Markers + reference

Dioscorea

42 species · Dioscoreaceae · Dioscoreales

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Species 42
Genome length 152–155 kb
Candidate markers 268
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-trnQ-UUG LSC 1617 0.0452 1.00 80.5 yes View details
trnS-GCU-trnG-UCC LSC 1016 0.0618 0.95 79.3 yes View details
atpF LSC 1543 0.0305 0.99 70.8 yes View details
rpoB-trnC-GCA LSC 1271 0.0386 0.98 82.0 yes View details
trnT-GGU-psbD LSC 1037 0.0389 0.94 71.5 no View details
ndhC-trnV-UAC LSC 986 0.0416 0.95 78.7 yes View details
ycf1 SSC 5589 0.0316 1.00 64.3 yes View details
trnL-UAG-rpl32 SSC 839 0.0533 1.00 80.0 no View details
rpl32-ndhF SSC 708 0.0948 0.85 76.4 no View details
ndhF SSC 2238 0.0262 0.97 67.7 yes View details
trnT-UGU-trnL-UAA LSC 857 0.0429 0.96 82.7 yes View details
trnC-GCA-petN LSC 946 0.0412 0.97 80.5 yes View details
trnF-GAA-ndhJ LSC 689 0.0402 0.99 76.7 yes View details
petA-psbJ LSC 891 0.0404 1.00 75.8 yes View details
psbM-trnD-GUC LSC 914 0.0286 0.99 74.6 yes View details
ycf1-rps15 SSC 290 0.0663 1.00 73.4 yes View details
trnP-UGG-psaJ LSC 377 0.0482 0.99 72.7 yes View details
trnG-UCC-trnR-UCU LSC 147 0.0576 0.98 72.6 yes View details
atpH-atpI LSC 798 0.0366 0.99 72.2 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
trnK-UUU-trnQ-UUG_p1 trnK-UUU-trnQ-UUG AAAGCCGAGTACTCTACCGT GAGGTTCGAATCCTTCCGTC 976–2657 1.000 90.0
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG AAGCCGAGTACTCTACCGTT GAGGTTCGAATCCTTCCGTC 975–2656 1.000 90.0
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG AAAGCCGAGTACTCTACCGT CTCGGAGGTTCGAATCCTTC 976–2661 1.000 89.0
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG AAGCCGAGTACTCTACCGTT CTCGGAGGTTCGAATCCTTC 975–2660 1.000 89.0
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG TACCGTTGAGTTAGCAACCC GAGGTTCGAATCCTTCCGTC 962–2643 1.000 87.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CCGTCGCTTTAATCCACTCA ACGAATCGCACTTTTACCACT 358–2278 1.000 82.1
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CCGTCGCTTTAATCCACTCA ACGAATCGCACTTTTACCAC 357–2278 1.000 82.0
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC TCGCTTTAATCCACTCAGCC ACGAATCGCACTTTTACCACT 355–2279 1.000 81.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TCGCTTTAATCCACTCAGCC ACGAATCGCACTTTTACCAC 354–2279 1.000 81.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAGATTAGCAATCCGTCGCT ACGAATCGCACTTTTACCACT 370–2279 1.000 81.0
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 220–2279 1.000 73.6
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 223–2279 1.000 73.3
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 226–2279 1.000 72.8
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 229–2279 1.000 72.5
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 224–2279 1.000 71.1
atpF_p1 atpF ACGAGCAATACCATCCCCTA GTGGCATTGGCGCTTTTATT 969–2277 0.976 90.2
atpF_p2 atpF CTAATTCGCCTGCCATCACT GTGGCATTGGCGCTTTTATT 1006–2279 0.952 89.7
atpF_p3 atpF CTAATTCGCCTGCCATCACT AAGCCGTAGAAGGTATTGCG 1008–2373 0.952 89.3
atpF_p4 atpF GAGCAATGCCTACTGTACCC GTGGCATTGGCGCTTTTATT 1039–2294 0.881 86.8
atpF_p5 atpF GCAATGCCTACTGTACCCTC GTGGCATTGGCGCTTTTATT 1037–2292 0.881 86.8
atpH-atpI_p1 atpH-atpI CGCAATACCTTCTACGGCTT AGCAAAGCCCAAATTGGAGA 1297–2571 1.000 91.4
atpH-atpI_p2 atpH-atpI AATAAAAGCGCCAATGCCAC AGCAAAGCCCAAATTGGAGA 1404–2573 0.976 90.9
atpH-atpI_p3 atpH-atpI AATAAAAGCGCCAATGCCAC TATGGTCCTTGGGTTCCCTT 1380–2549 0.976 90.4
atpH-atpI_p4 atpH-atpI AATAAAAGCGCCAATGCCAC CTGCGCCCACGAATGATATA 1268–2437 0.976 90.3
atpH-atpI_p5 atpH-atpI AATAAAAGCGCCAATGCCAC GCGAATCCATGGAAGGTCAT 932–2280 0.952 89.8
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TCCCTCATTTCCATCCCGAA TTAGGCGACACCCAGATTTG 900–2279 0.976 86.9
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TCCCTCATTTCCATCCCGAA TTGTTGATTAGGCGACACCC 900–2279 0.976 86.3
rpoB-trnC-GCA_p3 rpoB-trnC-GCA GTTCTTCCATCAAGCCCTGA TTAGGCGACACCCAGATTTG 979–2278 0.976 86.2
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TTCCCTCATTTCCATCCCGA TTAGGCGACACCCAGATTTG 901–2279 0.952 86.0
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TTCCCTCATTTCCATCCCGA TTGTTGATTAGGCGACACCC 901–2279 0.952 85.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (42)

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

Species Accession Length (bp) Link
Dioscorea abyssinica NC_039834.1 152552 View on NCBI ↗
Dioscorea alata NC_039707.1 153161 View on NCBI ↗
Dioscorea aspersa NC_039807.1 153337 View on NCBI ↗
Dioscorea banzhuana NC_077568.1 153989 View on NCBI ↗
Dioscorea baya NC_039850.1 152155 View on NCBI ↗
Dioscorea biformifolia NC_077569.1 154149 View on NCBI ↗
Dioscorea brevipetiolata NC_062811.1 153485 View on NCBI ↗
Dioscorea bulbifera NC_039708.1 153075 View on NCBI ↗
Dioscorea burkilliana MG805605.1 151908 View on NCBI ↗
Dioscorea cayenensis NC_039836.1 152367 View on NCBI ↗
Dioscorea cayenensis subsp. rotundata NC_024170.1 155406 View on NCBI ↗
Dioscorea collettii NC_037717.1 153870 View on NCBI ↗
Dioscorea coreana PZ211770.1 153654 View on NCBI ↗
Dioscorea deltoidea NC_077564.1 153947 View on NCBI ↗
Dioscorea depauperata NC_062812.1 153487 View on NCBI ↗
Dioscorea dumetorum NC_039691.1 152475 View on NCBI ↗
Dioscorea elephantipes NC_009601.1 152609 View on NCBI ↗
Dioscorea esculenta NC_052854.1 153437 View on NCBI ↗
Dioscorea fordii NC_070252.1 153161 View on NCBI ↗
Dioscorea futschauensis NC_039808.1 153946 View on NCBI ↗
Dioscorea glabra NC_062813.1 153503 View on NCBI ↗
Dioscorea gracillima NC_077565.1 153996 View on NCBI ↗
Dioscorea hirtiflora NC_039851.1 152287 View on NCBI ↗
Dioscorea hispida NC_066182.1 153438 View on NCBI ↗
Dioscorea japonica NC_057066.1 153293 View on NCBI ↗
Dioscorea nipponica NC_057065.1 153255 View on NCBI ↗
Dioscorea nipponica subsp. rosthornii OQ525996.1 153916 View on NCBI ↗
Dioscorea persimilis NC_057257.1 153221 View on NCBI ↗
Dioscorea polystachya NC_037716.1 152963 View on NCBI ↗
Dioscorea praehensilis NC_039837.1 152466 View on NCBI ↗
Dioscorea preussii NC_039852.1 152539 View on NCBI ↗
Dioscorea pyrifolia NC_062814.1 153370 View on NCBI ↗
Dioscorea quinquelobata NC_057067.1 153945 View on NCBI ↗
Dioscorea sagittifolia NC_039854.1 152549 View on NCBI ↗
Dioscorea sansibarensis NC_039838.1 152445 View on NCBI ↗
Dioscorea schimperiana NC_039855.1 152382 View on NCBI ↗
Dioscorea spongiosa NC_077566.1 153947 View on NCBI ↗
Dioscorea tenuipes PZ211775.1 153669 View on NCBI ↗
Dioscorea togoensis NC_039856.1 152264 View on NCBI ↗
Dioscorea tokoro NC_077567.1 153946 View on NCBI ↗
Dioscorea villosa NC_034686.1 153974 View on NCBI ↗
Dioscorea zingiberensis NC_027090.1 153970 View on NCBI ↗