Markers + reference

Ligularia

9 species · Asteraceae · Asterales

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Species 9
Genome length 151–151 kb
Candidate markers 265
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnC-GCA-petN LSC 810 0.0089 1.00 58.2 yes View details
trnR-UCU-trnG-UCC LSC 213 0.0078 1.00 38.3 yes View details
trnT-UGU-trnL-UAA LSC 622 0.0034 1.00 47.2 yes View details
rpl16 LSC 1436 0.0027 1.00 40.5 yes View details
ycf1 IRb 597 0.0004 1.00 41.6 no View details
rpl32-trnL-UAG SSC 792 0.0051 1.00 47.1 yes View details
ndhG-ndhI SSC 376 0.0056 1.00 38.3 yes View details
ndhA SSC 2157 0.0023 1.00 43.1 yes View details
ycf1 SSC 5094 0.0023 1.00 40.2 yes View details
atpF-atpA LSC 76 0.0124 0.99 54.1 yes View details
ndhC-trnV-UAC LSC 755 0.0032 1.00 53.9 yes View details
rpoC1 LSC 2822 0.0009 1.00 51.1 yes View details
clpP LSC 2029 0.0009 1.00 51.0 yes View details
atpB-rbcL LSC 716 0.0029 1.00 50.5 yes View details
accD-psaI LSC 666 0.0034 1.00 48.5 yes View details
trnM-CAU-atpE LSC 203 0.0107 1.00 48.3 yes View details
petN-psbM LSC 500 0.0036 1.00 48.2 yes View details
trnS-GCU-trnC-GCA LSC 735 0.0015 1.00 47.9 yes View details
atpI-atpH LSC 1095 0.0011 1.00 47.9 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnS-GCU-trnC-GCA_p1 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA CCGGATTTGAACTGGGGAAA 886–890 1.000 78.7
trnS-GCU-trnC-GCA_p2 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA AAAAGGATTTGCAGTCCCCC 868–872 1.000 76.5
trnS-GCU-trnC-GCA_p3 trnS-GCU-trnC-GCA CTTTCGTCCACTCAGCCATC CCGGATTTGAACTGGGGAAA 822–826 1.000 74.8
trnS-GCU-trnC-GCA_p4 trnS-GCU-trnC-GCA AACGGAAAGAGAGGGATTCG CCGGATTTGAACTGGGGAAA 887–891 1.000 74.5
trnS-GCU-trnC-GCA_p5 trnS-GCU-trnC-GCA CTTTCGTCCACTCAGCCATC AAAAGGATTTGCAGTCCCCC 804–808 1.000 72.7
trnC-GCA-petN_p1 trnC-GCA-petN GTTGTGTATCGTTTTGGCGG AGCCCAAGCGAGACTTACTA 916–928 1.000 82.2
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 859–871 1.000 82.1
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 877–889 1.000 79.8
trnC-GCA-petN_p4 trnC-GCA-petN TGTTGTGTATCGTTTTGGCG AGCCCAAGCGAGACTTACTA 917–929 1.000 77.1
trnC-GCA-petN_p5 trnC-GCA-petN GTTGTGTATCGTTTTGGCGG GCCCAAGCGAGACTTACTAT 915–927 1.000 76.3
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTT 657–662 1.000 60.6
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTTT 657–662 1.000 58.9
petN-psbM_p3 petN-psbM ATAGTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATTT 658–663 1.000 54.7
petN-psbM_p4 petN-psbM CTCGCTTGGGCTGCTTTAAT TGCTACTGCACTGTTCATTT 649–654 1.000 54.6
petN-psbM_p5 petN-psbM TGGGCTGCTTTAATGGTAGTC TGCTACTGCACTGTTCATTT 643–648 1.000 53.8
rpoC1_p1 rpoC1 TCTGAGAAGACTTTCCAGCT GTACCTCCATATTGCGCTGA 2966–2984 1.000 58.7
rpoC1_p2 rpoC1 TCTGAGAAGACTTTCCAGCT TCAGTACCTCCATATTGCGC 2969–2987 1.000 58.7
rpoC1_p3 rpoC1 TCTGAGAAGACTTTCCAGCT AGTACCTCCATATTGCGCTG 2967–2985 1.000 58.7
rpoC1_p4 rpoC1 TCTGAGAAGACTTTCCAGCT CAGTACCTCCATATTGCGCT 2968–2986 1.000 58.7
rpoC1_p5 rpoC1 TTCGGTTGTTCGTTCGAGAA GGTTTGAGTCAGTGATTGGA 2989–3000 0.667 43.7
atpI-atpH_p1 atpI-atpH TTTTTGCAACTTTAGCCGCG ATAACGGAAGCGGCAGAAAT 1180–1206 1.000 76.2
atpI-atpH_p2 atpI-atpH TTTTTGCAACTTTAGCCGCG TACCTTGACCAACTCCAGGT 1236–1262 1.000 75.6
atpI-atpH_p3 atpI-atpH TTTTTGCAACTTTAGCCGCG AGCCAATCCAGCAGCAATAA 1196–1222 1.000 75.3
atpI-atpH_p4 atpI-atpH TCAGTGGTTCCTATCCCTGT ATAACGGAAGCGGCAGAAAT 1241–1267 1.000 75.2
atpI-atpH_p5 atpI-atpH TTTTTGCAACTTTAGCCGCG AATAACGGAAGCGGCAGAAA 1181–1207 1.000 75.1
atpF-atpA_p1 atpF-atpA ATATTGGCATATTGGGGGCG GTCGGCTTGAATGGTTACCA 134–140 1.000 81.4
atpF-atpA_p2 atpF-atpA ATATTGGCATATTGGGGGCG ATTTCGTCGGCTTGAATGGT 139–145 1.000 81.3
atpF-atpA_p3 atpF-atpA ATATTGGCATATTGGGGGCG TCGTCGGCTTGAATGGTTAC 136–142 1.000 80.6
atpF-atpA_p4 atpF-atpA ATATTGGCATATTGGGGGCG CAATGCCGTCACCTACTTGA 231–237 1.000 80.5
atpF-atpA_p5 atpF-atpA ATATTGGCATATTGGGGGCG GCTCAATACGTTCGCGGATA 168–174 1.000 80.2

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
Ligularia biceps OK448480.1 151153 View on NCBI ↗
Ligularia fischeri NC_039352.1 151193 View on NCBI ↗
Ligularia hodgsonii NC_039381.1 151136 View on NCBI ↗
Ligularia intermedia NC_039382.1 151152 View on NCBI ↗
Ligularia jaluensis NC_039383.1 151148 View on NCBI ↗
Ligularia mongolica NC_039384.1 151118 View on NCBI ↗
Ligularia stenocephala NC_056964.1 151158 View on NCBI ↗
Ligularia veitchiana NC_039385.1 151253 View on NCBI ↗
Ligularia virgaurea NC_052864.1 151185 View on NCBI ↗