Markers + reference

Paeonia

26 species · Paeoniaceae · Saxifragales

Back to catalogue

Species 26
Genome length 152–154 kb
Candidate markers 269
Primer pairs 110

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 313 0.0451 1.00 76.2 yes View details
rps16-trnQ-UUG LSC 1298 0.0182 0.99 73.0 yes View details
rpoC1 LSC 2751 0.0056 1.00 41.8 yes View details
trnD-GUC-trnY-GUA LSC 324 0.0152 1.00 60.7 yes View details
psbC-trnS-UGA LSC 216 0.0238 1.00 49.9 yes View details
rps4-trnT-UGU LSC 376 0.0205 0.99 56.8 yes View details
accD-psaI LSC 534 0.0158 1.00 55.9 yes View details
petA-psbJ LSC 832 0.0196 1.00 84.6 yes View details
rps18-rpl20 LSC 435 0.0166 0.99 52.4 yes View details
ycf1 IRb 1078 0.0016 1.00 31.3 no View details
ndhF SSC 2211 0.0091 1.00 47.1 yes View details
ndhF-trnL-UAG SSC 1019 0.0132 1.00 65.8 yes View details
ycf1 SSC 5403 0.0095 1.00 48.2 yes View details
petN-psbM LSC 838 0.0080 1.00 67.1 yes View details
trnR-UCU-atpA LSC 207 0.0230 0.96 64.8 yes View details
rbcL-accD LSC 688 0.0104 1.00 64.1 yes View details
trnK-UUU-rps16 LSC 723 0.0123 1.00 63.5 yes View details
psbE-petL LSC 1132 0.0116 1.00 63.0 yes View details
ndhC-trnV-UAC LSC 999 0.0096 1.00 62.3 yes View details
atpH-atpI LSC 1177 0.0099 1.00 61.0 yes View details
psbM-trnD-GUC LSC 1087 0.0091 1.00 59.6 yes View details
trnS-UGA-psbZ LSC 292 0.0132 0.99 59.3 yes View details
psaI-ycf4 LSC 425 0.0111 1.00 58.8 yes View details
Candidate markers include all hotspot labels marked in the diversity plot, listed in genomic order, plus the top 10 remaining regions by MarkerSeek score. Primer design is attempted for every listed region. Primer available: yes means at least one valid primer pair was found; no means no valid pair passed screening; NA means primer design was skipped.

Primer pairs

Showing the top 30 of 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CATGGTGGATTCACAACCCA CGAAGCTCCATCTACAAATGG 381–402 1.000 73.4
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG CGAAGCTCCATCTACAAATGG 354–375 1.000 73.1
trnH-GUG-psbA_p3 trnH-GUG-psbA GATTCACAACCCACTGCCTT CGAAGCTCCATCTACAAATGG 374–395 1.000 71.1
trnH-GUG-psbA_p4 trnH-GUG-psbA GCCTTGATCCACTTGGCTAC CGAAGCTCCATCTACAAATGG 359–380 1.000 69.2
trnH-GUG-psbA_p5 trnH-GUG-psbA ATTCACAACCCACTGCCTTG CGAAGCTCCATCTACAAATGG 373–394 1.000 68.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG GGGGTTTTACATAATTTTGCCT 799–965 0.923 45.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 ATCAGTCGCGGTCTTTCAAA GGGGTTTTACATAATTTTGCCT 874–1040 0.923 44.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGTCGCGGTCTTTCAAACTC GGGGTTTTACATAATTTTGCCT 871–1037 0.923 44.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 GTCGCGGTCTTTCAAACTCT GGGGTTTTACATAATTTTGCCT 870–1036 0.923 44.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 ATCAGTCGCGGTCTTTCAAA GGGGTTTTACATAATTTTGCCTT 874–1040 0.923 44.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TATGTCCTTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 1119–1398 1.000 91.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1109–1388 1.000 90.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TATGTCCTTCAAGTCGCACG TTCGGAGGTTCGAATCCTTC 1123–1402 1.000 86.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1113–1392 1.000 85.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 1101–1380 1.000 85.0
trnR-UCU-atpA_p1 trnR-UCU-atpA ATGAAAGGCGTCCATTGTCT TCAGGAACAGATGGAACGTT 315–336 1.000 75.2
trnR-UCU-atpA_p2 trnR-UCU-atpA ATGAAAGGCGTCCATTGTCT TTCAGGAACAGATGGAACGT 316–337 1.000 75.1
trnR-UCU-atpA_p3 trnR-UCU-atpA ATGAAAGGCGTCCATTGTCT CGACTAAGACATTCACCGAGG 364–385 1.000 74.9
trnR-UCU-atpA_p4 trnR-UCU-atpA ATGAAAGGCGTCCATTGTCT CGGAAGCCCTTTTGAAAGAAG 340–361 1.000 74.3
trnR-UCU-atpA_p5 trnR-UCU-atpA ATGAAAGGCGTCCATTGTCT CGGAAGCCCTTTTGAAAGAA 340–361 1.000 72.9
atpH-atpI_p1 atpH-atpI AACGGAAGCAGCAGAAATCA CCGGTCATGTTCCTTGGATT 1306–1320 1.000 82.2
atpH-atpI_p2 atpH-atpI GCCAATCCAGCAGCAATAAC CCGGTCATGTTCCTTGGATT 1323–1337 1.000 81.3
atpH-atpI_p3 atpH-atpI TCCAGCAGCAATAACGGAAG CCGGTCATGTTCCTTGGATT 1318–1332 1.000 80.9
atpH-atpI_p4 atpH-atpI AACGGAAGCAGCAGAAATCA TACCGGTCATGTTCCTTGGA 1308–1322 1.000 80.4
atpH-atpI_p5 atpH-atpI CACTCCAGGCCCAATAGAAG CCGGTCATGTTCCTTGGATT 1354–1368 1.000 80.2
rpoC1_p1 rpoC1 GCTCGAATTCATACCATATCA TGCTCGTTCGAGAATTACGA 2924–2939 1.000 42.3
rpoC1_p2 rpoC1 GCTCGAATTCATACCATATCA TTGCTCGTTCGAGAATTACGA 2925–2940 1.000 42.3
rpoC1_p3 rpoC1 GCTCGAATTCATACCATATCAT TGCTCGTTCGAGAATTACGA 2924–2939 1.000 42.3
rpoC1_p4 rpoC1 GCTCGAATTCATACCATATCA TGCTCGTTCGAGAATTACGAT 2924–2939 1.000 42.3
rpoC1_p5 rpoC1 GCTCGAATTCATACCATATCA TACGATCTTTGGCTCTGGAG 2909–2924 1.000 42.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (26)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Paeonia anomala MT210549.1 152745 View on NCBI ↗
Paeonia brownii NC_037880.1 152228 View on NCBI ↗
Paeonia decomposita NC_039425.1 152601 View on NCBI ↗
Paeonia delavayi NC_035718.1 154405 View on NCBI ↗
Paeonia delavayi var. angustiloba OR187761.1 152748 View on NCBI ↗
Paeonia emodi MT210548.1 152828 View on NCBI ↗
Paeonia intermedia NC_071221.1 152766 View on NCBI ↗
Paeonia lactiflora NC_040983.1 152747 View on NCBI ↗
Paeonia lactiflora x Paeonia lutea NC_088565.1 152731 View on NCBI ↗
Paeonia lactiflora x Paeonia peregrina NC_088564.1 152731 View on NCBI ↗
Paeonia lactiflora x Paeonia x lemoinei NC_072909.1 152958 View on NCBI ↗
Paeonia ludlowii NC_035623.1 152687 View on NCBI ↗
Paeonia mairei NC_050998.1 152731 View on NCBI ↗
Paeonia mlokosewitschii NC_071855.1 152785 View on NCBI ↗
Paeonia obovata NC_026076.1 152698 View on NCBI ↗
Paeonia obovata subsp. willmottiae NC_049161.1 152713 View on NCBI ↗
Paeonia obovata var. japonica MT821944.1 152731 View on NCBI ↗
Paeonia ostii NC_036834.1 152153 View on NCBI ↗
Paeonia rockii NC_037772.1 152821 View on NCBI ↗
Paeonia rockii subsp. taibaishanica MW192444.1 153368 View on NCBI ↗
Paeonia sinjiangensis NC_071854.1 152760 View on NCBI ↗
Paeonia sterniana NC_071222.1 152621 View on NCBI ↗
Paeonia suffruticosa NC_037879.1 153119 View on NCBI ↗
Paeonia suffruticosa x Paeonia lactiflora NC_088566.1 152607 View on NCBI ↗
Paeonia veitchii NC_032401.1 152682 View on NCBI ↗
Paeonia x lemoinei PP476258.2 152519 View on NCBI ↗