Table 8

Shared repeats among eight angiosperm chloroplast genomes.

Repeat Size (AT%)

Nymphaea (reference genome)

Amborella

Nuphar

Calycanthus

Triticum

Ranunculus

Arabidopsis

Nicotiana

Location


49(64)

2

2

2

2

2

2

2

2

psaA, psaB

43(61)

4

4

4

4

0

4

2

2

ycf2

42(51)

5

6

7

7

5

5

6

7

intron ycf3, intron rpoC1, IGS psbH:petB, IGS petD:petB, IGS rpl16:rps3, IGS trnV:rps12 3'

40(54)

11

10

11

11

11

7

9

10

intron ycf3, intron ndhB, IGS trnV:rps12 3', IGS rpl16:rps3, IGS psbH:petB, IGS rps12 3':rps7

37(39)

2

2

2

2

1

2

2

2

IGS trnS:trnR

36(51)

3

2

3

2

2

3

2

3

trnV, trnA

35(75)

2

0

1

0

0

0

0

0

IGS rps12 5':clpP

35(47)

3

3

3

3

3

3

3

3

trnS

35(100)

3

2

4

1

0

2

4

1

intron trnL, IGS ndhC:trnV

34(91)

2

2

2

2

2

1

2

2

trnfM, trnP

34(86)

2

0

2

0

0

0

0

0

IGS atpH:atpI, IGS trnS:trnR

34(54)

4

1

1

0

1

0

4

0

intron trnL, IGS trnE:trnT

33(59)

2

3

2

2

3

2

3

2

intron atpF, IGS trnS:trnR

33(85)

2

2

1

1

0

1

1

2

intron clpP, rpoC2

33(47)

4

4

4

2

4

4

4

4

trnI, trnN

32(79)

2

0

1

1

0

0

0

0

IGS psbA:matK

32(94)

2

0

1

0

0

0

0

0

IGS trnP:psaJ

32(58)

3

3

3

3

4

3

3

3

trnT, trnM

32(64)

2

2

2

2

1

2

0

2

psaA, psaB

32(97)

3

1

0

1

1

1

4

1

intron trnL, IGS ndhC:trnV

32(69)

2

0

2

1

1

1

1

2

intron ndhA, rpoA

31(66)

4

2

4

4

0

6

2

4

ycf2

31(66)

2

2

2

2

2

2

2

2

IGS trnS:trnR, trnG

31(56)

2

1

2

2

1

2

2

2

Intron ndhA, IGS rpl16:rps3

31(59)

2

2

2

2

2

2

2

2

trnT

31(53)

2

1

2

1

3

1

1

3

intron ycf3, intron ndhA

31(66)

4

4

4

4

0

2

4

4

ycf2

31(75)

2

2

2

2

0

2

1

2

intron ndhB

31(88)

2

0

1

0

0

0

0

0

IGS rps16:trnQ, cemA

31(84)

2

1

2

1

0

1

0

0

intron ndhB, IGS trnT:psbD

31(34)

2

2

2

1

0

2

1

1

psaB, psaA

31(56)

2

2

2

1

1

1

1

1

psaB, psaA

31(59)

2

0

2

0

0

0

0

0

IGS rps12 5':clpP

31(75)

2

0

2

0

0

0

0

0

intron clpP, intron rps16

31(84)

2

0

1

0

0

0

0

0

IGS rps15:trnN

30(77)

2

1

0

0

0

0

0

0

intron ycf3

30(52)

2

2

2

2

2

2

2

2

trnS

30(71)

3

3

3

3

4

4

3

3

intron ndhB, IGS trnS:trnR

30(52)

3

3

3

3

3

3

3

4

intron ycf3, IGS trnV:rps12 3'

30(55)

2

1

2

0

0

0

0

0

IGS petA:psbJ

30(42)

4

2

4

2

2

2

2

2

IGS trnV:rps12 3', rrn23

30(39)

4

2

4

2

2

2

2

2

IGS trnV:rps12 3', rrn23

30(68)

2

2

2

1

2

2

2

1

intron ndhA, IGS trnS:trnR

30(84)

3

0

2

0

0

0

0

0

rpl23

30(68)

4

4

4

4

0

4

6

6

ycf2

30(74)

4

4

4

6

0

2

8

4

ycf2

30(55)

2

1

2

1

0

0

0

0

IGS trnH:psbA, rpoB

30(74)

2

0

2

0

0

0

0

0

IGS psbK:psbI, IGS psbF:psbE

30(97)

2

0

1

0

0

0

0

0

IGS atpH:atpI

30(90)

2

1

1

0

0

0

1

0

IGS atpH:atpI, IGS psaI:ycf4

30(68)

2

1

2

1

0

1

1

0

IGS accD:psaI, rpoB

30(74)

2

0

2

0

0

0

0

0

IGS ycf6:psbM, IGS psaI:ycf4

30(68)

3

3

3

3

0

3

3

3

IGS psbD:psbC, IGS rpl14:rpl16, ycf2

30(71)

2

2

2

2

2

2

2

1

psaB, psaA

30(55)

3

1

3

0

2

3

1

1

intron ycf3, IGS trnV:rps12 3'

30(65)

2

0

1

0

0

0

0

0

IGS trnS:rps4, IGS rps15:trnN

30(74)

2

2

2

2

1

1

2

1

rps4, ndhC

30(65)

2

1

2

2

0

1

0

2

ndhK, ndhD

30(61)

3

1

3

1

1

1

1

1

intron trnV, IGS trnV:rps12 3'

30(58)

2

2

1

0

0

1

1

1

atpE, ndhD

30(74)

2

1

1

1

1

1

1

0

IGS petB:petD, IGS rps15:trnN

30(71)

4

2

4

1

2

2

4

4

rpl2, ycf2

30(52)

4

2

4

1

2

2

2

2

rpl2, ycf2

30(29)

2

2

2

0

0

0

0

0

IGS trnI:rrn16


Repeats size is for Nymphaea, which was used the reference genome in Blast comparisons. Numbers in parentheses are percentage AT in each repeat. Numbers listed under each taxon indicate the number of copies of repeat shared with Nymphaea. The location indicates position of shared repeats. IGS = intergenic spacer.

Raubeson et al. BMC Genomics 2007 8:174   doi:10.1186/1471-2164-8-174

Open Data