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Table 3 Peptides fragments of PR-10 isoforms in pollen from five Betula species as identified by Q-TOF LC-MSE.

From: Characterization of PR-10 genes from eight Betula species and detection of Bet v 1 isoforms in birch pollen

Species

Fragment

I

III

IV

V

VII

VIII

X

XVI

XVII

Sequence coverage

 

Isoform

Gene

      

*2

   

B. pendula

01A01

1A

A

a

a

a

a

A

a?

a

a

79%

 

01A06

1A

A

a

a

b

a

A

a?

a

a

79%

 

01B01

1B

B

B

a

b

a

C

B

a

a

79%

 

01C04

1C

D

a

a

a

a

D

c?

a

a

71%

 

01C05

1C

D

a

a

a

a

D

c?

a

a

71%

 

01D01

1D

(E)

a

a

(C)

(C)

(E)

a?

a

a

-

 

02A01

2A

j

e

a

e

k

k

g?

(B* 3 )

a

74%

 

02B01

2B

j

e

a

e

k

k

g?

(c * 3 )

a

74%

 

02C01

2C

j

F

a

e

k

k

a?

(c * 3 )

a

74%

 

03 *1

 

(C), ( z )

e

( z ), (Y)

e

(Z), ( y )

( z ), (Y)

(z), (Y)

( z )

a

-

 

04 *1

 

(Y)

(Z)

(X), (W)

(Z)

(X)

(X)

(X)

(Y)

(Z), (Y)

-

 

05 *1

 

(X)

(Y)

(V)

(Y)

(W)

(W)

(W)

(X)

(X)

-

B. chichibuensis

01var09

1A

a

a

a

a

a

d

a?

a

a

79%

 

01var12

1B

C

a

a

a

a

d

a?

a

a

79%

 

01var17

1C

a

a

a

a

H

(H)

c?

a

a

-

 

01var18

1C

a

a

a

a

H

d

c?

a

a

71%

 

01var19

1D

(E)

a

a

(C)

(J)

(E)

a?

a

a

-

 

02var03

2A

j

e

B

e

k

k

a?

(c*3)

a

74%

 

02var08

2B

j

F

a

e

k

k

a?

(c*3)

a

74%

B. costata

01var01

1A

F

a

a

a

a

c

a

a

a

79%

 

01var02

1B

a

a

a

a

a

c

a

a

a

79%

 

01var04

1C

a

(C)

a

b

(E)

c

(D)

a

a

-

 

01var05

1D

a

a

a

b

a

c

(E)

a

a

71%

 

01var13

1E

D

a

a

a

a

D

a

a

a

79%

 

Unknown

 

E

        

?

 

02var05

2A

j

(J)

a

e

k

k

a

(c * 3 )

a

-

 

02var10

2B

j

G

a

e

k

k

a

(c * 3 )

a

74%

 

Unknown

 

F

        

?

B. lenta

01var10

1A

G

A

a

(A)

(F)

d

a

(a* 3 )

a

60%

 

01var11

1A

G

A

a

(A)

(G)

d

a

(a* 3 )

a

60%

 

01var16

1B

B

D

a

D

A

d

a

(a* 3 )

a

74%

 

02var01

2A

j

e

a

e

k

k

a

(c* 3 )

a

74%

 

02var04

2B

j

H

a

e

k

k

a

(c* 3 )

a

74%

 

02var07

2C

j

F

a

e

k

k

a

(c* 3 )

a

74%

B. nigra

01var03

1A

B

a

a

B

a

F

a

a

a

79%

 

01var06

1B

a

a

a

a

-

C

a

a

a

74%

 

01var07

1C

a

a

a

a

a

C

a

a

a

79%

 

01var08

1D

a

a

a

a

a

D

F

a

a

79%

 

02var06

2A

J

K

a

e

K

K

a

(c* 3 )

a

74%

 

unknown

  

F

       

?

  1. Each isoform is displayed on a separate line. When isoforms are encoded by the same gene this is indicated in the third column. Note that gene labels in one species do not correspond to gene labels in other species. Peptide fragments are shown at the top of the table and are labelled with Roman numbers as indicated in Fig. 3. Each variant of these fragments is displayed in the Table by a letter. Bold capital letters indicate that a fragment is unique for the isoforms of a particular gene. Bold italic letters indicate that a fragment is unique for the isoforms of a particular subfamily. Letters displayed between brackets indicate that a particular fragment was predicted, but was absent in the PR-10 mixture. Finally, the last column displays the coverage of the total protein sequence, including the fragments that were too small to be detected (II, VI, IX, XI, XII, XIII, XIV, XV). Fig. 3 displays the representative amino acid sequences of the isoforms 01A01 and 02A01.
  2. *1 The isoforms in subfamily 03 to 05 were summarized into a single row and not displayed for the other species, because specific peptides were not detected in any of the species.
  3. *2 Fragments Xa and Xg have exactly the same mass and cannot be distinguished. The peak of peptide Xc overlaps with the first isotope peak of peptide Xa = g because they differ exactly 1 Da in size and have the same charge. As a consequence, Xc cannot be identified separately.
  4. *3 The XVI-peptides are not always detected because of their small size.
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BMC Plant Biology

ISSN: 1471-2229

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