The Life Cycle
P
Neuroptera
Coleoptera
Hymenoptera
Lepidoptera
Mecoptera
Siphonoptera
Strepsiptera
Diptera
~250 Mya
Nematocera
Brachycera
Muscomorpha
Cyclorrhapha
Schizophora
Calyptrata
Acalyptrata
Camillidae
Steganinae
Cladocheata etc
Zaprionus etc
s.g. Drosophila
Chymomyza etc
s.g. Sophopora
Drosophila melanogaster subgroup
Drosophila melanogaster - cosmopolitan - 1830
Drosophila simulans - cosmopolitan - 1919
Drosophila mauritiana - Mauritius - 1974
Drosophila sechellia - Seychelles -1981
Drosophila yakuba - Equatorial Africa - 1954
Drosophila santomea - Sao Tome - 2000
Drosophila teissieri - Equatorial Africa - 1979
Drosophila erecta - Central West Africa - 1974
Drosophila orena - Cameroons - 1978
mel f x sim m
sim f x mel m
Viable, sterile f
Viable, sterile m
Larval lethal m
Embryo lethal f
aabb
AAbb
x
aaBB
AaBb
Hmr allele of melanogaster (transcription factor)
Lhr allele of simulans (chromatin binding protein)
“Eventually, the story of the chromosomal mechanisms and its
evolution will have to be entirely rewritten in molecular terms.”
Michael White, 1973, Animal Cytology & Evolution, 2nd edition.
Q
a r e
u ic k T im
e ™
a n d
d e c o m
p r e s s o r
n e e d e d
t o
s e e
a
t
h is
p ic t
u r e .
Paracentric inversions are the most common rearrangement
 Segregating in 106 out 183 species.
- 57% - (Powell 1997).
 22000-56000 inversions have
become fixed during the evolution
of the genus (Clayton & Guest 1986).
a b c d e f g h i j k l m n o p q r s t
a b j i h g f e d c k l m n o p q r s t
a b j l o n m l k c d e f h i p q r s t
a b c d e f g h i j k l m n o p q r s t
a b c d e f g h i o n m l k j p q r s t
a b k l m n o i h g f e d c j p q r s t
12 genomes have been sequenced in the genus Drosophila
Ectopic recombination between homologous fragments of DNA
1.
2.
3.
( Cáceres et al. Science 1999 )
~280 Kb
~450 Kb
BACs
BACR16N15
BACR42I20
BACR08K01
BACR07M14
BACR45A07
3R of D. melanogaster
centromere
84F1
telomere
93F6-7
centromere
telomere
3R of D. simulans
Inversion-mediated duplications can result from
staggered isochromatid breaks & repair.
A
C
B
D
E
F
G
H
I
J
K
5'
3'
3'
5'
5'
3'
3'
5'
3'
5'
5'
3'
5'
3'
A
5'
3'
B
C
D
I
H
5'
3'
5'
3'
5'
G
F
E
D
C
B
I
3'
3'
J
5'
5'5'
K
3'
3'
5'
5'
5'
3'
3'
5'
5'
Lemeunier & Ashburner, 1976
BLAST-N of D. mel 3R transcripts against D. yak 3R
J. Ranz, C. Bergman & M. Ashburner
Flanking duplications are a common by-product
of the genome reorganization between
D. melanogaster and D. yakuba.
20
9
20
18
16
14
12
10
8
6
4
2
0
with
without
Most inversions occurred in the D. yakuba lineage
1 ( 3.4 % )
D. melanogaster
28 ( 96.6 % )
D. yakuba
outgroup species
1:
A-B
A]-----[B
A-B
2:
A]-----[B
A-B
A-B
Large-scale comparison of the gene order between
D. melanogaster and D. yakuba.
55 breakpoints =
12
+
22
+
9
+
12
0.025
0.02
Breakpoints
Mb Myr
0.015
0.01
0.005
0
X
2L+2R
3L
3R
29 inversions
Comparison of total number of breakpoints that correspond to small and gross inversions
between D. melanogaster and other flies' genomes
2000
1800
1600
1400
1200
1000
800
600
400
200
D.
Gr
i.
D.
Vi
r.
D.
M
oj.
D.
W
il.
D.
Ps
e.
.
D.
Pe
r
D.
An
a.
.
D.
Ya
k
.
D.
Er
e
.
D.
Se
c
D.
Si
m
.
0
Cluster gram based on the number of breakpoints
that correspond to inversions
Comparison of total number of breakpoints that correspond to small and gross
inversions divided by the square of evolutionary distance
0.50
0.40
0.30
0.20
0.10
D.
G
ri.
D.
Vi
r.
D.
M
oj
.
D.
W
il.
D.
Ps
e.
D.
Pe
r.
D.
An
a.
D.
Ya
k.
D.
Er
e.
D.
Se
c.
.
0.00
D.
Si
m
Number of breakpoints / square of
evolutionary distance
0.60
Number of time the pair of genes has been broken
Distribution of breakpoints from X chromosome to 3L
7
6
5
4
3
2
1
0
1
1001
2001
3001
4001
5001
6001
7001
8001
9001
10001
Genes within genes within
genes
700
9000
350
4500
0
0
Number of nonoverlapping pairs
Number of overlapping pairs
Number of antisense/sense overlapping
pairs of genes in D. melanogaster
700
2000
350
1000
0
H. Sapiens
D. Melanogaster
D. melanogaster is different from H. sapiens.
0
RIKEN Group and FANTOM Consortium,
Antisense transcription in the mammalian transcriptome. Science 2005 309(5740)
100
Percentage of conserved pairs
90
80
3'-3' Antisense overlap
5'-5' Antisense overlap
70
5'-3' Sense overlap
3'-3' Nonoverlapping pair
60
5'-5' Nonoverlapping pair
5'-3' Nonoverlapping pair
50
40
M
el
a
no
g
as
t
er
Si
m
ul
an
s
Se
ch
el
lia
Ya
ku
ba
Er
ec
An
ta
a
na
Ps
ss
eu
ae
do
ob
sc
ur
a
Pe
rs
im
ilis
W
illi
st
on
M
oj
av i
en
si
s
Vi
ril
G
rim is
sh
aw
i
30
Thanks to:
Jose Ranz (Cambridge).
Casey Bergman (Manchester).
Marcin von Grotthuss (Cambridge).
Karen Eilbeck & Suzi Lewis (Berkeley).
Lincoln Stein (CSGL) & Richard Durbin (WTGC)
Hadi Quesneville (Paris).
The MRC for 25 years of continuous funding.
The BBSRC for a grant to Jose.
EMBO for support to Marcin.
The Royal Society for a Fellowship to Casey.
Depth of knowledge
Annotation
Detailed analysis
(typically biological) of
single genes
Annotated genome
Large-scale analysis
(typically computational)
of entire genome
Breadth of knowledge
Assemblies from the 12 ongoing Drosophila
sequencing projects are available right now
Comparison of number of annotated proteins
16000
GLEANR
BlastN/TblastN/PSI(NR70)-TBlastN
All Blasts + Syntenic Info
12000
10000
8000
6000
4000
2000
e
ct
iv
Ef
fe
on
Co
m
m
D.
G
ri.
D.
Vi
r.
D.
Er
e.
D.
Ya
k.
D.
An
a.
D.
Pe
r.
D.
Ps
e.
D.
W
il.
D.
M
oj
.
D.
Se
c.
.
0
D.
Si
m
Number of orthologs
14000
Comparison of total number of breakpoints that correspond to small and gross
inversions divided by evolutionary distance
Number of breakpoints / evolutionary
distance
30
25
20
15
10
5
D.
G
ri.
D.
Vi
r.
D.
M
oj
.
D.
W
il.
D.
Ps
e.
D.
Pe
r.
D.
An
a.
D.
Ya
k.
D.
Er
e.
D.
Se
c.
D.
Si
m
.
0
Number of time the pair of genes has been broken
Distribution of breakpoints along the chromosome X (Muller's element A)
7
6
5
4
3
2
1
0
1
201
401
601
801
1001
1201
Number of time the pair of genes has been broken
Distribution of breakpoints along the chromosome 3R (first 1283 pairs)
7
6
5
4
3
2
1
0
1
201
401
601
801
1001
1201