Supplemental Table 1. Comparison of intergenic spacer regions of O. sativa, T. aestivum and H. vulgare and A. stolonifera. BTG- A. stolonifera, BRL- H.vulgare, RCE- O. sativa, WHT- T. aestivum, AVG- Average.
Intergenic Spacer Region / BTG/BRL% Identity / RCE/BRL
% Identity / WHT/BRL
% Identity / BTG/RCE
% Identity / BTG/WHT
% Identity / RCE/WHT
% Identity / AVG.
% Identity
psbH:petB / 15 / 14 / 91 / 91 / 14 / 13 / 39.67
rpl16:rps3 / 11 / 10 / 11 / 88 / 88 / 84 / 48.67
rps16:trnQ-UUG / 40 / 36 / 36 / 56 / 56 / 100 / 54.00
petB:petD / 19 / 93 / 99 / 18 / 18 / 93 / 56.67
petN:trnC-GCA / 65 / 48 / 73 / 37 / 85 / 37 / 57.50
psbM:petN / 37 / 80 / 84 / 33 / 41 / 70 / 57.50
trnD-GUC:psbM / 82 / 43 / 92 / 47 / 82 / 43 / 64.83
trnL-UAA:trnF-GAA / 81 / 55 / 86 / 59 / 87 / 57 / 70.83
rps18:rpl20 / 85 / 41 / 96 / 62 / 86 / 59 / 71.50
rpl32:trnL-UAG / 77 / 59 / 93 / 66 / 76 / 61 / 72.00
atpI:atpH / 85 / 57 / 95 / 57 / 86 / 58 / 73.00
trnT-UGU:trnL-UAA / 65 / 67 / 95 / 80 / 67 / 67 / 73.50
ndhC:trnV-UAC / 70 / 76 / 77 / 65 / 89 / 68 / 74.17
trnF-GAA:ndhJ / 88 / 75 / 72 / 75 / 68 / 77 / 75.83
ndhF:rpl32 / 83 / 70 / 87 / 65 / 88 / 68 / 76.83
rpoC2:rps2 / 79 / 69 / 92 / 78 / 79 / 69 / 77.67
trnL-UAA:trnL-UAA / 69 / 86 / 92 / 71 / 68 / 84 / 78.33
trnY-GUA:trnD-GUC / 75 / 82 / 91 / 67 / 74 / 81 / 78.33
rpoA:rps11 / 81 / 80 / 88 / 88 / 75 / 61 / 78.83
ccsA:ndhD / 88 / 69 / 91 / 73 / 87 / 72 / 80.00
petG:trnW-CCA / 81 / 85 / 82 / 78 / 84 / 72 / 80.33
petA:psbJ / 89 / 72 / 95 / 71 / 89 / 71 / 81.17
trnS-GGA:rps4 / 80 / 80 / 92 / 80 / 79 / 79 / 81.67
ndhG:ndhI / 87 / 78 / 90 / 79 / 84 / 74 / 82.00
psbK:psbI / 75 / 83 / 92 / 78 / 79 / 86 / 82.17
rpl36:infA / 76 / 88 / 94 / 72 / 75 / 88 / 82.17
psbE:petL / 81 / 77 / 96 / 80 / 81 / 79 / 82.33
trnG-GCC:trnfM-CAU / 82 / 77 / 95 / 79 / 84 / 78 / 82.50
rpl33:rps18 / 86 / 77 / 95 / 74 / 87 / 79 / 83.00
psaI:ycf4 / 88 / 74 / 97 / 77 / 88 / 75 / 83.17
psbC:trnS-UGA / 82 / 79 / 95 / 79 / 84 / 80 / 83.17
trnL-UAG:ccsA / 84 / 76 / 93 / 85 / 86 / 77 / 83.50
ycf4:cemA / 87 / 76 / 94 / 82 / 86 / 76 / 83.50
rpl14:rpl16 / 80 / 83 / 93 / 82 / 82 / 82 / 83.67
psbI:trnS-GCU / 88 / 80 / 88 / 82 / 87 / 78 / 83.83
trnV-UAC:trnM-CAU / 83 / 78 / 97 / 85 / 83 / 77 / 83.83
rps14:psaB / 80 / 90 / 93 / 73 / 80 / 89 / 84.17
rps12_5end:clpP / 86 / 80 / 100 / 78 / 86 / 80 / 85.00
psaA:ycf3 / 89 / 80 / 91 / 84 / 88 / 79 / 85.17
ycf3:trnS-GGA / 89 / 80 / 94 / 84 / 88 / 80 / 85.83
psaC:ndhE / 86 / 81 / 93 / 87 / 87 / 83 / 86.17
ndhJ:ndhK / 89 / 81 / 92 / 82 / 93 / 81 / 86.33
trnC-GCA:rpoB / 90 / 80 / 96 / 80 / 91 / 81 / 86.33
petD:rpoA / 90 / 86 / 86 / 88 / 89 / 83 / 87.00
psaJ:rpl33 / 85 / 85 / 96 / 83 / 87 / 86 / 87.00
rps11:rpl36 / 87 / 87 / 90 / 86 / 88 / 85 / 87.17
petL:petG / 86 / 82 / 95 / 88 / 90 / 83 / 87.33
ndhA:ndhA / 91 / 82 / 95 / 84 / 91 / 84 / 87.83
atpH:atpF / 89 / 87 / 96 / 85 / 86 / 86 / 88.17
clpP:psbB / 86 / 88 / 93 / 87 / 86 / 90 / 88.33
rps8:rpl14 / 92 / 86 / 94 / 84 / 91 / 86 / 88.83
ndhI:ndhA / 90 / 84 / 91 / 89 / 95 / 87 / 89.33
cemA:petA / 88 / 89 / 94 / 89 / 88 / 89 / 89.50
rps2:atpI / 90 / 87 / 93 / 94 / 88 / 85 / 89.50
ndhD:psaC / 88 / 85 / 87 / 90 / 94 / 94 / 89.67
ndhH:rps15 / 87 / 86 / 95 / 94 / 88 / 88 / 89.67
rps15:ndhH / 87 / 86 / 95 / 94 / 88 / 88 / 89.67
trnS-GCU:psbD / 91 / 88 / 94 / 87 / 89 / 89 / 89.67
psbB:psbT / 90 / 86 / 90 / 89 / 94 / 91 / 90.00
trnN-GUU:trnR-ACG / 88 / 85 / 100 / 94 / 88 / 85 / 90.00
trnR-ACG:trnN-GUU / 88 / 85 / 100 / 94 / 88 / 85 / 90.00
rrn5:trnR-ACG / 95 / 84 / 98 / 85 / 95 / 85 / 90.33
trnR-ACG:rrn5 / 95 / 84 / 98 / 85 / 95 / 85 / 90.33
rpoC1:rpoC2 / 92 / 86 / 96 / 90 / 94 / 89 / 91.17
atpB:rbcL / 94 / 88 / 98 / 87 / 93 / 88 / 91.33
atpF:atpF / 94 / 89 / 97 / 90 / 93 / 89 / 92.00
rps19:trnH-GUG / 91 / 91 / 96 / 91 / 91 / 92 / 92.00
rps4:trnT-UGU / 93 / 89 / 95 / 90 / 95 / 90 / 92.00
trnE-UUC:trnY-GUA / 89 / 92 / 100 / 90 / 89 / 92 / 92.00
trnH-GUG:rps19 / 91 / 91 / 96 / 91 / 91 / 92 / 92.00
ndhE:ndhG / 93 / 90 / 97 / 90 / 93 / 90 / 92.17
ycf3:ycf3 / 92 / 89 / 98 / 91 / 93 / 91 / 92.33
rpl20:rps12_5end / 95 / 88 / 98 / 90 / 96 / 89 / 92.67
trnQ-UUG:psbK / 92 / 91 / 91 / 91 / 91 / 100 / 92.67
ndhB:trnL-CAA / 98 / 90 / 91 / 90 / 90 / 98 / 92.83
trnL-CAA:ndhB / 98 / 90 / 91 / 90 / 90 / 98 / 92.83
rrn23:rrn4.5 / 91 / 94 / 100 / 88 / 92 / 94 / 93.17
trnA-UGC:trnI-GAU / 100 / 94 / 91 / 92 / 91 / 91 / 93.17
psbJ:psbL / 92 / 92 / 96 / 94 / 93 / 93 / 93.33
psbN:psbH / 94 / 92 / 95 / 92 / 95 / 93 / 93.50
rrn4.5:rrn23 / 92 / 94 / 100 / 89 / 92 / 94 / 93.50
rrn23:trnA-UGC / 92 / 92 / 96 / 96 / 93 / 93 / 93.67
trnA-UGC:rrn23 / 92 / 92 / 96 / 96 / 93 / 93 / 93.67
trnH-GUG:rpl2 / 100 / 91 / 100 / 91 / 100 / 91 / 95.50
trnV-UAC:trnV-UAC / 97 / 94 / 98 / 93 / 97 / 94 / 95.50
rps7:ndhB / 98 / 94 / 94 / 94 / 94 / 100 / 95.67
rrn16:trnI-GAU / 97 / 95 / 98 / 95 / 97 / 95 / 96.17
ndhB:rps7 / 98 / 95 / 95 / 95 / 95 / 100 / 96.33
rrn16:trnV-GAC / 97 / 96 / 98 / 97 / 97 / 97 / 97.00
rrn4.5:rrn5 / 97 / 96 / 98 / 97 / 97 / 97 / 97.00
rrn5:rrn4.5 / 97 / 96 / 98 / 97 / 97 / 97 / 97.00
trnV-GAC:rrn16 / 97 / 96 / 98 / 97 / 97 / 97 / 97.00
rpl23:trnI-CAU / 97 / 97 / 100 / 97 / 97 / 97 / 97.50
trnI-CAU:rpl23 / 97 / 97 / 100 / 97 / 97 / 97 / 97.50
ndhB:ndhB / 99 / 98 / 98 / 98 / 98 / 98 / 98.17
trnA-UGC:trnA-UGC / 100 / 99 / 99 / 99 / 98 / 98 / 98.83
atpA:trnR-UCU / N/A / N/A / 78 / 82 / 86 / 85 / N/A
infA:rps8 / N/A / N/A / N/A / N/A / 86 / N/A / N/A
psbT:psbN / N/A / N/A / N/A / N/A / 79 / N/A / N/A
rpl22:rps19 / N/A / N/A / N/A / N/A / 83 / N/A / N/A
Supplemental Table 2. Comparison of intergenic spacer regions of Maize, Sorghum and Sugarcane.
Intergenic Spacer Region / Zea/Saccharum% Identity / Zea/Sorghum
% Identity / Saccharum/Sorghum
% Identity / Average
% Identity
rpl16:rps3 / 94 / 11 / 12 / 39.00
rps12_3end:rps7 / 9 / 9 / 100 / 39.33
psbH:petB / 15 / 15 / 98 / 42.67
petB:petD / 19 / 19 / 99 / 45.67
rps16:trnQ-UUG / 55 / 83 / 62 / 66.67
trnH-GUG:rpl2 / 91 / 69 / 71 / 77.00
psbT:psbN / 69 / 69 / 100 / 79.33
trnG-GCC:trnfM-CAU / 92 / 73 / 73 / 79.33
trnR-UCU:trnfM-CAU / 78 / 89 / 84 / 83.67
rps15:ndhF / 81 / 93 / 81 / 85.00
ycf4:cemA / 82 / 83 / 97 / 87.33
ndhH:rps15 / 84 / 95 / 85 / 88.00
trnV-UAC:trnM-CAU / 83 / 83 / 98 / 88.00
rpl33:rps18 / 90 / 86 / 92 / 89.33
rpoA:rps11 / 88 / 88 / 94 / 90.00
atpF:atpA / 91 / 88 / 92 / 90.33
petD:rpoA / 96 / 88 / 87 / 90.33
rps11:rpl36 / 91 / 88 / 92 / 90.33
trnA-UGC:trnI-GAU / 86 / 86 / 100 / 90.67
trnfM-CAU:rps14 / 89 / 88 / 97 / 91.33
atpA:trnR-UCU / 91 / 90 / 94 / 91.67
rpoC2:rps2 / 89 / 88 / 98 / 91.67
rps12_5end:clpP / 95 / 89 / 91 / 91.67
ndhE:ndhG / 96 / 91 / 90 / 92.33
ccsA:ndhD / 91 / 92 / 95 / 92.67
ndhF:rpl32 / 94 / 91 / 93 / 92.67
rps3:rpl22 / 89 / 89 / 100 / 92.67
atpB:rbcL / 93 / 90 / 96 / 93.00
atpI:atpH / 98 / 91 / 91 / 93.33
infA:rps8 / 92 / 94 / 94 / 93.33
ndhJ:ndhK / 90 / 90 / 100 / 93.33
psbI:trnS-GCU / 95 / 91 / 94 / 93.33
psbA:trnK-UUU / 92 / 92 / 97 / 93.67
trnC-GCA:rpoB / 93 / 91 / 97 / 93.67
trnL-UAG:ccsA / 94 / 93 / 94 / 93.67
cemA:petA / 91 / 91 / 100 / 94.00
matK:rps16 / 93 / 93 / 96 / 94.00
psbB:psbT / 93 / 92 / 97 / 94.00
petL:petG / 93 / 94 / 96 / 94.33
psbE:petL / 94 / 95 / 95 / 94.67
rpl14:rpl16 / 94 / 95 / 95 / 94.67
trnE-UUC:trnY-GUA / 92 / 92 / 100 / 94.67
trnF-GAA:ndhJ / 93 / 96 / 95 / 94.67
ndhC:trnV-UAC / 94 / 94 / 97 / 95.00
psaJ:rpl33 / 94 / 94 / 97 / 95.00
rpl20:rps12_5end / 98 / 93 / 94 / 95.00
rps8:rpl14 / 96 / 94 / 95 / 95.00
rpl32:trnL-UAG / 95 / 94 / 97 / 95.33
trnM-CAU:atpE / 93 / 93 / 100 / 95.33
petN:trnC-GCA / 95 / 96 / 96 / 95.67
psbK:psbI / 97 / 95 / 95 / 95.67
rps14:psaB / 95 / 96 / 96 / 95.67
trnY-GUA:trnD-GUC / 96 / 94 / 97 / 95.67
clpP:psbB / 95 / 97 / 96 / 96.00
rpl22:rps19 / 94 / 94 / 100 / 96.00
rpl36:infA / 94 / 94 / 100 / 96.00
rps18:rpl20 / 96 / 95 / 97 / 96.00
ycf3:ycf3 / 96 / 95 / 97 / 96.00
atpH:atpF / 95 / 95 / 99 / 96.33
ndhG:ndhI / 97 / 96 / 96 / 96.33
psbM:petN / 95 / 96 / 98 / 96.33
rpoC1:rpoC2 / 97 / 95 / 97 / 96.33
trnD-GUC:psbM / 97 / 95 / 97 / 96.33
trnT-UGU:trnL-UAA / 96 / 96 / 97 / 96.33
ndhI:ndhA / 95 / 100 / 95 / 96.67
psaC:ndhE / 96 / 97 / 97 / 96.67
psbC:trnS-UGA / 95 / 95 / 100 / 96.67
rrn23:rrn4.5 / 95 / 95 / 100 / 96.67
rrn4.5:rrn23 / 95 / 95 / 100 / 96.67
trnL-UAA:trnF-GAA / 97 / 96 / 97 / 96.67
trnS-GCU:psbD / 97 / 96 / 97 / 96.67
ycf3:trnS-GGA / 96 / 96 / 98 / 96.67
psaA:ycf3 / 98 / 96 / 97 / 97.00
trnL-UAA:trnL-UAA / 97 / 96 / 98 / 97.00
petG:trnW-CCA / 96 / 96 / 100 / 97.33
rps19:trnH-GUG / 100 / 96 / 96 / 97.33
trnH-GUG:rps19 / 100 / 96 / 96 / 97.33
trnK-UUU:trnK-UUU / 97 / 97 / 98 / 97.33
petA:psbJ / 97 / 97 / 99 / 97.67
rps4:trnT-UGU / 98 / 97 / 98 / 97.67
rrn5:trnR-ACG / 98 / 98 / 97 / 97.67
trnR-ACG:rrn5 / 98 / 98 / 97 / 97.67
ndhB:rps7 / 98 / 98 / 98 / 98.00
psaI:ycf4 / 98 / 98 / 98 / 98.00
rpl23:trnI-CAU / 97 / 97 / 100 / 98.00
rps2:atpI / 97 / 97 / 100 / 98.00
rps7:ndhB / 98 / 98 / 98 / 98.00
rps7:rps12_3end / 97 / 97 / 100 / 98.00
rrn4.5:rrn5 / 97 / 97 / 100 / 98.00
rrn5:rrn4.5 / 97 / 97 / 100 / 98.00
trnI-CAU:rpl23 / 97 / 97 / 100 / 98.00
trnQ-UUG:psbK / 98 / 98 / 98 / 98.00
rrn16:trnI-GAU / 98 / 98 / 99 / 98.33
trnS-GGA:rps4 / 99 / 98 / 98 / 98.33
trnV-UAC:trnV-UAC / 98 / 98 / 99 / 98.33
ndhA:ndhA / 99 / 98 / 99 / 98.67
rrn16:trnV-GAC / 98 / 98 / 100 / 98.67
trnN-GUU:trnR-ACG / 98 / 98 / 100 / 98.67
trnR-ACG:trnN-GUU / 98 / 98 / 100 / 98.67
trnV-GAC:rrn16 / 98 / 98 / 100 / 98.67
ndhB:ndhB / 99 / 100 / 99 / 99.33
ndhB:trnL-CAA / 100 / 99 / 99 / 99.33
rps12_3end:trnV-GAC / 99 / 99 / 100 / 99.33
trnA-UGC:trnA-UGC / 99 / 99 / 100 / 99.33
trnL-CAA:ndhB / 100 / 99 / 99 / 99.33
trnV-GAC:rps12_3end / 99 / 99 / 100 / 99.33
ndhD:psaC / 100 / 100 / 100 / 100.00
psbJ:psbL / 100 / 100 / 100 / 100.00
psbN:psbH / 100 / 100 / 100 / 100.00
rrn23:trnA-UGC / 100 / 100 / 100 / 100.00
trnA-UGC:rrn23 / 100 / 100 / 100 / 100.00
Supplemental Table 3. Simple sequence repeats identified by CUGISSR in the nine grass chloroplast genomes examined. Table shows motif, number of repeated elements, location, and presence within an ORF.
# SSRs / Motif / # Repeats / Start / Stop / INORF / ORF IDA.stolonifera / 140754 / 17 / ttat / 4 / 11012 / 11023 / Y / rpoC2
aat / 3 / 24240 / 24251 / N
at / 2 / 25539 / 25548 / N
tcct / 4 / 42353 / 42364 / N
cttat / 5 / 47561 / 47575 / N
aaat / 4 / 65509 / 65520 / N
agaa / 4 / 68264 / 68275 / N
ta / 2 / 84762 / 84771 / N
aacg / 4 / 98980 / 98991 / N
caa / 3 / 105494 / 105505 / N
aaca / 4 / 105501 / 105512 / N
atta / 4 / 105588 / 105599 / N
aata / 4 / 107654 / 107665 / N
ct / 2 / 114612 / 114623 / N
tcgt / 4 / 117977 / 117988 / N
ta / 2 / 132196 / 132205 / N
H.vulgare / 136462 / 21 / at / 5 / 26364 / 26373 / Y / rpoC2
at / 7 / 56573 / 56586 / N
ta / 6 / 15124 / 15135 / N
ta / 5 / 85456 / 85465 / N
ta / 5 / 132669 / 132678 / N
tc / 5 / 115218 / 115227 / N
aat / 4 / 25059 / 25070 / N
aat / 4 / 64188 / 64199 / N
taa / 4 / 50799 / 50810 / N
ttc / 4 / 65709 / 65720 / N
aaca / 3 / 106006 / 106017 / N
aacg / 3 / 99520 / 99531 / N
aaga / 3 / 72365 / 72376 / N
aata / 3 / 108235 / 108246 / N
agaa / 3 / 68964 / 68975 / N
taga / 3 / 116703 / 116714 / N
tcct / 3 / 43301 / 43312 / N
tcgt / 3 / 118602 / 118613 / N
tcta / 3 / 101420 / 101431 / N
ttca / 3 / 64665 / 64676 / N
ccata / 3 / 44175 / 44189 / N
O.sativa / 134525 / 16 / ag / 5 / 3223 / 3232 / N
at / 5 / 25478 / 25487 / Y / rpoC2
ct / 5 / 36589 / 36598 / N
tc / 5 / 113474 / 113483 / N
aat / 4 / 24183 / 24194 / N
tct / 4 / 80517 / 80528 / N
tat / 4 / 108670 / 108681 / N
taaa / 4 / 4152 / 4167 / N
cttt / 3 / 15220 / 15231 / N
gtag / 4 / 51285 / 51300 / N
aata / 3 / 55770 / 55781 / N
agaa / 3 / 68356 / 68367 / N
ttta / 3 / 71703 / 71714 / N
aacg / 3 / 98267 / 98278 / N
aata / 3 / 106600 / 106611 / N
tcgt / 3 / 116839 / 116850 / N
O.nivara / 134494 / 18 / ag / 5 / 3222 / 3231 / N
at / 5 / 25412 / 25421 / Y / rpoC2
ct / 5 / 36523 / 36532 / N
tc / 5 / 113440 / 113449 / N
aat / 4 / 24117 / 24128 / N
tct / 4 / 80469 / 80480 / N
tat / 4 / 108629 / 108640 / N
taaa / 4 / 4151 / 4166 / N
cttt / 3 / 15157 / 15168 / N
gtag / 4 / 51207 / 51222 / N
aata / 3 / 55705 / 55716 / N
agaa / 3 / 68286 / 68297 / N
ttta / 3 / 71634 / 71645 / N
aacg / 3 / 98218 / 98229 / N
aaca / 3 / 104470 / 104481 / N
aata / 3 / 106559 / 106570 / N
tcgt / 3 / 116809 / 116820 / N
aaagt / 3 / 57560 / 57574 / N
Sa.officinarum / 141182 / 16 / at / 5 / 28187 / 28196 / Y / rpoC2
ta / 5 / 67037 / 67046 / N
ta / 5 / 88487 / 88496 / N
tc / 5 / 117973 / 117982 / N
ta / 5 / 135735 / 135744 / N
ctt / 4 / 82941 / 82952 / N
aaag / 3 / 6174 / 6185 / N
tcct / 3 / 45521 / 45532 / N
gtag / 4 / 54633 / 54648 / N
agaa / 3 / 70894 / 70905 / N
aacg / 3 / 102837 / 102848 / N
attg / 3 / 108384 / 108395 / N
aata / 3 / 111094 / 111105 / N
atcc / 3 / 117870 / 117881 / N
tcgt / 3 / 121382 / 121393 / N
tataa / 3 / 21020 / 21034 / N
Sa.hybrid / 141182 / 16 / ta / 5 / 8930 / 8939 / N
tc / 5 / 38416 / 38425 / N
ta / 5 / 56179 / 56188 / N
at / 5 / 89814 / 89823 / Y / rpoC2
ta / 5 / 128664 / 128673 / N
ctt / 4 / 3384 / 3395 / N
aacg / 3 / 23280 / 23291 / N
attg / 3 / 28827 / 28838 / N
aata / 3 / 31537 / 31548 / N
atcc / 3 / 38313 / 38324 / N
tcgt / 3 / 41825 / 41836 / N
aaag / 3 / 67800 / 67811 / N
tcct / 3 / 107148 / 107159 / N
gtag / 4 / 116260 / 116275 / N
agaa / 3 / 132520 / 132531 / N
tataa / 3 / 82647 / 82661 / N
So..bicolor / 140754 / 16 / at / 5 / 28526 / 28535 / Y / rpoC2
ct / 5 / 53726 / 53735 / N
ta / 5 / 67248 / 67257 / N
ta / 5 / 88644 / 88653 / N
tc / 5 / 118078 / 118087 / N
ta / 5 / 135829 / 135838 / N
tta / 4 / 39073 / 39084 / N
ctt / 4 / 83099 / 83110 / N
tcct / 3 / 45723 / 45734 / N
gtag / 4 / 54852 / 54867 / N
agaa / 3 / 71090 / 71101 / N
aacg / 3 / 103001 / 103012 / N
attg / 3 / 108508 / 108519 / N
aata / 3 / 111197 / 111208 / N
atcc / 3 / 117975 / 117986 / N
tcgt / 3 / 121469 / 121480 / N
T.aestivum / 134545 / 21 / ag / 5 / 3235 / 3244 / N
tc / 5 / 14936 / 14945 / N
ta / 5 / 14959 / 14968 / N
at / 5 / 26191 / 26200 / Y / rpoC2
at / 6 / 41788 / 41799 / N
at / 5 / 56570 / 56579 / N
tc / 5 / 113634 / 113643 / N
aat / 5 / 24888 / 24902 / N
tat / 4 / 47730 / 47741 / N
ttc / 4 / 64988 / 64999 / N
tcct / 3 / 43164 / 43175 / N
ttca / 3 / 63925 / 63936 / N
ttct / 3 / 64227 / 64238 / N
agaa / 3 / 68245 / 68256 / N
aaga / 3 / 71631 / 71642 / N
aacg / 3 / 97881 / 97892 / N
aata / 3 / 106646 / 106657 / N
tcgt / 3 / 117001 / 117012 / N
ataga / 3 / 17184 / 17198 / N
ccata / 3 / 44040 / 44054 / N
tttat / 3 / 44785 / 44799 / N
Z.mays / 140384 / 19 / at / 5 / 27734 / 27743 / Y / rpoC2
at / 5 / 48185 / 48194 / N
ta / 6 / 66388 / 66399 / N
ta / 5 / 87788 / 87797 / N
tc / 5 / 117222 / 117231 / N
ta / 5 / 134940 / 134949 / N
tat / 5 / 20596 / 20610 / N
ctt / 4 / 82245 / 82256 / N
aaat / 3 / 18157 / 18168 / N
tcct / 3 / 44968 / 44979 / N
gtag / 4 / 54086 / 54101 / N
agaa / 3 / 70272 / 70283 / N
accg / 3 / 74068 / 74079 / N
aacg / 3 / 102116 / 102127 / N
attg / 3 / 107643 / 107654 / N
agat / 3 / 110050 / 110061 / N
aata / 3 / 110340 / 110351 / N
atcc / 3 / 117119 / 117130 / N
tcgt / 3 / 120609 / 120620 / N
Supplemental Figure 1. Alignment of a portion of the ndhK and matk genes illustrating a deletion withinH. vulgare, T. aestivum,A. stolonifera and both O. sativa chloroplast genes of ndhK and an insertion unique to S. bicolor in the matK gene.
ndhK
551 AGGATCGAACTCTATGTCAAAGTCAAAAGAAAAATAGATCTTTTACTACC S.hybrid
551 AGGATCGAACTCTATGTCAAAGTCAAAAGAAAAATAGATCTTTTACTACC S.officinarium
551 AGGATCGAACTCTATGTCAAAGTCAAAAGAAAAATAGATCTTTTACTACC S.bicolor
551 AGGATCGAACTCTATGTCAAAGTCAAAAGAAAAATAGATCTTTTACTACC Z.mays
551 AGGATCGAACTCTATCTCAAA------ATAAAAAAAGATGTTTTACTACC H.vulgare
551 AGGATCGAACTCGATCTCAAA------ATAAAAATAGATGTTTTACTACC A.stolonifera
551 AGGATCGAACTCTATCTCAAA------ATAAAAATAGATGTTTTACTACC T.aestivum
551 AGGATCGAACTCTATCTCAAA------AGAAAAATCGATGTTTTACTACC O.sativa
551 AGGATCGAACTCTATCTCAAA------AGAAAAATCGATGTTTTACTACC O.nivara
matK
1420 TTTTTTCTTTGATGTTCACCAAAAC------AACTCTTTTTTCTTTCAGT H.vulgare
1421 TTTTTTCTTTGATGTTCACCAAAAC------AAGCCTTTTTTCTTTCCGT A.stolonifera
1514 TTTTTTCTTTGATGTTCGCCAAAAC------AACTTACTTTTCTTTCCGG T.aestivum
1482 TTTTTTCTTTGATGTTCACCAAAAC------AATTCACTTTTCTTTCCAT S.officinarium
1514 TTTTTTCTTTGATGTTCACCAAAAC------AATTCACTTTTCTTTCCAT S.hybrid
1461 TTTTTTCTTTGATGTTCACCAAAACCAAAACAATTCACTTTTCTTTCCAT S.bicolor
1514 TTTTTTCTTTGATGTTCGCCAAAAC------AACTTACTTTTCTTTCCGT O.sativa
1514 TTTTTTCTTTGATGTTCGCCAAAAC------AACTTACTTTTCTTTCCGT O.nivara
1514 TTTTTTCTTTGATGTTCACCAAAAC------AATTCACTTTTCTTTCCAT Z.mays