Markers + reference

Gentiana

43 species · Gentianaceae · Gentianales

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Species 43
Genome length 128–151 kb
Candidate markers 267
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

8 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
trnH-GUG-psbA LSC 364 0.0963 0.91 68.5 yes View details
trnK-UUU-trnQ-UUG LSC 1342 0.0467 0.96 74.1 yes View details
psaA-ycf3 LSC 850 0.0443 0.98 72.4 yes View details
trnT-UGU-trnL-UAA LSC 743 0.0511 0.90 72.9 yes View details
petA-psbJ LSC 847 0.0513 0.98 76.9 yes View details
ycf1 IRb 1026 0.0133 0.99 49.5 no View details
rpl32-trnL-UAG SSC 979 0.0754 0.99 75.2 yes View details
ycf1 SSC 5484 0.0429 0.99 72.9 yes View details
trnS-GCU-trnS-CGA LSC 556 0.0522 1.00 80.5 yes View details
rpoB-trnC-GCA LSC 1246 0.0447 0.98 78.2 yes View details
trnT-GGU-psbD LSC 1211 0.0414 0.98 76.0 yes View details
trnC-GCA-petN LSC 899 0.0421 0.96 75.4 yes View details
psaI-ycf4 LSC 417 0.0510 1.00 72.6 yes View details
trnE-UUC-trnT-GGU LSC 496 0.0366 0.95 71.9 yes View details
trnL-UAA-trnF-GAA LSC 341 0.0556 0.98 71.8 yes View details
trnQ-UUG-psbK LSC 367 0.0501 0.98 71.7 yes View details
rpl20-rps12 LSC 805 0.0279 0.99 71.4 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TTCGGCGGTTCCTTATTCAG 657–875 1.000 90.8
trnH-GUG-psbA_p2 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TCAGTGCTATGCATGGTTCC 641–859 1.000 90.6
trnH-GUG-psbA_p3 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TTCGGCGGTTCCTTATTCAG 658–876 1.000 90.6
trnH-GUG-psbA_p4 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CAGTGCTATGCATGGTTCCT 640–858 1.000 90.5
trnH-GUG-psbA_p5 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TGCTGCTTGGCCTGTAATAG 448–666 0.651 76.6
trnK-UUU_p1 trnK-UUU CCAAGCACACGCATTCTCTA GCAGTTTGTTTGTTAGTTCAAGG 2850–2901 0.721 45.1
trnK-UUU_p2 trnK-UUU AAGCACACGCATTCTCTACA GCAGTTTGTTTGTTAGTTCAAGG 2848–2899 0.721 43.6
trnK-UUU_p3 trnK-UUU AGCACACGCATTCTCTACAA GCAGTTTGTTTGTTAGTTCAAGG 2847–2898 0.721 43.6
trnK-UUU_p4 trnK-UUU TACAGAAGCGACCCCATAGG GCAGTTTGTTTGTTAGTTCAAGG 2943–2994 0.721 42.5
trnK-UUU_p5 trnK-UUU ATCCAGTTACAGAAGCGACC GCAGTTTGTTTGTTAGTTCAAGG 2950–3000 0.698 40.8
trnK-UUU-trnQ-UUG_p1 trnK-UUU-trnQ-UUG CCGTTGAGTTAGCAACCC GAGGTTCGAATCCTTCCGTC 478–1495 1.000 57.0
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG CCGTTGAGTTAGCAACCC TTCGGAGGTTCGAATCCTTC 482–1499 1.000 52.2
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG CCGTTGAGTTAGCAACCC TAAGGCAACGGGTTTTGGTC 508–1525 1.000 52.1
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG CCGTTGAGTTAGCAACCC GGGTTTTGGTCCCGCTATTC 499–1516 1.000 52.0
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG CCGTTGAGTTAGCAACCC AAATCTAAATGGGGCGTGGC 535–1552 0.977 51.1
trnQ-UUG-psbK_p1 trnQ-UUG-psbK GATATGCTCTGGGACGGAAG CAGATCCCTATCAAACTACAA 437–502 0.907 48.3
trnQ-UUG-psbK_p2 trnQ-UUG-psbK GATATGCTCTGGGACGGAAG CAGATCCCTATCAAACTACAAA 437–502 0.907 48.3
trnQ-UUG-psbK_p3 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA CAGATCCCTATCAAACTACAA 395–460 0.907 48.3
trnQ-UUG-psbK_p4 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA CAGATCCCTATCAAACTACAAA 395–460 0.907 48.3
trnQ-UUG-psbK_p5 trnQ-UUG-psbK GAATAGCGGGACCAAAACCC CAGATCCCTATCAAACTACAA 404–469 0.907 48.3
trnS-GCU-trnS-CGA_p1 trnS-GCU-trnS-CGA CAATCCGTCGCTTTAGTCCA ACCACTAAACTATACCCGCT 503–659 1.000 73.1
trnS-GCU-trnS-CGA_p2 trnS-GCU-trnS-CGA AATCCGTCGCTTTAGTCCAC ACCACTAAACTATACCCGCT 502–658 1.000 73.1
trnS-GCU-trnS-CGA_p3 trnS-GCU-trnS-CGA AGCAATCCGTCGCTTTAGTC ACCACTAAACTATACCCGCT 505–661 1.000 70.3
trnS-GCU-trnS-CGA_p4 trnS-GCU-trnS-CGA CGTCGCTTTAGTCCACTCAG ACCACTAAACTATACCCGCT 498–654 1.000 70.1
trnS-GCU-trnS-CGA_p5 trnS-GCU-trnS-CGA GCTTTAGTCCACTCAGCCAT ACCACTAAACTATACCCGCT 494–650 1.000 69.9
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCTCATTTCCATCAACGAGC CCGGATTTGAACTGGGGAAA 874–1360 0.930 79.6
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ACTCCCTCATTTCCATCAACG CCGGATTTGAACTGGGGAAA 878–1364 0.884 78.6
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCCCTCATTTCCATCAACGAG CCGGATTTGAACTGGGGAAA 876–1362 0.930 78.4
rpoB-trnC-GCA_p4 rpoB-trnC-GCA ACTCCCTCATTTCCATCAACG AAAAGGATTTGCAGTCCCCC 860–1346 0.907 77.4
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CTCCCTCATTTCCATCAACGA CCGGATTTGAACTGGGGAAA 877–1363 0.884 76.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (43)

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

Species Accession Length (bp) Link
Gentiana acaulis PP203118.1 150449 View on NCBI ↗
Gentiana algida NC_065764.1 143715 View on NCBI ↗
Gentiana arethusae NC_058687.1 137458 View on NCBI ↗
Gentiana atropurpurea NC_053884.1 145757 View on NCBI ↗
Gentiana atuntsiensis NC_063902.1 144238 View on NCBI ↗
Gentiana bavarica MN199162.1 147894 View on NCBI ↗
Gentiana cephalantha OM961143.1 146913 View on NCBI ↗
Gentiana clusii PP203119.1 149395 View on NCBI ↗
Gentiana crassa subsp. rigescens NC_053841.1 146891 View on NCBI ↗
Gentiana crassicaulis NC_027442.1 148776 View on NCBI ↗
Gentiana crassuloides MN199150.1 128392 View on NCBI ↗
Gentiana cruciata MN199136.1 148933 View on NCBI ↗
Gentiana cruciata subsp. cruciata PP203120.1 148936 View on NCBI ↗
Gentiana dahurica NC_039572.1 148803 View on NCBI ↗
Gentiana davidii MN199156.1 147565 View on NCBI ↗
Gentiana delavayi NC_052850.1 149040 View on NCBI ↗
Gentiana frigida NC_063903.1 143661 View on NCBI ↗
Gentiana georgei MN234135.1 149354 View on NCBI ↗
Gentiana handeliana MN199143.1 143813 View on NCBI ↗
Gentiana haynaldii MN234137.1 127889 View on NCBI ↗
Gentiana lhassica NC_059703.1 148653 View on NCBI ↗
Gentiana lutea MN199129.1 150466 View on NCBI ↗
Gentiana lutea subsp. vardjanii PP203121.1 150414 View on NCBI ↗
Gentiana manshurica NC_053840.1 149185 View on NCBI ↗
Gentiana nubigena MN199157.1 143378 View on NCBI ↗
Gentiana officinalis NC_039574.1 148879 View on NCBI ↗
Gentiana pneumonanthe PP203122.1 149114 View on NCBI ↗
Gentiana punctata PP203123.1 150429 View on NCBI ↗
Gentiana purdomii NC_063904.1 144290 View on NCBI ↗
Gentiana purpurea MN199160.1 150559 View on NCBI ↗
Gentiana robusta KT159969.1 148911 View on NCBI ↗
Gentiana scabra NC_053842.1 146915 View on NCBI ↗
Gentiana sikkimensis MN199154.1 146103 View on NCBI ↗
Gentiana siphonantha NC_039573.1 148908 View on NCBI ↗
Gentiana straminea NC_027441.1 148991 View on NCBI ↗
Gentiana szechenyii MN199158.1 149334 View on NCBI ↗
Gentiana terglouensis MN199132.1 147840 View on NCBI ↗
Gentiana ternifolia MN199147.1 137516 View on NCBI ↗
Gentiana tibetica NC_030319.1 148765 View on NCBI ↗
Gentiana triflora NC_058535.1 149125 View on NCBI ↗
Gentiana urnula NC_050655.1 149076 View on NCBI ↗
Gentiana waltonii MK780032.1 148705 View on NCBI ↗
Gentiana yunnanensis MN199140.1 147461 View on NCBI ↗