Markers + reference

Rhododendron

22 species · Ericaceae · Ericales

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Species 22
Genome length 194–208 kb
Candidate markers 285
Primer pairs 95

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 285 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnM-CAU-trnI-CAU LSC 241 0.0740 1.00 72.5 yes View details
trnI-CAU-rpoB LSC 1402 0.0854 0.98 84.5 yes View details
trnT-GGU-rpl16 LSC 6538 0.0611 0.72 73.3 yes View details
rpoA-rps15 LSC 7382 0.0552 0.65 69.7 yes View details
trnI-CAU-rrn16S IRb 2457 0.0832 0.99 82.8 yes View details
trnI-CAU-trnM-CAU IRb 2455 0.1029 0.92 75.5 yes View details
trnI-CAU-rps16 IRb 4069 0.0780 0.95 76.8 yes View details
rps19-trnI-CAU IRa 2910 0.0978 0.96 83.9 yes View details
trnM-CAU-trnI-CAU IRa 2455 0.1047 0.95 76.7 yes View details
rrn16S-trnI-CAU IRa 2457 0.0797 0.99 78.5 yes View details
rps16-rps19 IRa 979 0.0633 0.98 82.9 yes View details
rpl32-ndhF IRb 709 0.0453 0.97 82.7 yes View details
psaI-rps19 IRa 1984 0.0235 1.00 76.3 yes View details
trnK-UUU-ycf3 LSC 2498 0.0267 0.99 73.4 yes View details
trnT-UGU-trnL-UAA LSC 836 0.0169 0.99 71.7 yes View details
trnE-UUC-psbB LSC 1787 0.0169 1.00 71.5 yes View details
rps19-rps16 IRa 1690 0.0244 1.00 71.4 yes View details
psbE-petL LSC 1291 0.0147 1.00 70.0 yes View details
rps16-psaI IRb 3824 0.0233 1.00 69.9 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-ycf3_p1 trnK-UUU-ycf3 CGAATCCCTTGCTTCATCCA GAAGCCGCTCAGTATTGGAA 2140–2624 0.909 87.8
trnK-UUU-ycf3_p2 trnK-UUU-ycf3 ACGAATCCCTTGCTTCATCC GAAGCCGCTCAGTATTGGAA 2141–2625 0.909 87.8
trnK-UUU-ycf3_p3 trnK-UUU-ycf3 ATGGACGAATCCCTTGCTTC GAAGCCGCTCAGTATTGGAA 2145–2629 0.909 87.8
trnK-UUU-ycf3_p4 trnK-UUU-ycf3 GGACGAATCCCTTGCTTCAT GAAGCCGCTCAGTATTGGAA 2143–2627 0.909 87.8
trnK-UUU-ycf3_p5 trnK-UUU-ycf3 CGATGGTATGGACGAATCCC GAAGCCGCTCAGTATTGGAA 2152–2636 0.909 87.5
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 915–2356 1.000 86.1
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 923–2364 1.000 85.5
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 883–2324 0.955 84.7
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 891–2332 0.955 84.1
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG AGTCCGTAGCGTCTACCAAT 897–2338 0.955 82.7
trnM-CAU-trnI-CAU_p1 trnM-CAU-trnI-CAU CTCTCAGACGAGCTAGGACA GAATGGTTAAAGCGCCCAAC 647–2358 0.909 86.8
trnM-CAU-trnI-CAU_p2 trnM-CAU-trnI-CAU ACCGCGAAGGCTATGAATTT GAATGGTTAAAGCGCCCAAC 1043–2754 0.909 83.7
trnM-CAU-trnI-CAU_p3 trnM-CAU-trnI-CAU CTCTCAGACGAGCTAGGACA TCGAACAAAAGAAGACGGCA 1107–2823 0.227 60.2
trnM-CAU-trnI-CAU_p4 trnM-CAU-trnI-CAU ACCGCGAAGGCTATGAATTT TCGAACAAAAGAAGACGGCA 1503–2892 0.182 57.0
trnM-CAU-trnI-CAU_p5 trnM-CAU-trnI-CAU TTGAACCAATGACTCCTGCC GAATGGTTAAAGCGCCCAAC 363 0.045 41.0
trnI-CAU-rpoB_p1 trnI-CAU-rpoB GTTGGGCGCTTTAACCATTC CTTCATTTCCATCCCAGAGCA 991–2902 0.955 82.0
trnI-CAU-rpoB_p2 trnI-CAU-rpoB GTTGGGCGCTTTAACCATTC TTCATTTCCATCCCAGAGCA 990–2901 0.955 80.5
trnI-CAU-rpoB_p3 trnI-CAU-rpoB AGTTGGGCGCTTTAACCATT CTTCATTTCCATCCCAGAGCA 992–2903 0.955 79.1
trnI-CAU-rpoB_p4 trnI-CAU-rpoB TTGGGCGCTTTAACCATTCA CTTCATTTCCATCCCAGAGCA 990–2901 0.955 79.1
trnI-CAU-rpoB_p5 trnI-CAU-rpoB GTTGGGCGCTTTAACCATTC TCATTTCCATCCCAGAGCAT 989–2900 0.955 78.6
trnT-GGU-rpl16_p1 trnT-GGU-rpl16 TATTCACGCAGGGAGCATTC GCGATTTTCTGAACCAGCAC 684–696 0.591 75.0
trnT-GGU-rpl16_p2 trnT-GGU-rpl16 TCAGCTTGATGCAAATGGGT GCGATTTTCTGAACCAGCAC 924–936 0.591 74.8
trnT-GGU-rpl16_p3 trnT-GGU-rpl16 AACGAATCTGAGGGCAATCC GCGATTTTCTGAACCAGCAC 374–392 0.545 73.2
trnT-GGU-rpl16_p4 trnT-GGU-rpl16 TGCCGGCATCTACCACTATA GCGATTTTCTGAACCAGCAC 463 0.091 43.4
trnT-GGU-rpl16_p5 trnT-GGU-rpl16 TGCCGGCATCTACCACTATA CGAAGGACTGTGACATAGCC 554 0.091 43.0
rpoA-rps15_p1 rpoA-rps15 GTTGAGGGAAAGGACGATGG TGGCGTTGGATCAGAATAGC 1505 0.045 39.4
rpoA-rps15_p2 rpoA-rps15 CGATGGCCCCAAATACTCTT TGGCGTTGGATCAGAATAGC 1491 0.045 38.7
rpoA-rps15_p3 rpoA-rps15 GTTGAGGGAAAGGACGATGG CTGCAATCTCAGGGTTTGTT 1485 0.045 25.5
rpoA-rps15_p4 rpoA-rps15 CGATGGCCCCAAATACTCTT CTGCAATCTCAGGGTTTGTT 1471 0.045 24.8
rpoA-rps15_p5 rpoA-rps15 GACGATGGCCCCAAATACTC CTGCAATCTCAGGGTTTGTT 1473 0.045 24.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (22)

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

Species Accession Length (bp) Link
Rhododendron ambiguum NC_083984.1 207478 View on NCBI ↗
Rhododendron anthopogonoides NC_069024.1 207719 View on NCBI ↗
Rhododendron aureum OM574972.1 207900 View on NCBI ↗
Rhododendron brachycarpum OM574995.1 206422 View on NCBI ↗
Rhododendron capitatum NC_067871.1 200257 View on NCBI ↗
Rhododendron catawbiense OM575017.1 199538 View on NCBI ↗
Rhododendron concinnum MT239366.1 207236 View on NCBI ↗
Rhododendron delavayi MN711645.4 202169 View on NCBI ↗
Rhododendron delavayi var. delavayi NC_047438.1 193798 View on NCBI ↗
Rhododendron griersonianum NC_050162.1 206467 View on NCBI ↗
Rhododendron henanense subsp. lingbaoense MT239363.1 208015 View on NCBI ↗
Rhododendron huadingense NC_063113.1 198952 View on NCBI ↗
Rhododendron maximum OM575018.1 206382 View on NCBI ↗
Rhododendron micranthum NC_065477.1 201398 View on NCBI ↗
Rhododendron nivale subsp. boreale PQ536991.1 202882 View on NCBI ↗
Rhododendron ovatum OR129260.1 195987 View on NCBI ↗
Rhododendron purdomii NC_086505.1 208062 View on NCBI ↗
Rhododendron schlippenbachii OM575019.1 202789 View on NCBI ↗
Rhododendron shanii MW374796.1 204170 View on NCBI ↗
Rhododendron thymifolium NC_067870.1 201186 View on NCBI ↗
Rhododendron vialii PQ536992.1 195319 View on NCBI ↗
Rhododendron williamsianum NC_088748.1 205424 View on NCBI ↗