Markers + reference

Ligusticum

12 species · Apiaceae · Apiales

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Species 12
Genome length 145–156 kb
Candidate markers 264
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 711 0.0284 1.00 73.7 yes View details
trnE-UUC-trnT-GGU LSC 781 0.0386 0.97 71.7 yes View details
petA-psbJ LSC 971 0.0405 0.99 89.8 yes View details
ycf1 IRb 2028 0.0114 1.00 53.0 no View details
ndhF SSC 2247 0.0125 1.00 53.0 yes View details
ndhF-rpl32 SSC 1048 0.0255 0.98 73.5 yes View details
rpl32-trnL-UAG SSC 933 0.0329 0.99 71.7 yes View details
ycf1 SSC 5478 0.0148 1.00 54.3 yes View details
trnL-CAA-trnH-GUG IRa 2275 0.0943 0.98 79.4 no View details
ndhG-ndhI SSC 361 0.0260 1.00 79.3 yes View details
trnT-UGU-trnL-UAA LSC 810 0.0217 0.99 78.3 yes View details
psbA-trnK-UUU LSC 200 0.0529 0.99 76.8 yes View details
psbK-psbI LSC 286 0.0314 1.00 75.9 yes View details
trnH-GUG-psbA LSC 186 0.0759 0.99 74.3 yes View details
psaI-ycf4 LSC 411 0.0201 0.99 73.4 yes View details
ccsA-ndhD SSC 223 0.0541 1.00 73.2 yes View details
rps16-trnQ-UUG LSC 1238 0.0226 0.99 72.3 yes View details
ndhC-trnV-UAC LSC 1078 0.0218 1.00 71.8 yes View details
trnS-GCU-trnG-UCC LSC 553 0.0172 1.00 69.0 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 90 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 CCTCTAGACCTAGCTGCTGT 228–288 1.000 90.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 242–302 1.000 90.4
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 241–301 1.000 90.4
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 243–303 1.000 90.4
trnH-GUG-psbA_p5 trnH-GUG-psbA CGCATGGTGGATTCACAATC CCTCTAGACCTAGCTGCTGT 257–317 1.000 87.6
psbA-trnK-UUU_p1 psbA-trnK-UUU TAAAGACGGTTTTCGGTGCT CTAGTTCCGGGTTCGAATCC 308–339 1.000 86.5
psbA-trnK-UUU_p2 psbA-trnK-UUU GTAAAGACGGTTTTCGGTGC CTAGTTCCGGGTTCGAATCC 309–340 1.000 86.0
psbA-trnK-UUU_p3 psbA-trnK-UUU TTTTCGGTGCTGGTTATCCA CTAGTTCCGGGTTCGAATCC 299–330 1.000 84.0
psbA-trnK-UUU_p4 psbA-trnK-UUU TAAAGACGGTTTTCGGTGCT ACTCCATCCGACTAGTTCCG 319–350 1.000 83.4
psbA-trnK-UUU_p5 psbA-trnK-UUU TACAGAAGCGACCCCATAGG CTAGTTCCGGGTTCGAATCC 277–308 0.917 80.7
trnK-UUU_p1 trnK-UUU ACTCCCAAGCACACGAATTT TGTCCGAGCGGTTTGATTTT 2933–2972 0.917 79.5
trnK-UUU_p2 trnK-UUU ACTCCCAAGCACACGAATTT TTGTCCGAGCGGTTTGATTT 2934–2973 0.750 70.1
trnK-UUU_p3 trnK-UUU ACTCCCAAGCACACGAATTT TTTGTCCGAGCGGTTTGATT 2935–2974 0.750 70.1
trnK-UUU_p4 trnK-UUU ACTCCCAAGCACACGAATTT TTTTGTCCGAGCGGTTTGAT 2936–2975 0.750 70.1
trnK-UUU_p5 trnK-UUU ACTCCCAAGCACACGAATTT ATTTTTGTCCGAGCGGTTTG 2938–2977 0.750 70.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TCTATCCCAATGAGCCGTCT 857–1052 0.917 86.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG GCCGTACGAGGAGAAAACTT 918–1113 0.917 85.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG GCCGTACGAGGAGAAAACTT 917–1112 0.917 85.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG AAGTGTATCACGCGGGAATC 1535–1561 0.750 73.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAGTGTATCACGCGGGAATC 1534–1560 0.750 73.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TGCTTTCTACCACAGCGTTT GGGTTTTGGTCCCGGTATTC 627–1549 1.000 86.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TTGCTTTCTACCACAGCGTT GGGTTTTGGTCCCGGTATTC 628–1550 1.000 86.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GGGTTTTGGTCCCGGTATTC 638–1560 1.000 85.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TGCTTTCTACCACAGCGTTT TCGGAGGTTCGAATCCTTTC 609–1531 1.000 85.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TTGCTTTCTACCACAGCGTT TCGGAGGTTCGAATCCTTTC 610–1532 1.000 85.0
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGCCCCGGATCATTAGATA 400–533 1.000 88.8
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TACGCCCCGGATCATTAGAT 401–534 1.000 88.8
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTACGCCCCGGATCATTAGA 402–535 1.000 87.0
psbK-psbI_p4 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACGCCCCGGATCATTAGATA 397–530 1.000 86.8
psbK-psbI_p5 psbK-psbI TGGCAAGCTGCTGTAAGTTT TACGCCCCGGATCATTAGAT 398–531 1.000 86.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (12)

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

Species Accession Length (bp) Link
Ligusticum chuanxiong NC_061684.1 148564 View on NCBI ↗
Ligusticum glaucifolium ON470822.1 146985 View on NCBI ↗
Ligusticum jeholense NC_061748.1 148487 View on NCBI ↗
Ligusticum mucronatum NC_066699.1 147384 View on NCBI ↗
Ligusticum mutellina OR896882.1 155832 View on NCBI ↗
Ligusticum nematophyllum NC_063844.1 148608 View on NCBI ↗
Ligusticum nullivittatum ON470830.1 148470 View on NCBI ↗
Ligusticum oliverianum NC_063843.1 148378 View on NCBI ↗
Ligusticum reptans PV613225.1 148540 View on NCBI ↗
Ligusticum sikiangense ON470833.1 155449 View on NCBI ↗
Ligusticum thomsonii NC_049058.1 147462 View on NCBI ↗
Ligusticum yushuense NC_071795.1 145335 View on NCBI ↗