Markers + reference

Codonopsis

9 species · Campanulaceae · Asterales

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Species 9
Genome length 169–172 kb
Candidate markers 272
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpoC2-atpH LSC 1135 0.2216 0.99 83.6 yes View details
rps2-clpP LSC 1482 0.2586 0.81 76.8 yes View details
clpP LSC 2010 0.0367 1.00 73.9 yes View details
rpl36-rps8 LSC 777 0.0703 0.99 85.3 yes View details
rpl2-trnI-CAU IRb 1090 0.0300 0.96 76.1 yes View details
ycf1 IRb 6981 0.0191 0.99 59.5 no View details
ycf1 IRa 6981 0.0205 1.00 60.5 yes View details
trnI-CAU-rpl2 IRa 1090 0.0298 0.96 76.0 yes View details
trnA-UGC-trnI-GAU IRa 144 0.0602 0.73 79.6 yes View details
trnI-GAU-trnA-UGC IRb 144 0.0599 0.69 75.0 yes View details
ndhF-rpl32 SSC 973 0.0313 0.94 74.5 yes View details
trnT-GGU-trnM-CAU LSC 429 0.0355 0.99 74.4 yes View details
psaJ-rpl33 LSC 448 0.0339 1.00 73.9 yes View details
trnV-UAC-trnM-CAU LSC 1317 0.0229 1.00 73.4 yes View details
rps16-trnT-UGU LSC 1254 0.0280 0.95 73.1 yes View details
trnW-CAA-trnP-UGG LSC 177 0.0381 1.00 73.0 yes View details
rpl32-trnL-UAG SSC 403 0.0345 0.96 71.8 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnT-UGU_p1 rps16-trnT-UGU CGGTGCTTTTTACCACATCG CTAACCACGGAGCTAAGCAG 1275–1446 1.000 87.1
rps16-trnT-UGU_p2 rps16-trnT-UGU CGGTGCTTTTTACCACATCG CTCTAACCACGGAGCTAAGC 1277–1448 1.000 86.0
rps16-trnT-UGU_p3 rps16-trnT-UGU CGGGATCGAACATCAATTGC CTAACCACGGAGCTAAGCAG 1314–1485 1.000 85.7
rps16-trnT-UGU_p4 rps16-trnT-UGU ATAAGTCGCACGGTGCTTTT CTAACCACGGAGCTAAGCAG 1285–1456 1.000 85.1
rps16-trnT-UGU_p5 rps16-trnT-UGU CGGGATCGAACATCAATTGC CTCTAACCACGGAGCTAAGC 1316–1487 1.000 84.6
trnT-GGU-trnM-CAU_p1 trnT-GGU-trnM-CAU ACGCCTTACCATGGTGTTAC TCGGTCAACAAACTGAGCAA 1143–1180 1.000 88.0
trnT-GGU-trnM-CAU_p2 trnT-GGU-trnM-CAU AACAGAAGGGAGGAGGTCAA TCGGTCAACAAACTGAGCAA 1455–1492 1.000 86.5
trnT-GGU-trnM-CAU_p3 trnT-GGU-trnM-CAU CTTGCGGAGTCCAAAGAACT TCGGTCAACAAACTGAGCAA 1490–1512 0.444 58.9
trnT-GGU-trnM-CAU_p4 trnT-GGU-trnM-CAU GCGGAGTCCAAAGAACTGAA TCGGTCAACAAACTGAGCAA 1487–1509 0.444 58.9
trnT-GGU-trnM-CAU_p5 trnT-GGU-trnM-CAU TCTTGCGGAGTCCAAAGAAC TCGGTCAACAAACTGAGCAA 1491–1513 0.444 58.8
rpoC2-atpH_p1 rpoC2-atpH TTTTTCACCCGGAGAACTGG CTCGCGATACCTTCTACAGC 1678–2852 1.000 91.5
rpoC2-atpH_p2 rpoC2-atpH GAACTGGTTGGATTGTTGCG CTCGCGATACCTTCTACAGC 1665–2839 1.000 91.3
rpoC2-atpH_p3 rpoC2-atpH TTTTTCACCCGGAGAACTGG GATTACGAAGGGGAAGGCTG 1983–2833 0.889 87.0
rpoC2-atpH_p4 rpoC2-atpH ACGCAAGGTCTTCCAAAAGT CTCGCGATACCTTCTACAGC 1977–2827 0.889 86.8
rpoC2-atpH_p5 rpoC2-atpH GAACTGGTTGGATTGTTGCG GATTACGAAGGGGAAGGCTG 1970–2820 0.889 86.8
trnV-UAC-trnM-CAU_p1 trnV-UAC-trnM-CAU TACCCACTGAGCTATAGCCC GTATTGCTTTCATACGGCGG 1376–2417 1.000 81.1
trnV-UAC-trnM-CAU_p2 trnV-UAC-trnM-CAU AGTAAGACGGGGAAAGGTGA GTATTGCTTTCATACGGCGG 1459–2500 1.000 80.8
trnV-UAC-trnM-CAU_p3 trnV-UAC-trnM-CAU AAGGGCCCCTTTGAAAAACA GTATTGCTTTCATACGGCGG 1422–2463 1.000 80.1
trnV-UAC-trnM-CAU_p4 trnV-UAC-trnM-CAU AGGGCCCCTTTGAAAAACAT GTATTGCTTTCATACGGCGG 1421–2462 1.000 80.1
trnV-UAC-trnM-CAU_p5 trnV-UAC-trnM-CAU TGAAGGGCCCCTTTGAAAAA GTATTGCTTTCATACGGCGG 1424–2465 1.000 79.6
trnW-CAA-trnP-UGG_p1 trnW-CAA-trnP-UGG GTTTTGGAGACCCACGTTCT GGGTACAAAATGTCACGGGT 251–266 1.000 86.7
trnW-CAA-trnP-UGG_p2 trnW-CAA-trnP-UGG TGCCGAACTGAACTAAGAGC ATTGAAGGGATGTAGCGCAG 272–287 1.000 86.2
trnW-CAA-trnP-UGG_p3 trnW-CAA-trnP-UGG GTTTTGGAGACCCACGTTCT ATTGAAGGGATGTAGCGCAG 291–306 1.000 86.1
trnW-CAA-trnP-UGG_p4 trnW-CAA-trnP-UGG TTTTGGAGACCCACGTTCTG ATTGAAGGGATGTAGCGCAG 290–305 1.000 86.1
trnW-CAA-trnP-UGG_p5 trnW-CAA-trnP-UGG ACCTACGACATCGGGTTTTG ATTGAAGGGATGTAGCGCAG 305–320 1.000 85.4
psaJ-rpl33_p1 psaJ-rpl33 TTTTGGGAAATGCTCGGGAA TAACACCCTTTCGCACACAA 842–932 0.778 75.5
psaJ-rpl33_p2 psaJ-rpl33 TTTTGGGAAATGCTCGGGAA TTAACACCCTTTCGCACACA 843–933 0.667 69.5
psaJ-rpl33_p3 psaJ-rpl33 TTTTTGGGAAATGCTCGGGA TAACACCCTTTCGCACACAA 843–933 0.667 69.5
psaJ-rpl33_p4 psaJ-rpl33 TTTTTGGGAAATGCTCGGGA TTAACACCCTTTCGCACACA 844–934 0.667 69.5
psaJ-rpl33_p5 psaJ-rpl33 TCGATTTCACCGAATCCACC TAACACCCTTTCGCACACAA 1178–1268 0.444 57.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

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

Species Accession Length (bp) Link
Codonopsis bhutanica NC_063738.1 169718 View on NCBI ↗
Codonopsis canescens PV364364.1 170726 View on NCBI ↗
Codonopsis lanceolata MH251613.1 170075 View on NCBI ↗
Codonopsis minima NC_036311.1 169321 View on NCBI ↗
Codonopsis subglobosa PX582132.1 171644 View on NCBI ↗
Codonopsis thalictrifolia PV364366.1 171564 View on NCBI ↗
Codonopsis tsinlingensis NC_056284.1 170253 View on NCBI ↗
Codonopsis tubulosa PX582131.1 171802 View on NCBI ↗
Codonopsis viridiflora PV364367.1 171306 View on NCBI ↗