drosophila transposable elements.bergmanlab.genetics.uga.edu/wp-content/uploads/2010/02/... ·...
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Casey M. Bergman
Faculty of Life SciencesUniversity of Manchester
[email protected]://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