Markers + reference

Polystichum

4 species · Dryopteridaceae · Polypodiales

Back to catalogue

Species 4
Genome length 149–150 kb
Candidate markers 206
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 7 remaining regions by MarkerSeek score (out of 206 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnN-GUU-rpl32 SSC 3545 0.2054 1.00 79.5 yes View details
rpl32-trnP-GGG SSC 646 0.3093 0.99 84.4 yes View details
trnP-GGG-trnL-UAG SSC 282 0.3435 0.91 75.9 yes View details
ccsA-ndhD SSC 398 0.2645 0.96 76.7 yes View details
ndhE SSC 303 0.2492 1.00 76.4 yes View details
ndhE-ndhI SSC 841 0.2665 1.00 84.2 yes View details
ndhI SSC 516 0.2678 1.00 82.9 yes View details
ndhA SSC 2073 0.2344 1.00 82.1 yes View details
ycf1 SSC 3909 0.2395 1.00 79.0 yes View details
ycf1-chlN SSC 1572 0.2295 0.99 82.9 yes View details
chlN SSC 1386 0.2278 1.00 83.9 yes View details
trnN-GUU-trnH-GUG IRa 7096 0.0277 0.99 60.9 yes View details
trnT-GGU-rps14 LSC 674 0.0692 1.00 84.8 yes View details
ndhH SSC 1179 0.2221 1.00 84.3 yes View details
psbK-psbI LSC 556 0.0650 1.00 84.2 yes View details
chlN-trnN-GUU SSC 1395 0.2484 1.00 84.1 yes View details
trnS-GCU-ycf12 LSC 578 0.0715 0.98 83.6 yes View details
ndhD SSC 1509 0.2279 1.00 83.4 yes View details
ccsA SSC 945 0.2208 1.00 82.9 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
psbK-psbI_p1 psbK-psbI CGCAGTTAGCTTCCGGTAA ACAAATAGTTTGAGGGTAAGCA 583–602 1.000 50.2
psbK-psbI_p2 psbK-psbI CGCAGTTAGCTTCCGGTAA AGACAAATAGTTTGAGGGTAAGCA 585–604 1.000 50.1
psbK-psbI_p3 psbK-psbI CGCAGTTAGCTTCCGGTAA TGCATAGACAAATAGTTTGAGGGT 590–609 1.000 50.1
psbK-psbI_p4 psbK-psbI CGCAGTTAGCTTCCGGTAA GACAAATAGTTTGAGGGTAAGCA 584–603 1.000 50.1
psbK-psbI_p5 psbK-psbI CGCAGTTAGCTTCCGGTAA CTGCATAGACAAATAGTTTGAGGG 591–610 1.000 50.1
trnS-GCU-ycf12_p1 trnS-GCU-ycf12 TGCAGGCGGAGATATCAGTA AATGGTCCCGATGCAACTAC 1268–1305 1.000 90.0
trnS-GCU-ycf12_p2 trnS-GCU-ycf12 TGCAGGCGGAGATATCAGTA ACTAATGGTCCCGATGCAAC 1271–1308 1.000 90.0
trnS-GCU-ycf12_p3 trnS-GCU-ycf12 TGCAGGCGGAGATATCAGTA TTCACGGTTATGCTGCCTAC 1348 0.500 59.9
trnS-GCU-ycf12_p4 trnS-GCU-ycf12 TGCAGGCGGAGATATCAGTA CACGGTTATGCTGCCTACAT 1346 0.500 59.7
trnS-GCU-ycf12_p5 trnS-GCU-ycf12 GGGATTTGAACCCTCGGTAC TTCACGGTTATGCTGCCTAC 779 0.500 59.7
trnT-GGU-rps14_p1 trnT-GGU-rps14 CTCTACCGCTGAGTTAAGGG GAGTATCCAAATCAAGTTGGT 715–772 1.000 50.4
trnT-GGU-rps14_p2 trnT-GGU-rps14 GGATTTGAACCGACGGCTTA GAGTATCCAAATCAAGTTGGT 753–810 1.000 50.3
trnT-GGU-rps14_p3 trnT-GGU-rps14 GGATTTGAACCGACGGCTTA AGTATCCAAATCAAGTTGGT 752–809 1.000 50.3
trnT-GGU-rps14_p4 trnT-GGU-rps14 GATTTGAACCGACGGCTTAC GAGTATCCAAATCAAGTTGGT 752–809 1.000 50.3
trnT-GGU-rps14_p5 trnT-GGU-rps14 CCCCTTGTCGGATTTGAACC GAGTATCCAAATCAAGTTGGT 762–819 1.000 50.3
trnV-UAC_p1 trnV-UAC GAAGACCGCGAAAACCAAAG GAGAGAGCTGCCGAAATTGA 2030–2045 1.000 89.3
trnV-UAC_p2 trnV-UAC GAAGACCGCGAAAACCAAAG CAAGTAGGCCGCCAGTAATT 1662–1678 1.000 89.3
trnV-UAC_p3 trnV-UAC GAAGACCGCGAAAACCAAAG GCGATACTCTAACCGCTGAG 1683–1699 1.000 89.3
trnV-UAC_p4 trnV-UAC GAAGACCGCGAAAACCAAAG AATTGATCCCGACGAAGCTC 2016–2031 1.000 88.9
trnV-UAC_p5 trnV-UAC GAAGACCGCGAAAACCAAAG GACGAAGCTCGAAGAACCTT 2006–2021 1.000 88.9
trnN-GUU-rpl32_p1 trnN-GUU-rpl32 ACGAAAGTAGCAGCTTACGG CCGCTATCCTGTTTCTGGTC 1021–1028 0.750 77.5
trnN-GUU-rpl32_p2 trnN-GUU-rpl32 ACGAAAGTAGCAGCTTACGG GTATACCCCCGCTATCCTGT 1029–1036 0.750 77.4
trnN-GUU-rpl32_p3 trnN-GUU-rpl32 ACGAAAGTAGCAGCTTACGG ACTCCACGATGTCCCAGTTA 1287–1294 0.750 77.4
trnN-GUU-rpl32_p4 trnN-GUU-rpl32 ACGAAAGTAGCAGCTTACGG TACTCCACGATGTCCCAGTT 1288–1295 0.750 77.4
trnN-GUU-rpl32_p5 trnN-GUU-rpl32 ACGAAAGTAGCAGCTTACGG CGCTATCCTGTTTCTGGTCC 1020 0.500 66.4
rpl32-trnP-GGG_p1 rpl32-trnP-GGG TAATCGCGCGTGGAAAACTA CTCTGGCACTGCTTCCTAAG 1157–1189 0.750 81.0
rpl32-trnP-GGG_p2 rpl32-trnP-GGG TAATCGCGCGTGGAAAACTA CTGGCACTGCTTCCTAAGAG 1155–1187 0.750 81.0
rpl32-trnP-GGG_p3 rpl32-trnP-GGG TAATCGCGCGTGGAAAACTA GAGGTCACAGGTTCGAATCC 798–847 0.750 78.8
rpl32-trnP-GGG_p4 rpl32-trnP-GGG TAATCGCGCGTGGAAAACTA GGAGGTCACAGGTTCGAATC 799–848 0.750 78.8
rpl32-trnP-GGG_p5 rpl32-trnP-GGG ACGGATCTGGCATCAACTTC GAGGTCACAGGTTCGAATCC 1234–1283 0.500 66.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Polystichum jinfoshanense MT789702.1 149099 View on NCBI ↗
Polystichum piceopaleaceum PP236762.1 150343 View on NCBI ↗
Polystichum tripteron NC_050009.1 148539 View on NCBI ↗
Polystichum yaanense NC_063670.1 149052 View on NCBI ↗