Markers + reference

Physalis

15 species · Solanaceae · Solanales

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Species 15
Genome length 157–157 kb
Candidate markers 280
Primer pairs 70

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 10 remaining regions by MarkerSeek score (out of 280 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 440 0.0287 1.00 73.6 yes View details
trnL-UAA-trnF-GAA LSC 637 0.0322 1.00 81.9 yes View details
rpl2 LSC 1491 0.0069 1.00 50.5 yes View details
ycf1 SSC 1137 0.0013 1.00 42.2 no View details
ycf1 SSC 5727 0.0091 1.00 54.4 yes View details
rpl23-trnH-GUG LSC 1703 0.0057 1.00 54.3 no View details
petA-psbJ LSC 1071 0.0070 1.00 66.3 yes View details
rpoB-trnC-GCA LSC 1322 0.0026 1.00 65.0 yes View details
atpH-atpI LSC 1231 0.0038 0.99 63.6 yes View details
ndhF-rpl32 SSC 786 0.0034 1.00 58.9 yes View details
rpl32-trnL-UAG SSC 976 0.0039 0.96 58.9 yes View details
rps19-rpl2 LSC 71 0.0131 1.00 57.4 yes View details
clpP LSC 2004 0.0039 1.00 56.4 yes View details
ndhC-trnV-UAC LSC 1135 0.0028 0.98 55.9 yes View details
petD-rpoA LSC 172 0.0141 1.00 54.7 yes View details
infA-rps8 LSC 117 0.0065 1.00 54.7 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCGAAGCTCCATCTACAAATGG 480–512 0.867 67.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TCGAAGCTCCATCTACAAATGG 494–526 0.867 67.2
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TCGAAGCTCCATCTACAAATGG 493–525 0.867 67.2
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TCGAAGCTCCATCTACAAATGG 495–527 0.867 67.2
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CGAAGCTCCATCTACAAATGG 479–511 0.867 67.2
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TACCTGTCATGCTCCTTGGA 1346–1387 1.000 83.0
atpH-atpI_p2 atpH-atpI TACCCTCTACAGCTTGACCC TACCTGTCATGCTCCTTGGA 1429–1470 1.000 81.9
atpH-atpI_p3 atpH-atpI GCGATACCCTCTACAGCTTG TACCTGTCATGCTCCTTGGA 1433–1474 1.000 81.9
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA TACCTGTCATGCTCCTTGGA 1347–1388 1.000 81.8
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC TACCTGTCATGCTCCTTGGA 1361–1402 1.000 81.5
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CTCATTTCCATCCCCGAGC CCGGATTTGAACTGGGGAAA 1346–1407 1.000 75.9
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ATTCCCTCATTTCCATCCCC CCGGATTTGAACTGGGGAAA 1351–1412 1.000 75.3
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCATTTCCATCCCCGAGCAT CCGGATTTGAACTGGGGAAA 1345–1406 1.000 74.7
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CTCATTTCCATCCCCGAGC AGTCCTCTGCCTTACCACTC 1315–1376 1.000 73.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CATTTCCATCCCCGAGCAT CCGGATTTGAACTGGGGAAA 1344–1405 1.000 72.6
trnL-UAA-trnF-GAA_p1 trnL-UAA-trnF-GAA CAATGCCGGCAACAATGAAA TTTGAACTGGTGACACGAGG 692–842 1.000 88.9
trnL-UAA-trnF-GAA_p2 trnL-UAA-trnF-GAA CAATGCCGGCAACAATGAAA AATCATGTGCCAGGAACCAG 713–863 1.000 87.9
trnL-UAA-trnF-GAA_p3 trnL-UAA-trnF-GAA AATCGTGAGGGTTCAAGTCC TTTGAACTGGTGACACGAGG 639–789 1.000 87.2
trnL-UAA-trnF-GAA_p4 trnL-UAA-trnF-GAA CAATGCCGGCAACAATGAAA GTGCCAGGAACCAGATTTGA 707–857 0.933 85.2
trnL-UAA-trnF-GAA_p5 trnL-UAA-trnF-GAA CAATGCCGGCAACAATGAAA CATGTGCCAGGAACCAGATT 710–860 0.933 84.7
ndhC-trnV-UAC_p1 ndhC-trnV-UAC CTCCGGAAATGAAAAATGCCA AGAAGGTCTACGGTTCGAGT 1206–1267 1.000 70.2
ndhC-trnV-UAC_p2 ndhC-trnV-UAC ACTCCGGAAATGAAAAATGCC AGAAGGTCTACGGTTCGAGT 1207–1268 1.000 70.1
ndhC-trnV-UAC_p3 ndhC-trnV-UAC TCCGGAAATGAAAAATGCCA AGAAGGTCTACGGTTCGAGT 1205–1266 1.000 68.5
ndhC-trnV-UAC_p4 ndhC-trnV-UAC CTCCGGAAATGAAAAATGCCA GAAGGTCTACGGTTCGAGTC 1205–1266 1.000 67.4
ndhC-trnV-UAC_p5 ndhC-trnV-UAC ACTCCGGAAATGAAAAATGCC GAAGGTCTACGGTTCGAGTC 1206–1267 1.000 67.4
petA-psbJ_p1 petA-psbJ GAGAAGGTTCAATTGGCCGA GGTTCATATTCCGGGTTGGG 872–1153 1.000 82.4
petA-psbJ_p2 petA-psbJ TCGAGAAGGTTCAATTGGCC GGTTCATATTCCGGGTTGGG 874–1155 1.000 82.4
petA-psbJ_p3 petA-psbJ AGAAGGTTCAATTGGCCGAA GGTTCATATTCCGGGTTGGG 871–1152 1.000 81.5
petA-psbJ_p4 petA-psbJ GAGAAGGTTCAATTGGCCGA CATATTCCGGGTTGGGTTCA 868–1149 1.000 81.5
petA-psbJ_p5 petA-psbJ GAGAAGGTTCAATTGGCCGA TGGTTCATATTCCGGGTTGG 873–1154 1.000 81.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (15)

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

Species Accession Length (bp) Link
Physalis ampla OR296714.1 156821 View on NCBI ↗
Physalis angulata NC_039457.1 156706 View on NCBI ↗
Physalis angulata var. villosa OM257167.1 156898 View on NCBI ↗
Physalis chenopodiifolia MN508249.2 156900 View on NCBI ↗
Physalis cinerascens OR296712.1 156663 View on NCBI ↗
Physalis cordata ON018728.1 157000 View on NCBI ↗
Physalis gracilis OR296713.1 156731 View on NCBI ↗
Physalis grisea PP952506.1 157007 View on NCBI ↗
Physalis ixocarpa NC_085278.1 156871 View on NCBI ↗
Physalis longifolia var. subglabrata OP748222.1 156735 View on NCBI ↗
Physalis minima NC_048515.1 156692 View on NCBI ↗
Physalis peruviana NC_026570.1 156706 View on NCBI ↗
Physalis philadelphica NC_070364.1 156856 View on NCBI ↗
Physalis pruinosa NC_039458.1 156706 View on NCBI ↗
Physalis pubescens NC_048514.1 157007 View on NCBI ↗