Markers + reference

Lycium

52 species · Solanaceae · Solanales

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Species 52
Genome length 155–156 kb
Candidate markers 270
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 418 0.0077 1.00 42.4 yes View details
atpH-atpI LSC 1223 0.0048 0.99 57.7 yes View details
rbcL LSC 1455 0.0069 1.00 35.4 yes View details
rbcL-accD LSC 794 0.0043 1.00 42.5 yes View details
ycf4-cemA LSC 727 0.0057 1.00 39.7 yes View details
rpl36-rps8 LSC 446 0.0088 1.00 45.3 yes View details
ycf1 IRb 1038 0.0033 1.00 43.6 no View details
ndhF SSC 2223 0.0023 1.00 32.9 yes View details
rpl32-trnL-UAG SSC 763 0.0081 1.00 55.8 yes View details
ccsA SSC 942 0.0023 1.00 31.2 yes View details
ndhG SSC 531 0.0032 1.00 30.7 yes View details
ycf1 SSC 5676 0.0036 1.00 40.6 yes View details
trnK-UUU-rps16 LSC 690 0.0052 1.00 59.8 yes View details
ndhC-trnV-UAC LSC 1132 0.0047 0.97 58.3 yes View details
petA-psbJ LSC 1077 0.0041 1.00 57.7 yes View details
rpoB-trnC-GCA LSC 1305 0.0033 1.00 55.1 yes View details
rps16-trnQ-UUG LSC 902 0.0037 1.00 54.9 yes View details
rpoC1-rpoB LSC 26 0.0099 1.00 54.4 yes View details
clpP1 LSC 2035 0.0024 1.00 53.4 yes View details
psbM-trnD-GUC LSC 1075 0.0031 0.99 52.5 yes View details
rpl2-trnH-GUG IRa 145 0.0198 0.99 52.4 no View details
trnS-GGA-rps4 LSC 337 0.0077 1.00 51.7 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 100 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 TTCCCTCTAGACCTAGCTGC 488–498 1.000 83.3
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 502–512 1.000 83.1
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 501–511 1.000 83.1
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 503–513 1.000 83.1
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 537–547 1.000 80.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC TTGAAAAAGGGGCTCAACCT 816–916 1.000 81.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAAGACACTAGCCGCACTT TTGAAAAAGGGGCTCAACCT 752–852 1.000 81.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 CAGTCGTGGTCTTCCAAACT TTGAAAAAGGGGCTCAACCT 815–915 1.000 81.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC AAAAGGGGCTCAACCTACAG 812–912 1.000 80.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 CAGTCGTGGTCTTCCAAACT AAAAGGGGCTCAACCTACAG 811–911 1.000 80.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 975–1007 1.000 85.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 958–990 1.000 84.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAGGTTCGAATCCTTCCGTC 976–1008 1.000 84.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 973–1005 1.000 82.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 972–1004 1.000 82.7
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TACCTGTCATGCTCCTTGGA 1298–1389 1.000 85.6
atpH-atpI_p2 atpH-atpI TACCCTCTACAGCTTGACCC TACCTGTCATGCTCCTTGGA 1381–1472 1.000 84.7
atpH-atpI_p3 atpH-atpI GCGATACCCTCTACAGCTTG TACCTGTCATGCTCCTTGGA 1385–1476 1.000 84.7
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA TACCTGTCATGCTCCTTGGA 1299–1390 1.000 84.5
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC TACCTGTCATGCTCCTTGGA 1313–1404 1.000 84.2
rpoC1-rpoB_p1 rpoC1-rpoB TGGCCCAAGCACTTATTTGT TTGCTCGTTCGAGAACTACG 187–192 1.000 84.2
rpoC1-rpoB_p2 rpoC1-rpoB TTTTAGTGGCCCAAGCACTT TTGCTCGTTCGAGAACTACG 193–198 1.000 83.5
rpoC1-rpoB_p3 rpoC1-rpoB TGGCCCAAGCACTTATTTGT CCCGAAGATGCTCCAGAATC 214–219 1.000 83.0
rpoC1-rpoB_p4 rpoC1-rpoB AGGATTTTAGTGGCCCAAGC TTGCTCGTTCGAGAACTACG 197–202 1.000 82.9
rpoC1-rpoB_p5 rpoC1-rpoB TTTTAGTGGCCCAAGCACTT CCCGAAGATGCTCCAGAATC 220–225 1.000 82.3
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CTCATTTCCATCCCCGAGC CCGGATTTGAACTGGGGAAA 1374–1405 1.000 75.6
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ATTCCCTCATTTCCATCCCC CCGGATTTGAACTGGGGAAA 1379–1410 1.000 75.0
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCATTTCCATCCCCGAGCAT CCGGATTTGAACTGGGGAAA 1373–1404 1.000 74.4
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CTCATTTCCATCCCCGAGC AGTCCTCTGCCTTACCACTC 1343–1374 1.000 72.8
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CATTTCCATCCCCGAGCAT CCGGATTTGAACTGGGGAAA 1372–1403 1.000 72.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (52)

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

Species Accession Length (bp) Link
Lycium acutifolium PP952461.1 155919 View on NCBI ↗
Lycium amarum NC_086884.1 155677 View on NCBI ↗
Lycium ameghinoi PP952462.1 155907 View on NCBI ↗
Lycium americanum PP952463.1 155636 View on NCBI ↗
Lycium andersonii PP952464.1 155731 View on NCBI ↗
Lycium barbarum NC_041110.1 155656 View on NCBI ↗
Lycium barbarum var. auranticarpum PX641346.1 154967 View on NCBI ↗
Lycium barbarum var. implicatum NC_084120.1 154888 View on NCBI ↗
Lycium berlandieri PP952467.1 155604 View on NCBI ↗
Lycium brevipes PP952468.1 155712 View on NCBI ↗
Lycium brevipes var. brevipes PP952495.1 155710 View on NCBI ↗
Lycium californicum PP952469.1 155749 View on NCBI ↗
Lycium californicum subsp. carinatum PP952470.1 155664 View on NCBI ↗
Lycium carolinianum PP952471.1 155712 View on NCBI ↗
Lycium cestroides PP952472.1 155953 View on NCBI ↗
Lycium chilense PP952473.1 155756 View on NCBI ↗
Lycium chinense NC_042204.1 155745 View on NCBI ↗
Lycium chinense var. potaninii PX804860.1 155029 View on NCBI ↗
Lycium ciliatum PP952475.1 155748 View on NCBI ↗
Lycium cooperi PP952476.1 155772 View on NCBI ↗
Lycium cuneatum PP952477.1 155866 View on NCBI ↗
Lycium cylindricum NC_086885.1 155662 View on NCBI ↗
Lycium dasystemum NC_067978.1 155656 View on NCBI ↗
Lycium dasystemum var. rubricaulium PQ835017.1 155638 View on NCBI ↗
Lycium densifolium PP952480.1 155639 View on NCBI ↗
Lycium elongatum PP952481.1 155702 View on NCBI ↗
Lycium exsertum PP952482.1 155618 View on NCBI ↗
Lycium ferocissimum PP952483.1 155892 View on NCBI ↗
Lycium fremontii PP952484.1 155712 View on NCBI ↗
Lycium infaustum PP952485.1 155695 View on NCBI ↗
Lycium macrodon PP952486.1 155924 View on NCBI ↗
Lycium megacarpum PP952487.1 155718 View on NCBI ↗
Lycium morongii PP952488.1 155760 View on NCBI ↗
Lycium ningxiaense NC_086883.1 154892 View on NCBI ↗
Lycium nodosum PP952489.1 155797 View on NCBI ↗
Lycium oxycarpum PP952465.1 155857 View on NCBI ↗
Lycium pallidum PP952490.1 155758 View on NCBI ↗
Lycium parishii PP952491.1 155750 View on NCBI ↗
Lycium puberulum PP952492.1 155792 View on NCBI ↗
Lycium qingshuiheense NC_084119.1 154945 View on NCBI ↗
Lycium rachidocladum PP952494.1 155689 View on NCBI ↗
Lycium ruthenicum NC_039651.1 154996 View on NCBI ↗
Lycium sandwicense PP952497.1 155775 View on NCBI ↗
Lycium schaffneri PP952498.1 155879 View on NCBI ↗
Lycium schweinfurthii PP952499.1 155763 View on NCBI ↗
Lycium shawii PQ824997.1 155936 View on NCBI ↗
Lycium shockleyi PP952500.1 155877 View on NCBI ↗
Lycium tenuispinosum PP952501.1 155717 View on NCBI ↗
Lycium tetrandrum PP952502.1 156034 View on NCBI ↗
Lycium torreyi PP952503.1 155696 View on NCBI ↗
Lycium truncatum NC_086880.1 155638 View on NCBI ↗
Lycium yunnanense NC_086881.1 155620 View on NCBI ↗