Markers + reference

Yucca

7 species · Asparagaceae · Asparagales

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Species 7
Genome length 158–158 kb
Candidate markers 271
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 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0015 1.00 37.5 yes View details
trnK-UUU-rps16 LSC 694 0.0085 1.00 60.4 yes View details
rps16-trnQ-UUG LSC 1393 0.0055 1.00 64.8 yes View details
trnS-GCU-trnG-GCC LSC 1172 0.0113 1.00 56.9 yes View details
trnT-GGU-psbD LSC 1095 0.0049 1.00 53.3 yes View details
psaJ-rpl33 LSC 490 0.0076 1.00 35.0 yes View details
rpl16 LSC 1412 0.0112 1.00 58.4 yes View details
rpl32-trnL-UAG SSC 661 0.0137 1.00 59.7 yes View details
ndhD SSC 1503 0.0058 1.00 54.2 yes View details
ndhA SSC 2200 0.0051 1.00 52.8 yes View details
rps19-psbA LSC 118 0.0511 1.00 71.3 no View details
ndhC-trnV-UAC LSC 1608 0.0033 1.00 61.1 yes View details
trnR-ACG-trnN-GUU IRb 624 0.0038 1.00 58.5 yes View details
trnN-GUU-trnR-ACG IRa 624 0.0038 1.00 58.5 yes View details
accD LSC 1497 0.0029 1.00 57.7 yes View details
ndhF-rpl32 SSC 963 0.0036 1.00 54.7 yes View details
psbM-trnD-GUC LSC 1060 0.0043 1.00 54.4 yes View details
trnE-UUC-trnT-GGU LSC 502 0.0048 1.00 54.2 yes View details
ycf3 LSC 1982 0.0015 1.00 53.9 yes View details
atpH-atpI LSC 492 0.0046 1.00 53.2 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
psbA_p1 psbA GGTATGGCTCCTTCAACGAT GTGCTTGGGAGTCCTTGAAA 1149 1.000 75.2
psbA_p2 psbA TGGCTCCTTCAACGATTCTT GTGCTTGGGAGTCCTTGAAA 1145 1.000 73.3
psbA_p3 psbA GGTATGGCTCCTTCAACGAT TAGTACGTGTGCTTGGGAGT 1157 1.000 72.3
psbA_p4 psbA GGTATGGCTCCTTCAACGAT GTTAGTACGTGTGCTTGGGA 1159 1.000 71.7
psbA_p5 psbA GGTATGGCTCCTTCAACGAT AGTTAGTACGTGTGCTTGGG 1160 1.000 71.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAA GGTGCTCAACCTACAGGAAC 808–812 1.000 79.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC GGTGCTCAACCTACAGGAAC 783–787 1.000 76.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 TAGTCGCACTTAAAAGCCGA GGTGCTCAACCTACAGGAAC 809–813 1.000 74.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAA GTGCTCAACCTACAGGAACT 807–811 1.000 74.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 GCCGAATACTCTACCGTTGA GGTGCTCAACCTACAGGAAC 794–798 1.000 73.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ATCATGTCCTTCAAGTCGCG GAGGTTCGAATCCTTCCGTC 1461–1486 1.000 78.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATCATGTCCTTCAAGTCGCG GTCACTCGGAGGTTCGAATC 1469–1494 1.000 78.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG ATCATGTCCTTCAAGTCGCG TAAACCTAAATGGGGCGTGG 1519–1544 1.000 78.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ATCATGTCCTTCAAGTCGCG CTCGGAGGTTCGAATCCTTC 1465–1490 1.000 77.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GCGTTGCTTTCTACCACATC GAGGTTCGAATCCTTCCGTC 1442–1467 1.000 77.4
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC TGATCAGAGAGAGCGGAGAG CGAACGAATCACACTTTTACCA 1310–1329 1.000 61.8
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCTGCCGCTTTAGTCCAC CGAACGAATCACACTTTTACCA 1243–1262 1.000 60.2
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCTGCCGCTTTAGTCCA CGAACGAATCACACTTTTACCA 1244–1263 1.000 60.2
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC GATCAGAGAGAGCGGAGAGA CGAACGAATCACACTTTTACCA 1309–1328 1.000 60.1
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC ATCAGAGAGAGCGGAGAGAG CGAACGAATCACACTTTTACCA 1308–1327 1.000 60.0
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT ATAGGGGAATCCATGGAGGG 551–556 1.000 80.8
atpH-atpI_p2 atpH-atpI CGCAATACCTTCTACGGCTT ATAGGGGAATCCATGGAGGG 639–644 1.000 80.3
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 576–581 1.000 80.2
atpH-atpI_p4 atpH-atpI TACCTTGACCAACTCCAGGT ATAGGGGAATCCATGGAGGG 607–612 1.000 80.0
atpH-atpI_p5 atpH-atpI CGCAATACCTTCTACGGCTT TTTTGCAACTTTAGCTGCGG 664–669 1.000 79.7
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC CCTCGCTGGGATTGTAGTTC 1188–1214 1.000 63.0
psbM-trnD-GUC_p2 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TACACCTCGCTGGGATTGTA 1192–1218 1.000 62.3
psbM-trnD-GUC_p3 psbM-trnD-GUC AGTGCGAGAATATTGACTTCCA CCTCGCTGGGATTGTAGTTC 1164–1190 1.000 61.1
psbM-trnD-GUC_p4 psbM-trnD-GUC AGTGCGAGAATATTGACTTCCA TACACCTCGCTGGGATTGTA 1168–1194 1.000 60.4
psbM-trnD-GUC_p5 psbM-trnD-GUC AGGAACTAGAATGAACAGTGCA CCTCGCTGGGATTGTAGTTC 1195–1221 1.000 59.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Yucca brevifolia NC_032711.1 158008 View on NCBI ↗
Yucca brevifolia x Yucca jaegeriana MW281812.1 157942 View on NCBI ↗
Yucca filamentosa NC_032712.1 157785 View on NCBI ↗
Yucca gloriosa NC_086555.1 157690 View on NCBI ↗
Yucca jaegeriana MW281815.1 157975 View on NCBI ↗
Yucca queretaroensis NC_032713.1 157814 View on NCBI ↗
Yucca treculeana NC_061319.1 157579 View on NCBI ↗