) or LTR (10%) retrotransposons

Population genomics of TEs in 9 strains of D. melanogaster based on ~1X 454 shotgun data

• ~12% TE sequence in each genome

• ~97% of known TE families are found in all strains

Sackton, Kulathinal, Bergman, et al (2009) submitted

• LTR > non-LTR > DNA in all strains

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

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

• Drosophila is an excellent system for studying the impact of TE insertion on genome structure and evolution

Hadi QuesnevilleRuqiang Li

Douda Bensasson

Andy Clark