Markers + reference

Ligustrum

13 species · Oleaceae · Lamiales

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Species 13
Genome length 162–167 kb
Candidate markers 274
Primer pairs 65

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 7 remaining regions by MarkerSeek score (out of 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rbcL-trnT-GGU LSC 943 0.0960 0.54 66.2 yes View details
trnT-GGU-accD LSC 2513 0.1451 0.32 62.4 yes View details
accD LSC 2184 0.0955 0.83 72.4 yes View details
clpP1 LSC 2111 0.0432 1.00 74.2 yes View details
ycf1 IRb 5859 0.0247 0.95 59.5 yes View details
ycf1 IRa 5859 0.0250 0.95 59.7 yes View details
rpl22-rps19 LSC 64 0.0520 1.00 68.7 yes View details
rps2-rpoC2 LSC 199 0.0254 1.00 63.6 yes View details
psaA-pafI LSC 708 0.0107 1.00 60.8 yes View details
psaI-pafII LSC 452 0.0133 0.99 57.6 yes View details
trnH-GUG-psbA LSC 429 0.0178 0.99 57.1 yes View details
psbI-trnS-GCU LSC 130 0.0108 0.97 57.1 yes View details
atpB-rbcL LSC 798 0.0177 1.00 57.1 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 65 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CCGTGCTAACCTTGGTATGG 543–555 1.000 82.0
trnH-GUG-psbA_p2 trnH-GUG-psbA TTAGTTATGGGCGAACGACG CCGTGCTAACCTTGGTATGG 598–610 1.000 81.9
trnH-GUG-psbA_p3 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC CCGTGCTAACCTTGGTATGG 544–556 1.000 81.8
trnH-GUG-psbA_p4 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT ACCGTGCTAACCTTGGTATG 544–556 1.000 81.6
trnH-GUG-psbA_p5 trnH-GUG-psbA TTAGTTATGGGCGAACGACG ACCGTGCTAACCTTGGTATG 599–611 1.000 81.4
psbI-trnS-GCU_p1 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA TGGACTAAAGCGTCGGATTG 221–227 0.923 74.1
psbI-trnS-GCU_p2 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA GTGGACTAAAGCGTCGGATT 222–228 0.923 74.0
psbI-trnS-GCU_p3 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA ATTGGGAGAGATGGCTGAGT 240–246 0.923 72.9
psbI-trnS-GCU_p4 psbI-trnS-GCU CGTAATCCTGGACGTGAAGAA TGGACTAAAGCGTCGGATTG 221–227 0.923 71.7
psbI-trnS-GCU_p5 psbI-trnS-GCU CGTAATCCTGGACGTGAAGAA GTGGACTAAAGCGTCGGATT 222–228 0.923 71.7
rps2-rpoC2_p1 rps2-rpoC2 GCCAAAATGAACTCCTGCCT TCCATGATACATCAGAACAATCA 304–321 1.000 47.4
rps2-rpoC2_p2 rps2-rpoC2 CCATGGCCAAAATGAACTCC TCCATGATACATCAGAACAATCA 309–326 1.000 47.3
rps2-rpoC2_p3 rps2-rpoC2 TTGCCGAGATATAAGGTGCC TCCATGATACATCAGAACAATCA 353–370 1.000 46.7
rps2-rpoC2_p4 rps2-rpoC2 TGCCGAGATATAAGGTGCCA TCCATGATACATCAGAACAATCA 352–369 1.000 46.7
rps2-rpoC2_p5 rps2-rpoC2 GCCGAGATATAAGGTGCCAT TCCATGATACATCAGAACAATCA 351–368 1.000 46.7
psaA-pafI_p1 psaA-pafI GCCCATTCCTCGAAAGAAGT GGAAACAGGCTATAGCGCTT 861–874 1.000 82.7
psaA-pafI_p2 psaA-pafI GCCCATTCCTCGAAAGAAGT TGGTTTGATCAAGCAGCTGA 886–899 1.000 80.7
psaA-pafI_p3 psaA-pafI GCCCATTCCTCGAAAGAAGT AGGCTATAGCGCTTACTCCT 855–868 1.000 80.7
psaA-pafI_p4 psaA-pafI GCCCATTCCTCGAAAGAAGT TTGGAAACAGGCTATAGCGC 863–876 1.000 80.3
psaA-pafI_p5 psaA-pafI GCCCATTCCTCGAAAGAAGT GCTATAGCGCTTACTCCTGG 853–866 1.000 80.2
atpB-rbcL_p1 atpB-rbcL GGAAACCCCAGAACCAGAAG AACACCCGCTTTGAATCCAA 809–900 1.000 84.3
atpB-rbcL_p2 atpB-rbcL GGAAACCCCAGAACCAGAAG TAACACCCGCTTTGAATCCA 810–901 1.000 82.1
atpB-rbcL_p3 atpB-rbcL ACCCCAGAACCAGAAGTAGT AACACCCGCTTTGAATCCAA 805–896 1.000 81.6
atpB-rbcL_p4 atpB-rbcL GGAAACCCCAGAACCAGAAG CCCGCTTTGAATCCAACACT 805–896 1.000 80.7
atpB-rbcL_p5 atpB-rbcL TTTTTCAAGCGTGGAAACCC AACACCCGCTTTGAATCCAA 821–912 1.000 80.2
rbcL-trnT-GGU_p1 rbcL-trnT-GGU ACTACAGTTCGGTGGAGGAA GTGGTAGAGTAACGCCATGG 1239 0.231 48.7
rbcL-trnT-GGU_p2 rbcL-trnT-GGU GGCTTCAGGGGGTATTCATG GTGGTAGAGTAACGCCATGG 1305 0.231 48.6
rbcL-trnT-GGU_p3 rbcL-trnT-GGU TTGAATGCTACTGCGGGTAC GTGGTAGAGTAACGCCATGG 1718 0.231 48.6
rbcL-trnT-GGU_p4 rbcL-trnT-GGU ACTACAGTTCGGTGGAGGAA TCAGTGGTAGAGTAACGCCA 1242 0.231 48.5
rbcL-trnT-GGU_p5 rbcL-trnT-GGU GGCTTCAGGGGGTATTCATG TCAGTGGTAGAGTAACGCCA 1308 0.231 48.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (13)

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

Species Accession Length (bp) Link
Ligustrum foliosum NC_071945.1 165731 View on NCBI ↗
Ligustrum gracile NC_042425.1 163110 View on NCBI ↗
Ligustrum henryi PP848118.1 163751 View on NCBI ↗
Ligustrum ibota OM640183.1 163268 View on NCBI ↗
Ligustrum leucanthum OM640181.1 163287 View on NCBI ↗
Ligustrum obtusifolium NC_071249.1 163087 View on NCBI ↗
Ligustrum ovalifolium NC_056242.1 166800 View on NCBI ↗
Ligustrum quihoui NC_057246.1 163575 View on NCBI ↗
Ligustrum quihoui var. latifolium OM640188.1 163099 View on NCBI ↗
Ligustrum sempervirens OM640189.1 162167 View on NCBI ↗
Ligustrum sinense NC_071248.1 162272 View on NCBI ↗
Ligustrum vulgare NC_042274.1 162185 View on NCBI ↗
Ligustrum x vicaryi NC_071250.1 166268 View on NCBI ↗