Markers + reference

Liriodendron

3 species · Magnoliaceae · Magnoliales

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Species 3
Genome length 159–160 kb
Candidate markers 271
Primer pairs 85

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 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 408 0.0278 1.00 45.6 yes View details
rps16-trnQ-UUG LSC 1921 0.0073 1.00 59.2 yes View details
petA-psbJ LSC 1174 0.0108 1.00 53.9 yes View details
petL-petG LSC 177 0.0075 1.00 31.5 yes View details
ycf1 IRb 1110 0.0030 1.00 34.6 no View details
ndhF SSC 2223 0.0039 1.00 32.8 yes View details
ndhF-rpl32 SSC 1136 0.0076 1.00 51.1 yes View details
ccsA SSC 966 0.0035 1.00 38.4 yes View details
ycf1 SSC 5490 0.0060 1.00 35.4 yes View details
atpF-atpH LSC 492 0.0068 1.00 66.4 yes View details
trnfM-CAU-rps14 LSC 192 0.0041 0.84 56.0 yes View details
petG-trnW-CCA LSC 114 0.0351 1.00 55.5 yes View details
rpl2-trnH-GUG IRa 73 0.0365 1.00 53.2 no View details
rps14-psaB LSC 142 0.0188 1.00 52.8 yes View details
trnI-CAU-ycf2 IRb 68 0.0196 1.00 52.5 yes View details
ycf2-trnI-CAU IRa 68 0.0196 1.00 52.5 yes View details
psbI-trnS-GCU LSC 142 0.0141 1.00 51.2 yes View details
ccsA-ndhD SSC 227 0.0235 1.00 50.9 yes View details
atpH-atpI LSC 1091 0.0067 1.00 50.5 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 TCACAATCCACTGCCTTGAG CCTCTAGACCTAGCTGCTGT 492 1.000 80.9
trnH-GUG-psbA_p2 trnH-GUG-psbA TCACAATCCACTGCCTTGAG GTTGACAGTCAAGGTCGTGT 591 1.000 80.4
trnH-GUG-psbA_p3 trnH-GUG-psbA TCACAATCCACTGCCTTGAG TCAGTGCTATGCATGGTTCC 878 1.000 79.8
trnH-GUG-psbA_p4 trnH-GUG-psbA TCACAATCCACTGCCTTGAG CAGTGCTATGCATGGTTCCT 877 1.000 79.7
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAAAGGAATGATGGGCGAA TCAGTGCTATGCATGGTTCC 928 0.667 64.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAAGAATCCACAGCCGATCA GAGGTTCGAATCCTTCCGTC 2021–2023 1.000 80.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 2011–2013 1.000 80.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 2009–2011 1.000 80.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AATCCACAGCCGATCATGTC GAGGTTCGAATCCTTCCGTC 2017–2019 1.000 80.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GAATCCACAGCCGATCATGT GAGGTTCGAATCCTTCCGTC 2018–2020 1.000 80.2
psbI-trnS-GCU_p1 psbI-trnS-GCU AATCCTGGACGCGAGGAATA TGGACTAAAGCGACGGATTG 232–236 1.000 77.6
psbI-trnS-GCU_p2 psbI-trnS-GCU ATCCTGGACGCGAGGAATAA TGGACTAAAGCGACGGATTG 231–235 1.000 77.6
psbI-trnS-GCU_p3 psbI-trnS-GCU TAATCCTGGACGCGAGGAAT TGGACTAAAGCGACGGATTG 233–237 1.000 77.6
psbI-trnS-GCU_p4 psbI-trnS-GCU AATCCTGGACGCGAGGAATA GTGGACTAAAGCGACGGATT 233–237 1.000 77.6
psbI-trnS-GCU_p5 psbI-trnS-GCU ATCCTGGACGCGAGGAATAA GTGGACTAAAGCGACGGATT 232–236 1.000 77.6
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG AATTTACGGACTGGTCGTGG 587–616 1.000 82.8
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG TCGTGGCATTAGCGCTTTTA 573–602 1.000 81.5
atpF-atpH_p3 atpF-atpH CCAGTAACCCAAGGAAACGA AATTTACGGACTGGTCGTGG 560–589 1.000 79.5
atpF-atpH_p4 atpF-atpH CCAGTAACCCAAGGAAACGA TCGTGGCATTAGCGCTTTTA 546–575 1.000 78.1
atpF-atpH_p5 atpF-atpH GGCCAGTAACCCAAGGAAAC AATTTACGGACTGGTCGTGG 562–591 1.000 78.0
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 1179–1191 1.000 76.3
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT CAAGCGGGATTCAAGCTCTT 1200–1212 1.000 76.1
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT TTTTTGCAACTTTAGCCGCG 1235–1247 1.000 75.7
atpH-atpI_p4 atpH-atpI GATACCTTCTACGGCTTGGC TTTTTGCAACTTTAGCCGCG 1264–1276 1.000 75.5
atpH-atpI_p5 atpH-atpI CGATACCTTCTACGGCTTGG TTTTTGCAACTTTAGCCGCG 1265–1277 1.000 75.5
trnfM-CAU-rps14_p1 trnfM-CAU-rps14 GCTACCAAACTGCTCTACCC CGTTGTTTTTCGACCGGAAG 306–336 1.000 83.9
trnfM-CAU-rps14_p2 trnfM-CAU-rps14 AAGGTTATGAGCCTTGCGAG CGTTGTTTTTCGACCGGAAG 325–355 1.000 83.9
trnfM-CAU-rps14_p3 trnfM-CAU-rps14 GATGTTGCGGAGACAGGATT CGTTGTTTTTCGACCGGAAG 360–390 1.000 83.9
trnfM-CAU-rps14_p4 trnfM-CAU-rps14 TTTGAACCCGTGACCTCAAG CGTTGTTTTTCGACCGGAAG 342–372 1.000 83.8
trnfM-CAU-rps14_p5 trnfM-CAU-rps14 ACAGGATTTGAACCCGTGAC CGTTGTTTTTCGACCGGAAG 348–378 1.000 83.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Liriodendron chinense NC_030504.1 159429 View on NCBI ↗
Liriodendron chinense x Liriodendron tulipifera NC_062941.1 159397 View on NCBI ↗
Liriodendron tulipifera NC_008326.1 159886 View on NCBI ↗