fungal genome size and intron evolution

Fungal Genome Size and Intron Evolution

Kemin Zhou, Oct 4, 2012

Figures Only, Tables will be in the manuscript word file

Percent Relative Intron Location from 5’-End of mRNA

Co

un

t

10

02

00

30

04

00

Aspni1

10

01

50

20

02

50

Mycfi1

10

01

50

20

02

50

30

0

Mycgr1

20

03

00

40

05

00 Necha2

10

30

50

70

Picst3

10

02

00

30

04

00

Trive1

50

15

02

50

35

0

Trire2

30

05

00

70

0 copci1

10

02

00

30

04

00

cryneo1

40

06

00

80

01

000 Lacbi1

20

03

00

40

05

00 Phchr1

20

03

00

40

05

00

Pospl1

0 20 40 60 80 100

50

15

02

50

35

0

Sporo1

0 20 40 60 80 100

40

60

80

10

0

ustma1

0 20 40 60 80 100

10

02

00

30

04

00

Batde5

0 20 40 60 80 100

20

04

00

60

08

00

Phybl1

Fig 1.

Relative Intron Location0.0 0.2 0.4 0.6 0.8 1.0

0600

Avg = 0.501

Exon Length0 200 400 600 800 1000

01500

Avg = 214.8

Number of Introns per Gene0 10 20 30 40

0600

Avg = 7.6 round = 0

Relative Intron Location0.0 0.2 0.4 0.6 0.8 1.0

0600 Avg = 0.476

Exon Length0 200 400 600 800 1000

02000 Avg = 246.2

Number of Introns per Gene0 10 20 30 40

0600 Avg = 6.5 round = 1

Relative Intron Location0.0 0.2 0.4 0.6 0.8 1.0

0400

Avg = 0.456

Exon Length0 200 400 600 800 1000

02000 Avg = 276.9

Number of Introns per Gene0 10 20 30 40

0600 Avg = 5.7 round = 2

Relative Intron Location0.0 0.2 0.4 0.6 0.8 1.0

0400

Avg = 0.427

Exon Length0 200 400 600 800 1000

01500 Avg = 332.3

Number of Introns per Gene0 5 10 15 20 25 30 35

01000 Avg = 4.6 round = 4

Relative Intron Location0.0 0.2 0.4 0.6 0.8 1.0

0400 Avg = 0.407

Exon Length0 200 400 600 800 1000

01000 Avg = 412.1

Number of Introns per Gene0 5 10 15 20 25 30 35

01500 Avg = 3.5 round = 8

Relative Intron Location0.0 0.2 0.4 0.6 0.8 1.0

0300

Avg = 0.419

Exon Length0 200 400 600 800 1000

0800 Avg = 493.3

Number of Introns per Gene0 5 10 15 20 25 30 35

03000

Avg = 2.7 round = 16

Relative Intron Location0.0 0.2 0.4 0.6 0.8 1.0

0300 Avg = 0.453

Exon Length0 200 400 600 800 1000

0600 Avg = 551.9

Number of Introns per Gene0 5 10 15 20 25 30

03000 Avg = 2.4 round = 32

0.0 0.2 0.4 0.6 0.8 1.0

0200 Avg = 0.481

0 200 400 600 800 1000

0600 Avg = 583.7

0 5 10 15 20 25 30

04000 Avg = 2.2 round = 64

Fig 2.

RIL Exon Length IPG

0.42 0.44 0.46 0.48 0.50

23

45

67

8

Relative Intron Location

IPG

0.42 0.44 0.46 0.48 0.50

4.5

5.5

6.5

7.5

Relative Intron Location

IPG

0 50000 150000 250000

23

45

67

Number of RT

2 4 6 8 10 12

23

45

67

ln(Number of RT)

-0.13

Fig 3.

A.

B.

C.

D.Number of RT Events

Ln (Number of RT Events)

789.210089.2948.4 610718.4 5

xey x

Mean Relative Intron Location

Me

an

Nu

mb

er

of

Co

din

g E

xon

s p

er

Ge

ne

0.40 0.42 0.44 0.46 0.48 0.50

12

34

56

78

Aspni1

Batde5

copci1

cryneo1

Lacbi1

Mycfi1Mycgr1

Necha2

Phchr1

Phybl1

Picst3

Pospl1

Sporo1

Trire2Trive1

ustma1

7.66y = 61.94x – 23.313p-value = 2.566E-07

Fig 4.

0 200 400 600 800 1000 1200 1400

23

45

67

8

Number of RT

EP

G

Fig 5.

Number of RTF

389.210089.2848.4 510118.2 3

xey x

Fig 6.

Intercept: 9.69 ± 1.99Slope: -0.30 ± 0.16

Intercept: 4.04 ± 0.35Slope: -0.11 ± 0.03

9 10 11 12 13 14

23

45

67

ln (Total RTF Length (nt))

Ave

rag

e E

PG

Aspni1

Batde5

copci1

cryneo1

Lacbi1

Mycfi1

Mycgr1Necha2

Phchr1

Phybl1

Picst3

Pospl1

Sporo1

Trire2

Trive1

ustma1

0 100 200 300 400

010

0020

0030

00

Cou

nt3n3n+13n+2

0 100 200 300 400

050

150

250

Cou

nt

3n3n+13n+2

Exon Length (nt)

C. reinhardtii

FungiA.

B.

Fig 7.

75

Number of Introns per Gene

Ave

rag

e E

xon

Le

ng

th (

nt) 5.1988961.11.1060 7812.0 xey x

020

060

010

00

0 10 20 30 40 50 60 70

Fig 8.

Percent relative intron location from 5’-end of mRNA

Diff

ere

nce

of

fre

qu

en

cy (

no

n-c

on

serv

ed

- c

on

serv

ed

)

-0.0

40.

000.

04 1.204E-07

Aspni1

1.482E-18

Mycfi1

2.228E-10

Mycgr1

1.390E-25

Necha2

-0.0

40.

000.

04 1.303E-03

Picst3

1.397E-35

Trive1

5.121E-18

Trire2

4.021E-08

copci1

-0.0

40.

000.

04 5.447E-01

cryneo1

1.770E-35

Lacbi1

1.330E-01

Phchr1

4.135E-02

Pospl1

0 20 40 60 80

-0.0

40.

000.

04 8.968E-02

Sporo1

0 20 40 60 80

2.997E-03

ustma1

0 20 40 60 80

8.028E-11

Batde5

0 20 40 60 80

1.047E-22

Phybl1

Fig 9.

Fig 10.

allbetween phylaphylumspecies

0

2

4

6

8

0

1

2

3

4

5

6

7

copc

i1

cryn

eo1

Lacb

i1

Phchr

1

Pospl1

Sporo

1

ustm

a1

Batde

5

Phybl1

Aspni1

Myc

fi1

Myc

gr1

Necha

2

Picst3

Trire

2

Trive

1

A.

B.

EP

G p

er

40

0 a

aE

PG

EPG of Genes Conserved in All Species

EP

G o

f S

pe

cie

s-sp

eci

fic G

en

es

2 3 4 5 6 7 8

23

45

67

Aspni1

Batde5

copci1

cryneo1

Lacbi1

Mycfi1

Mycgr1

Necha2

Phchr1

Phybl1

Picst3

Pospl1

Sporo1

Trire2

Trive1

ustma1

y = 0.503 x + 1.172

Excluding Sporo1, p-val=8.196E-07

Fig 11.