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

are needed to see this picture.

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