Markers + reference

Passiflora

21 species · Passifloraceae · Malpighiales

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Species 21
Genome length 136–152 kb
Candidate markers 267
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 9 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpoB-clpP LSC 1018 0.0441 0.93 76.0 yes View details
clpP LSC 699 0.0964 1.00 81.1 yes View details
accD LSC 2457 0.1354 0.92 78.7 yes View details
trnC-GCA-psbB LSC 872 0.0514 0.98 86.0 yes View details
ycf1 IRb 4752 0.0184 0.78 54.9 yes View details
ycf1 IRa 4752 0.0182 0.78 54.6 no View details
psbA-trnH-GUG LSC 264 0.0524 1.00 85.8 yes View details
ycf3-psaA LSC 977 0.0229 1.00 85.6 yes View details
trnY-GUA-trnD-GUC LSC 511 0.0278 0.98 83.9 yes View details
trnT-GGU-trnE-UUC LSC 825 0.0423 0.98 82.7 yes View details
rpl32-trnL-UAG SSC 752 0.0327 1.00 79.8 yes View details
ndhF-rpl32 SSC 529 0.0327 1.00 79.7 yes View details
psbM-petN LSC 1386 0.0272 0.99 77.8 yes View details
rps19-psbA LSC 383 0.0473 0.98 77.8 no View details
rps8-rpl14 LSC 217 0.0326 1.00 77.7 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 65 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-trnH-GUG_p1 psbA-trnH-GUG CCTCTAGACCTAGCTGCTGT CAATCCACCGCCTTTATCCA 296–354 1.000 91.1
psbA-trnH-GUG_p2 psbA-trnH-GUG CCTCTAGACCTAGCTGCTGT AATCCACCGCCTTTATCCAC 295–353 1.000 91.1
psbA-trnH-GUG_p3 psbA-trnH-GUG CCTCTAGACCTAGCTGCTGT ACAATCCACCGCCTTTATCC 297–355 1.000 91.1
psbA-trnH-GUG_p4 psbA-trnH-GUG TTCCCTCTAGACCTAGCTGC CAATCCACCGCCTTTATCCA 299–357 1.000 91.0
psbA-trnH-GUG_p5 psbA-trnH-GUG TTCCCTCTAGACCTAGCTGC AATCCACCGCCTTTATCCAC 298–356 1.000 91.0
rpoB-clpP_p1 rpoB-clpP CACGAGCCCATATTCTTGCT GGCCAGGATAAAAGATGCCA 1817–1892 0.810 82.3
rpoB-clpP_p2 rpoB-clpP CACGAGCCCATATTCTTGCT TGTCATCGTTATCGTCGTCG 1959–2034 0.762 80.7
rpoB-clpP_p3 rpoB-clpP AGAGGTTCCCAGGGAATTCA TGGCGATGTCTTCCTGAATG 1850–1925 0.714 79.4
rpoB-clpP_p4 rpoB-clpP CACGAGCCCATATTCTTGCT TGGCGATGTCTTCCTGAATG 2025–2100 0.714 78.7
rpoB-clpP_p5 rpoB-clpP CCGGGGCTTTGCAATATTTG TGGCGATGTCTTCCTGAATG 1903–1978 0.667 76.4
clpP_p1 clpP GCGGAAGAGGGCTTTATGAA TGACCCTGTTAGTCCGTTCT 1646–1790 1.000 91.6
clpP_p2 clpP TGCAGTTCGATTCTGGACAG TGACCCTGTTAGTCCGTTCT 1589–1709 1.000 91.3
clpP_p3 clpP GCGGAAGAGGGCTTTATGAA CGAGTACATATTCCTCGGCG 1357–1444 0.952 89.5
clpP_p4 clpP ATTTGGGTTCTGGGGTTGAC TGACCCTGTTAGTCCGTTCT 1518–1605 0.810 84.3
clpP_p5 clpP ATTTGGGTTCTGGGGTTGAC CGAGTACATATTCCTCGGCG 1172–1259 0.810 84.0
accD_p1 accD AAGTTAGGACTCCGCTGAAT ACTATCCATCCGCTTGTTACT 2650–2892 0.619 43.0
accD_p2 accD AGTTAGGACTCCGCTGAATT ACTATCCATCCGCTTGTTACT 2649–2891 0.619 43.0
accD_p3 accD AGTTAGGACTCCGCTGAATT TCGAATAACTATCCATCCGCT 2656–2898 0.619 42.1
accD_p4 accD TTTCTTCTTATGCCACCCCT ACTATCCATCCGCTTGTTACT 2928–2948 0.095 17.5
accD_p5 accD TTTCTTCTTATGCCACCCCT TCGAATAACTATCCATCCGCT 2935–2955 0.095 16.6
ycf3-psaA_p1 ycf3-psaA AGCGCAGAATTGGTTGAAGA GCCCATTCCTCGAAAGAAGT 1055–1264 1.000 90.2
ycf3-psaA_p2 ycf3-psaA TGAAGCGCAGAATTGGTTGA GCCCATTCCTCGAAAGAAGT 1058–1267 1.000 87.9
ycf3-psaA_p3 ycf3-psaA TTGAAGCGCAGAATTGGTTG GCCCATTCCTCGAAAGAAGT 1059–1268 1.000 87.7
ycf3-psaA_p4 ycf3-psaA AGCGCAGAATTGGTTGAAGA GAAGTTTTGACGGGATCCCT 1040–1249 1.000 87.2
ycf3-psaA_p5 ycf3-psaA AGCGCAGAATTGGTTGAAGA TGTTCTTGAGAAATGGCCGG 1122–1289 0.952 82.9
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC GAACCGATGACTTACGCCTT CGTTGCCTCCTTGAAAGAGA 587–971 1.000 90.6
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC TACCGCTGAGTTAAAAGGGC CGTTGCCTCCTTGAAAGAGA 552–936 1.000 89.8
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC CCGATGACTTACGCCTTACC CGTTGCCTCCTTGAAAGAGA 584–968 1.000 89.4
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC GAACCGATGACTTACGCCTT TCGTAATACCCTACCCCCAG 622–1006 1.000 88.9
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC GAACCGATGACTTACGCCTT ATCCCCGATCCACTTCCTTT 641–1025 0.905 84.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (21)

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

Species Accession Length (bp) Link
Passiflora actinia NC_038118.1 146255 View on NCBI ↗
Passiflora alata NC_053304.1 147773 View on NCBI ↗
Passiflora caerulea NC_053697.1 151362 View on NCBI ↗
Passiflora cincinnata NC_037690.1 150783 View on NCBI ↗
Passiflora cristalina NC_053307.1 145054 View on NCBI ↗
Passiflora edulis NC_034285.1 151406 View on NCBI ↗
Passiflora elegans MN062356.1 145644 View on NCBI ↗
Passiflora incarnata MN062357.1 151337 View on NCBI ↗
Passiflora laurifolia NC_038121.1 151422 View on NCBI ↗
Passiflora ligularis NC_038122.1 150827 View on NCBI ↗
Passiflora maliformis MN062359.1 148868 View on NCBI ↗
Passiflora miniata NC_050970.1 149573 View on NCBI ↗
Passiflora nitida NC_038123.1 151400 View on NCBI ↗
Passiflora oerstedii NC_038124.1 147073 View on NCBI ↗
Passiflora quadrangularis NC_038126.1 148106 View on NCBI ↗
Passiflora retipetala NC_038188.1 146678 View on NCBI ↗
Passiflora serratifolia NC_038129.1 143111 View on NCBI ↗
Passiflora serratodigitata NC_038127.1 151509 View on NCBI ↗
Passiflora vitifolia NC_038128.1 143845 View on NCBI ↗
Passiflora watsoniana NC_053315.1 146520 View on NCBI ↗
Passiflora xishuangbannaensis NC_059723.1 135742 View on NCBI ↗