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Table 3 Repeat sequences for Ananas comosus chloroplast genome

From: Complete chloroplast genome sequence of MD-2 pineapple and its comparative analysis among nine other plants from the subclass Commelinidae

No.

Type

Location

Region

Repeat unit

Period size (bp)

Copy number

1

T

trnS-GCU and trnG-GCC

LSC

TACATTAAACAATATTAAAT

20

2

2

D

psbI and trnG-GCC psbE and petL

LSC

TAAAAATATATATATATATATAAATATATTATAGTA

36

2

3

T

accD and psaI

LSC

TAATTAAGATAGACAA

16

2

4

T

accD and psaI

LSC

TTTTCATAAGAAAACTCCT

18

2

5

T

accD and psaI

LSC

ATTTGAGATTTCCAAATAATA

20

2

6

P

accD and psaI

LSC

GTATAATATGAAGTTTGAATAT

22

2

7

T

clpP (intron)

LSC

TTAGGACAAAATTGTATCTC

20

2

8

T

clpP (intron)

LSC

AGTAATAGTAGGTATAA

17

3

9

T

ndhB and trnL-CAA

IRA

GTCATTCAAGCGTAT

15

2

10

T

ndhC and trnV-UAC

LSC

ATTCTAAATAATAAAAG

17

2

11

T

ndhF and rpl32

SSC

TATTTATTAGATTTTGC

16

2

12

T

ndhF and rpl33

SSC

TCGGAAATCTTATGATACTCCTT

23

2

13

T

petD (intron)

LSC

TTATATGGGTTTATTTCTGTTA

22

2

14

P

petN and psbM

LSC

CTAAAGAGTGGTAGAAAGGACTA

24

2

15

D

psaB (CDS) and psaA (CDS)

LSC

TGCAATAGCTAAATGATGATGAGCAATATCGGTCA

34

2

16

P

psbA

LSC

AAAAAATACCCAATATCTTGT

21

2

17

P

psbT and psbH

LSC

ATTGAAGTAATGAGCCTCCCA

21

2

18

T

rbcL and accD

LSC

TATATACAAG

10

5

19

T

rpoC2 (CDS)

LSC

TGTCTCATGTAAATT

15

2

20

T

rps11 (CDS)

LSC

TACGCCCATTCTTACGTGAACCAA

24

2

21

P

trnD-GUC and trnE-UUC

LSC

TTTCATGATACTTTACTTA

19

2

22

T

trnF-GAA and ndhJ

LSC

TATTCTATTTCGTCA

15

2

23

T

trnL-CAA ndhB

IRB

ACATACGCTTGAATG

15

2

24

P

ycf1 (CDS)

SSC

TTTTATTTTGACTTGTATTTTTAT

22

2

25

T

ycf15 and trnL-CAA

IRB

GAATAACTAAAGAAAATAGATA

22

2

26

T

ycf15 and trnL-CAA

IRA

TCTATCTATTTTCTTTACTTAT

22

2

27

T

ycf2 (CDS)

IRB

TTTGTCCAAGTCACTTCTCTT

21

3

28

T

ycf2 (CDS)

IRB/IRA

CTTTTTGTCCAAGTCACTTCC

21

3

29

T

ycf2 (CDS)

IRB/IRA

GATATCGATATTGATGATAGTGAC

24

2

30

T

ycf2 (CDS)

IRA

GAAGTGACTTGGACAAAAAGA

21

3

31

D/P

ycf3 (intron) petB (intron) rps12 and trnV-GAC

LSC/IRA/IRB

CCAGAACCGTACATGAGATTTTCATCTCATACGGCTCCTC

39

3

  1. *Letter T, D, and P in Region column represents Tandem, Dispersed and Palindromic repeats, respectively. IRA, IRB, LSC and SSC represents inverted region A, inverted region B, long single copy and short single copy, respectively. All of the repeat locations are in intergenic spacer regions, except otherwise indicated