Post on 16-Dec-2015
The Life Cycle
P
Neuroptera
Coleoptera
Hymenoptera
Lepidoptera
Mecoptera
SiphonopteraStrepsiptera
Diptera
~250 Mya
Nematocera
BrachyceraMuscomorpha
CyclorrhaphaSchizophora
CalyptrataAcalyptrata
Camillidae
Steganinae
Cladocheata etc
Zaprionus etc
s.g. Drosophila
Chymomyza etc
s.g. Sophopora
Drosophila melanogaster subgroup
Drosophila melanogaster - cosmopolitan - 1830Drosophila simulans - cosmopolitan - 1919
Drosophila mauritiana - Mauritius - 1974Drosophila sechellia - Seychelles -1981
Drosophila yakuba - Equatorial Africa - 1954Drosophila santomea - Sao Tome - 2000
Drosophila teissieri - Equatorial Africa - 1979
Drosophila erecta - Central West Africa - 1974Drosophila 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 itsevolution will have to be entirely rewritten in molecular terms.”
Michael White, 1973, Animal Cytology & Evolution, 2nd edition.
QuickTime™ and a decompressor
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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 12 genomes have been sequenced in the genus DrosophilaDrosophila
( Cáceres et al. Science 1999 )
Ectopic recombination between homologous fragments of DNA
1.
2.
3.
centromere telomere3R of D. melanogaster
centromere telomere
3R of D. simulans
BACs
84F1 93F6-7
BACR07M14BACR45A07
BACR16N15BACR42I20BACR08K01
~280 Kb~450 Kb
Inversion-mediated duplications can result from Inversion-mediated duplications can result from staggered isochromatid breaks & repair.staggered isochromatid breaks & repair.
5'
5'3'
3'
5'3'
5'
3'
5'
3'5'
3'
5'
3' 5'
3'
5'
3'
3'
5'
A B C D E
3'
5'5' 3'
5'
3'
F G H I J K
5'3'
5'
5'
3'
3'
5'5'
5'
A B C D I J KEFG BCDI H
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-productFlanking duplications are a common by-product
of the genome reorganization betweenof the genome reorganization between
D. melanogasterD. melanogaster and and D. yakuba.D. yakuba.
0
2
4
6
8
10
12
14
16
18
20
withwith withoutwithout
2020 99
outgroup speciesD. yakubaD. melanogaster
Most inversions occurred in the Most inversions occurred in the D. yakuba D. yakuba lineagelineage
A-B A-B
A]-----[B A-B A-B
A]-----[B
28 ( 96.6 % )1 ( 3.4 % )
1:
2:
Large-scale comparison of the gene order betweenLarge-scale comparison of the gene order between
D. melanogasterD. melanogaster and and D. yakuba.D. yakuba.
0
0.005
0.01
0.015
0.02
0.025
X 2L+2R 3L 3R
BreakpointsBreakpoints Mb MyrMb Myr
1212 2222 99 121255 breakpoints =55 breakpoints = ++ ++ ++ 29 inversions29 inversions
Comparison of total number of breakpoints that correspond to small and gross inversions between D. melanogaster and other flies' genomes
0
200
400
600
800
1000
1200
1400
1600
1800
2000
Num
ber o
f bre
akpo
ints
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
0.00
0.10
0.20
0.30
0.40
0.50
0.60
Nu
mb
er o
f b
reak
po
ints
/ s
qu
are
of
evo
luti
on
ary
dis
tan
ce
Distribution of breakpoints from X chromosome to 3L
0
1
2
3
4
5
6
7
1 1001 2001 3001 4001 5001 6001 7001 8001 9001 10001
Nu
mb
er
of t
ime
the
pa
ir o
f ge
ne
s h
as
be
en
bro
ken
Genes within genes within genes
Number of antisense/sense overlapping pairs of genes in D. melanogaster
0
350
700
Nu
mb
er
of
ov
erl
ap
pin
g p
air
s
0
4500
9000
Nu
mb
er
of
no
no
ve
rla
pp
ing
pa
irs
D. melanogaster is different from H. sapiens.
RIKEN Group and FANTOM Consortium, Antisense transcription in the mammalian transcriptome. Science 2005 309(5740)
0
350
700
D. M
ela
no
ga
ste
r
0
1000
2000
H. S
ap
ien
s
30
40
50
60
70
80
90
100
Mela
noga
ster
Simul
ans
Seche
llia
Yakub
a
Erecta
Anana
ssae
Pseud
oobs
cura
Persim
ilis
Willi
stoni
Moja
vens
isViril
is
Grimsh
awi
Per
cen
tag
e o
f co
nse
rved
pai
rs
3'-3' Antisense overlap
5'-5' Antisense overlap
5'-3' Sense overlap
3'-3' Nonoverlapping pair
5'-5' Nonoverlapping pair
5'-3' Nonoverlapping pair
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.
Annotated genome
AnnotationD
epth
of
know
ledge
Breadth of knowledge
Detailed analysis (typically biological)
of single genes
Large-scale analysis (typically
computational) of entire genome
Assemblies from the 12 ongoing Drosophila sequencing projects are available right now
Comparison of number of annotated proteins
0
2000
4000
6000
8000
10000
12000
14000
16000
Nu
mb
er o
f o
rth
olo
gs
GLEANR BlastN/TblastN/PSI(NR70)-TBlastN All Blasts + Syntenic Info
Comparison of total number of breakpoints that correspond to small and gross inversions divided by evolutionary distance
0
5
10
15
20
25
30
Nu
mb
er
of
bre
ak
po
ints
/ e
vo
luti
on
ary
d
ista
nc
e
Distribution of breakpoints along the chromosome X (Muller's element A)
0
1
2
3
4
5
6
7
1 201 401 601 801 1001 1201
Nu
mb
er
of t
ime
the
pa
ir o
f ge
ne
s h
as
be
en
bro
ken
Distribution of breakpoints along the chromosome 3R (first 1283 pairs)
0
1
2
3
4
5
6
7
1 201 401 601 801 1001 1201
Nu
mb
er
of t
ime
the
pa
ir o
f ge
ne
s h
as
be
en
bro
ken