Markers + reference

Rheum

19 species · Polygonaceae · Caryophyllales

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Species 19
Genome length 161–162 kb
Candidate markers 267
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 381 0.0648 0.97 83.8 yes View details
rps16-trnQ-UUG LSC 1517 0.0202 0.94 68.7 yes View details
trnS-GCU-trnG-UCC LSC 1075 0.0175 0.95 65.4 yes View details
trnE-UUC-trnT-GGU LSC 988 0.0201 0.98 70.2 yes View details
trnT-GGU-psbD LSC 1423 0.0177 0.89 69.4 yes View details
rbcL-accD LSC 491 0.0297 0.98 72.1 yes View details
rpl33-rps18 LSC 474 0.0226 0.96 59.4 yes View details
clpP LSC 2396 0.0160 0.98 59.4 yes View details
ndhF-rpl32 SSC 957 0.0275 0.99 77.6 yes View details
rpl32-trnL-UAG SSC 872 0.0197 0.43 51.1 yes View details
ndhG SSC 531 0.0066 1.00 40.1 yes View details
trnR-UCU-atpA LSC 185 0.0422 0.96 75.9 yes View details
atpH-atpI LSC 651 0.0096 1.00 70.5 yes View details
trnG-UCC-trnR-UCU LSC 73 0.0417 1.00 68.9 yes View details
petN-psbM LSC 1044 0.0148 1.00 68.9 yes View details
ndhE-ndhG SSC 216 0.0458 0.99 68.0 yes View details
trnT-UGU-trnL-UAA LSC 810 0.0175 0.96 67.2 yes View details
atpB-rbcL LSC 792 0.0139 0.99 67.2 yes View details
psbM-trnD-GUC LSC 935 0.0147 0.97 66.6 yes View details
trnL-UAG-ccsA SSC 135 0.0249 0.96 66.4 yes View details
ccsA-ndhD SSC 203 0.0371 1.00 65.3 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 110 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 GCGCTAACCTTGGTATGGAA 355–590 1.000 90.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 369–604 1.000 90.7
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 368–603 1.000 90.7
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 370–605 1.000 90.7
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCCCCTAGACTTAGCTGCTA 306–541 1.000 87.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GCGTTGCTTTCTACCACATC GAGGTTCGAATCCTTCCGTC 1430–1633 1.000 85.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 1429–1632 1.000 83.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCGTTGCTTTCTACCACATC AGAAATCTAAGTGGGGCGTG 1489–1692 1.000 83.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GCGTTGCTTTCTACCACATC GAAATCTAAGTGGGGCGTGG 1488–1691 1.000 81.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG AGAAATCTAAGTGGGGCGTG 1488–1691 1.000 80.9
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TACCACTAAACTATACCCGC 1128–1184 1.000 56.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CTCGTACAGCGGATTAGCAA TACCACTAAACTATACCCGC 1091–1147 1.000 56.3
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC GACTCGTACAGCGGATTAGC TACCACTAAACTATACCCGC 1093–1149 1.000 56.0
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TTACCACTAAACTATACCCGC 1129–1185 1.000 55.4
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CTCGTACAGCGGATTAGCAA TTACCACTAAACTATACCCGC 1092–1148 1.000 55.2
trnG-UCC_p1 trnG-UCC CCGTTTCTGAATCTCCTCCG TGCTCAAACAATCCCAAGCT 1451–1536 0.947 85.4
trnG-UCC_p2 trnG-UCC CCGTTTCTGAATCTCCTCCG TGGCGGTAGAAGAGCAGATA 1424–1509 0.947 85.0
trnG-UCC_p3 trnG-UCC AAAGGCCTTTTAGTCCCACG TGCTCAAACAATCCCAAGCT 1814–1897 0.947 84.5
trnG-UCC_p4 trnG-UCC AAAGGCCTTTTAGTCCCACG TGGCGGTAGAAGAGCAGATA 1787–1870 0.947 84.1
trnG-UCC_p5 trnG-UCC ATCCGTCAAAACTCTCTGCC TGCTCAAACAATCCCAAGCT 1505–1590 0.895 82.8
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 130–165 1.000 74.2
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 133–168 1.000 73.8
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 136–171 1.000 73.3
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 139–174 1.000 72.9
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 134–169 1.000 71.6
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CATTCACTGAGGAAGCGGAA 267–349 1.000 77.7
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AGACATTCACTGAGGAAGCG 270–352 1.000 75.4
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ATTCACTGAGGAAGCGGAAG 266–348 1.000 75.3
trnR-UCU-atpA_p4 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT CATTCACTGAGGAAGCGGAA 302–384 1.000 74.8
trnR-UCU-atpA_p5 trnR-UCU-atpA AGTCGTAATGATAAGCGTCCA CATTCACTGAGGAAGCGGAA 331–413 1.000 74.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (19)

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

Species Accession Length (bp) Link
Rheum acuminatum MN564922.1 161306 View on NCBI ↗
Rheum alexandrae NC_061617.1 161634 View on NCBI ↗
Rheum delavayi NC_063092.1 162284 View on NCBI ↗
Rheum franzenbachii MN564923.1 161688 View on NCBI ↗
Rheum hotaoense MN564924.1 162048 View on NCBI ↗
Rheum lhasaense MZ475341.1 161768 View on NCBI ↗
Rheum nobile NC_046506.1 161250 View on NCBI ↗
Rheum officinale NC_058627.1 161563 View on NCBI ↗
Rheum palmatum NC_027728.1 161541 View on NCBI ↗
Rheum przewalskyi MN564926.1 161740 View on NCBI ↗
Rheum pumilum NC_058530.1 162213 View on NCBI ↗
Rheum racemiferum NC_066816.1 161915 View on NCBI ↗
Rheum rhabarbarum NC_060489.1 161723 View on NCBI ↗
Rheum rhomboideum NC_066819.1 161833 View on NCBI ↗
Rheum spiciforme NC_066818.1 161589 View on NCBI ↗
Rheum tanguticum NC_046695.1 161515 View on NCBI ↗
Rheum tanguticum var. liupanshanense PP937055.1 161144 View on NCBI ↗
Rheum uninerve NC_066817.1 161927 View on NCBI ↗
Rheum webbianum PQ963207.1 162150 View on NCBI ↗