Markers + reference

Berberis

17 species · Berberidaceae · Ranunculales

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Species 17
Genome length 165–167 kb
Candidate markers 285
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 285 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
petN-psbM LSC 649 0.0189 1.00 71.1 yes View details
rbcL-psaI LSC 2923 0.0255 0.91 66.9 yes View details
rps12-clpP LSC 521 0.0213 0.98 65.8 yes View details
trnN-GUU-ndhF SSC 2720 0.0228 0.76 58.9 yes View details
ndhD SSC 1503 0.0043 1.00 36.1 yes View details
rps15-trnN-GUU SSC 6882 0.0095 0.95 50.9 yes View details
ccsA-ndhD SSC 240 0.0398 0.98 79.5 yes View details
trnI-CAU-ycf2 IRb 285 0.0271 1.00 70.4 yes View details
ndhC-trnV-UAC LSC 1576 0.0090 0.99 67.0 yes View details
trnK-UUU-rps16 LSC 575 0.0122 1.00 65.6 yes View details
trnF-GAA-ndhJ LSC 720 0.0052 0.98 59.0 yes View details
trnH-GUG-psbA LSC 462 0.0131 0.97 57.6 yes View details
ycf2-trnI-CAU IRa 285 0.0135 1.00 57.4 yes View details
ndhF-rpl32 SSC 1027 0.0138 0.98 56.6 yes View details
rps4-trnT-UGU LSC 399 0.0067 1.00 56.4 yes View details
rpl32-trnL-UAG SSC 528 0.0130 1.00 56.3 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CAATCCACTGCCTTAACCCA TGGGCTGATATCATCAACCG 508–635 1.000 80.4
trnH-GUG-psbA_p2 trnH-GUG-psbA AATCCACTGCCTTAACCCAC TGGGCTGATATCATCAACCG 507–634 1.000 80.4
trnH-GUG-psbA_p3 trnH-GUG-psbA ACAATCCACTGCCTTAACCC TGGGCTGATATCATCAACCG 509–636 1.000 80.4
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACTGCCTTAACCCA GGGCTGATATCATCAACCGT 507–634 1.000 80.4
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTGCCTTAACCCAC GGGCTGATATCATCAACCGT 506–633 1.000 80.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCTACCAACGGTATGGACGA AAAAAGGCGCTCAACCTACA 716–755 1.000 85.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAAGGCGCTCAACCTACA 651–690 1.000 85.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAAGGCGCTCAACCTACA 650–689 1.000 85.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC AAAAAGGCGCTCAACCTACA 665–704 1.000 84.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AAAAAGGCGCTCAACCTACA 660–699 1.000 84.3
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCTACTGCATTGTTCATTCT 798–808 1.000 60.4
petN-psbM_p2 petN-psbM AGTAAGTCTTGCTTGGGCTG TGCTACTGCATTGTTCATTCT 804–814 1.000 58.8
petN-psbM_p3 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCATTGTTCATTCT 744–754 1.000 58.0
petN-psbM_p4 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCTACTGCATTGTTCATTC 798–808 1.000 55.7
petN-psbM_p5 petN-psbM TTGCTTGGGCTGCTTTAATG TGCTACTGCATTGTTCATTCT 796–806 1.000 54.5
rps4-trnT-UGU_p1 rps4-trnT-UGU CTCCCAGACGGCGTATTTTT CTCAGAGGTTAGAGCATCGC 509–534 1.000 82.1
rps4-trnT-UGU_p2 rps4-trnT-UGU GTAAGTCCCGGTAAAGCTCC CTCAGAGGTTAGAGCATCGC 525–550 1.000 81.6
rps4-trnT-UGU_p3 rps4-trnT-UGU CTCCCAGACGGCGTATTTTT ATGGTCATCGGTTCGATTCC 477–502 1.000 81.5
rps4-trnT-UGU_p4 rps4-trnT-UGU GTAAGTCCCGGTAAAGCTCC ATGGTCATCGGTTCGATTCC 493–518 1.000 81.0
rps4-trnT-UGU_p5 rps4-trnT-UGU GCGATTGGTTTCGAGGATCA CTCAGAGGTTAGAGCATCGC 569–594 1.000 80.9
trnF-GAA-ndhJ_p1 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA TTTGATGCCCGAAAGTTGGA 808–847 1.000 84.7
trnF-GAA-ndhJ_p2 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA GATAATCATCCGCGCCTGAA 834–873 1.000 83.0
trnF-GAA-ndhJ_p3 trnF-GAA-ndhJ TATGGAAATGATGCACCGCA TTTGATGCCCGAAAGTTGGA 907–915 0.412 56.5
trnF-GAA-ndhJ_p4 trnF-GAA-ndhJ TATGGAAATGATGCACCGCA GATAATCATCCGCGCCTGAA 933–941 0.412 55.0
trnF-GAA-ndhJ_p5 trnF-GAA-ndhJ TATGGAAATGATGCACCGCA TTGATGCCCGAAAGTTGGAT 906–914 0.412 54.9
ndhC-trnV-UAC_p1 ndhC-trnV-UAC CCGGTCCTTCACTAATTGGG AGAAGGTCTACGGTTCGAGT 1671–1726 1.000 84.2
ndhC-trnV-UAC_p2 ndhC-trnV-UAC CGGTCCTTCACTAATTGGGG AGAAGGTCTACGGTTCGAGT 1670–1725 1.000 84.2
ndhC-trnV-UAC_p3 ndhC-trnV-UAC CCTTCACTAATTGGGGCCAA AGAAGGTCTACGGTTCGAGT 1666–1721 1.000 82.7
ndhC-trnV-UAC_p4 ndhC-trnV-UAC GGTCCTTCACTAATTGGGGC AGAAGGTCTACGGTTCGAGT 1669–1724 1.000 82.6
ndhC-trnV-UAC_p5 ndhC-trnV-UAC GTCCTTCACTAATTGGGGCC AGAAGGTCTACGGTTCGAGT 1668–1723 1.000 82.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (17)

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

Species Accession Length (bp) Link
Berberis amurensis NC_030062.1 166636 View on NCBI ↗
Berberis amurensis var. latifolia MN510463.1 166513 View on NCBI ↗
Berberis amurensis var. quelpaertensis KM057376.1 166630 View on NCBI ↗
Berberis aquifolium NC_066183.1 165689 View on NCBI ↗
Berberis dasystachya MZ983398.1 167036 View on NCBI ↗
Berberis diaphana MZ962404.1 166225 View on NCBI ↗
Berberis eurybracteata NC_066187.1 165612 View on NCBI ↗
Berberis fordii NC_066188.1 165689 View on NCBI ↗
Berberis fortunei NC_042167.1 165611 View on NCBI ↗
Berberis ganpinensis MN417307.1 165562 View on NCBI ↗
Berberis gracilipes NC_066189.1 165909 View on NCBI ↗
Berberis japonica NC_066191.1 165711 View on NCBI ↗
Berberis koreana NC_030063.1 166758 View on NCBI ↗
Berberis napaulensis NC_066192.1 165216 View on NCBI ↗
Berberis nitens NC_066193.1 165692 View on NCBI ↗
Berberis polyodonta NC_066195.1 165526 View on NCBI ↗
Berberis weiningensis NC_056989.1 166275 View on NCBI ↗