Markers + reference

Populus

57 species · Salicaceae · Malpighiales

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Species 57
Genome length 155–158 kb
Candidate markers 258
Primer pairs 95

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 258 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnR-UCU LSC 1683 0.0138 0.98 60.6 yes View details
psbZ-trnG-UCC LSC 506 0.0180 0.94 69.5 yes View details
ndhC-trnV-UAC LSC 1332 0.0205 0.94 73.7 yes View details
trnR-ACG-trnN-GUU SSC 677 0.0128 0.97 65.1 yes View details
ndhF SSC 2289 0.0044 1.00 43.2 yes View details
ndhF-trnL-UAG SSC 566 0.0133 0.94 58.9 yes View details
psaC SSC 246 0.0047 1.00 29.5 yes View details
ndhH-ycf1 SSC 811 0.0082 1.00 57.3 yes View details
trnN-GUU-trnR-ACG SSC 673 0.0120 0.99 64.6 yes View details
atpA-atpF LSC 60 0.0747 0.98 72.1 yes View details
psbJ-psbL LSC 187 0.0274 0.98 69.9 yes View details
petA-psbJ LSC 945 0.0074 0.99 67.7 yes View details
rpl36-rps8 LSC 477 0.0074 1.00 62.7 yes View details
trnF-GAA-ndhJ LSC 746 0.0087 0.98 62.3 yes View details
ccsA-ndhD SSC 226 0.0201 0.99 60.6 yes View details
psbH-petD LSC 2567 0.0026 1.00 59.8 yes View details
rps12-clpP LSC 193 0.0162 0.99 59.1 yes View details
ycf4-cemA LSC 375 0.0114 0.99 58.9 yes View details
psbM-trnD-GUC LSC 1200 0.0051 1.00 58.4 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU GCTTTAGTCCACTCAGCCAT AGAAGACCTCTGTCCTATCCA 1710–1902 1.000 70.6
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU GCTTTAGTCCACTCAGCCAT AGGTTTAGAAGACCTCTGTCCT 1716–1908 1.000 69.9
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU AGTCCACTCAGCCATCTCTC AGAAGACCTCTGTCCTATCCA 1705–1897 1.000 69.8
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU AGTCCACTCAGCCATCTCTC AGGTTTAGAAGACCTCTGTCCT 1711–1903 1.000 69.1
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU TAGTCCACTCAGCCATCTCT AGAAGACCTCTGTCCTATCCA 1706–1898 1.000 67.2
atpA-atpF_p1 atpA-atpF TACTAATCTCGTCGGCTCGA TGTTTGGGGCGATGAAAGAA 113–125 1.000 90.1
atpA-atpF_p2 atpA-atpF CACTTGAAGTACGGTCCCAG TGTTTGGGGCGATGAAAGAA 187–199 1.000 89.8
atpA-atpF_p3 atpA-atpF CACCCACTTGAAGTACGGTC TGTTTGGGGCGATGAAAGAA 191–203 1.000 88.7
atpA-atpF_p4 atpA-atpF CCGTCACCCACTTGAAGTAC TGTTTGGGGCGATGAAAGAA 195–207 1.000 88.6
atpA-atpF_p5 atpA-atpF GTCACCCACTTGAAGTACGG TGTTTGGGGCGATGAAAGAA 193–205 1.000 88.6
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 1232–1436 1.000 66.1
psbM-trnD-GUC_p2 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TTTCGTTTCCCTGGGATTGT 1254–1458 0.982 63.7
psbM-trnD-GUC_p3 psbM-trnD-GUC AGGAACTAGAATGAACAGTGCA TTCAATTGGTCAGAGCACCG 1239–1443 1.000 62.9
psbM-trnD-GUC_p4 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC CGTTTCCCTGGGATTGTAGT 1251–1455 0.982 62.8
psbM-trnD-GUC_p5 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC GTTCAATTGGTCAGAGCACC 1233–1437 1.000 62.0
psbZ-trnG-UCC_p1 psbZ-trnG-UCC CGGTTGGTCAAGCAACAAAA AAATCGACTTGGGCGGATAG 676–887 0.982 84.7
psbZ-trnG-UCC_p2 psbZ-trnG-UCC CGGTTGGTCAAGCAACAAAA CGTCTTCTCCTTGGCAAAGA 641–852 0.947 83.8
psbZ-trnG-UCC_p3 psbZ-trnG-UCC TTTCTTCTCCTGACGGTTGG AAATCGACTTGGGCGGATAG 689–900 1.000 83.4
psbZ-trnG-UCC_p4 psbZ-trnG-UCC TTTCTTCTCCTGACGGTTGG CGTCTTCTCCTTGGCAAAGA 654–865 0.965 82.5
psbZ-trnG-UCC_p5 psbZ-trnG-UCC TTCTTCTCCTGACGGTTGGT CGTCTTCTCCTTGGCAAAGA 653–864 0.965 82.2
trnF-GAA-ndhJ_p1 trnF-GAA-ndhJ GGGATAGCTCAGCAGGTAGA CCGGAAAGTTGGATAGGGTG 490–920 1.000 87.6
trnF-GAA-ndhJ_p2 trnF-GAA-ndhJ GGGATAGCTCAGCAGGTAGA CGGAAAGTTGGATAGGGTGG 489–919 1.000 87.6
trnF-GAA-ndhJ_p3 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA CCGGAAAGTTGGATAGGGTG 454–884 1.000 87.2
trnF-GAA-ndhJ_p4 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA CGGAAAGTTGGATAGGGTGG 453–883 1.000 87.2
trnF-GAA-ndhJ_p5 trnF-GAA-ndhJ CAGGTAGAGCAGAGGACTGA CGGAAAGTTGGATAGGGTGG 477–907 1.000 86.5
ndhC-trnV-UAC_p1 ndhC-trnV-UAC GGGGATAAAAGGCCCGAAAT AGAAGGTCTACGGTTCGAGT 1304–1556 1.000 89.3
ndhC-trnV-UAC_p2 ndhC-trnV-UAC AATTGGGGATAAAAGGCCCG AGAAGGTCTACGGTTCGAGT 1308–1560 1.000 88.3
ndhC-trnV-UAC_p3 ndhC-trnV-UAC GGGGATAAAAGGCCCGAAAT GAAGGTCTACGGTTCGAGTC 1303–1555 1.000 86.6
ndhC-trnV-UAC_p4 ndhC-trnV-UAC AATTGGGGATAAAAGGCCCG GAAGGTCTACGGTTCGAGTC 1307–1559 1.000 85.5
ndhC-trnV-UAC_p5 ndhC-trnV-UAC GGCCCGAAATTAGAAATGCC AGAAGGTCTACGGTTCGAGT 1294–1546 0.965 84.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (57)

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

Species Accession Length (bp) Link
Populus afghanica NC_045396.1 155975 View on NCBI ↗
Populus alba NC_008235.1 156505 View on NCBI ↗
Populus alba var. pyramidalis MK341061.1 156225 View on NCBI ↗
Populus alba x Populus glandulosa NC_058277.1 156505 View on NCBI ↗
Populus angustifolia NC_037413.1 156698 View on NCBI ↗
Populus balsamifera NC_024735.1 157094 View on NCBI ↗
Populus butuoensis PP565779.1 156454 View on NCBI ↗
Populus cathayana NC_040874.1 156789 View on NCBI ↗
Populus ciliata MW376769.1 156953 View on NCBI ↗
Populus dafengensis PP565785.1 156511 View on NCBI ↗
Populus davidiana NC_032717.1 155853 View on NCBI ↗
Populus deltoides NC_040929.1 156957 View on NCBI ↗
Populus deltoides x Populus alba PV241163.1 157144 View on NCBI ↗
Populus euphratica NC_024747.1 156766 View on NCBI ↗
Populus fremontii NC_024734.1 157446 View on NCBI ↗
Populus glandulosa NC_058278.1 155374 View on NCBI ↗
Populus glauca MW376847.1 155713 View on NCBI ↗
Populus gonggaensis NC_040873.1 156466 View on NCBI ↗
Populus grandidentata MW376776.1 155170 View on NCBI ↗
Populus haoana NC_040872.1 156523 View on NCBI ↗
Populus heterophylla MW376780.1 157072 View on NCBI ↗
Populus hopeiensis NC_040871.1 155367 View on NCBI ↗
Populus ilicifolia NC_031371.1 158017 View on NCBI ↗
Populus iliensis MW376784.1 156561 View on NCBI ↗
Populus intramongolica MW376785.1 156689 View on NCBI ↗
Populus kangdingensis NC_040870.1 156523 View on NCBI ↗
Populus maximowiczii NC_060732.1 156892 View on NCBI ↗
Populus nigra subsp. nigra PP541867.1 156450 View on NCBI ↗
Populus ningshanica MW376801.1 155533 View on NCBI ↗
Populus pamirica MW376803.1 157193 View on NCBI ↗
Populus platyphylla MW376804.1 156472 View on NCBI ↗
Populus pseudoglauca NC_040869.1 156512 View on NCBI ↗
Populus pseudomaximowiczii MW376810.1 156577 View on NCBI ↗
Populus qamdoensis NC_040868.1 156526 View on NCBI ↗
Populus qiongdaoensis NC_031398.1 156074 View on NCBI ↗
Populus rotundifolia var. duclouxiana MK267306.1 155177 View on NCBI ↗
Populus schneideri NC_040867.1 156513 View on NCBI ↗
Populus shanxiensis MW376822.1 156753 View on NCBI ↗
Populus suaveolens MW376825.1 156904 View on NCBI ↗
Populus szechuanica var. rockii MW376815.1 156541 View on NCBI ↗
Populus szechuanica var. tibetica MW376831.1 157438 View on NCBI ↗
Populus talassica MW376834.1 156878 View on NCBI ↗
Populus tomentosa NC_040866.1 156446 View on NCBI ↗
Populus tremula NC_027425.1 156067 View on NCBI ↗
Populus tremula x Populus alba NC_028504.1 156641 View on NCBI ↗
Populus tremuloides NC_058279.1 156192 View on NCBI ↗
Populus trichocarpa NC_009143.1 157033 View on NCBI ↗
Populus ussuriensis MW376844.1 156872 View on NCBI ↗
Populus wenxianica MW376846.1 156974 View on NCBI ↗
Populus wulianensis NC_058847.1 156553 View on NCBI ↗
Populus x beijingensis PV191314.1 157070 View on NCBI ↗
Populus x canadensis NC_040928.1 156957 View on NCBI ↗
Populus x jrtyschensis MW376854.1 156365 View on NCBI ↗
Populus x xiaohei PV200281.1 156632 View on NCBI ↗
Populus xiangchengensis NC_040953.1 156465 View on NCBI ↗
Populus yatungensis MW376856.1 157439 View on NCBI ↗
Populus yunnanensis var. microphylla MW376821.1 156381 View on NCBI ↗