Markers + reference

Pyrrosia

10 species · Polypodiaceae · Polypodiales

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Species 10
Genome length 155–163 kb
Candidate markers 268
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
matK LSC 1506 0.0643 1.00 75.1 yes View details
matK-chlB LSC 1782 0.0855 0.99 79.8 yes View details
psbM-petN LSC 962 0.0762 0.97 77.5 yes View details
petA-psbJ LSC 1799 0.1039 0.72 75.3 yes View details
psbE-petL LSC 773 0.0699 0.99 82.7 yes View details
ndhF SSC 2220 0.0567 1.00 79.2 yes View details
rpl32-trnP-GGG SSC 603 0.1099 0.99 72.6 yes View details
ycf1 SSC 5109 0.0562 1.00 75.4 yes View details
rpoB-trnD-GUC LSC 673 0.0790 0.99 83.5 yes View details
trnS-GCU-ycf12 LSC 547 0.0685 0.99 80.5 yes View details
petB LSC 1469 0.0422 0.99 76.8 yes View details
trnL-UAA-trnF-GAA LSC 251 0.0774 0.98 76.3 yes View details
atpH-atpI LSC 757 0.0670 0.95 76.2 yes View details
rpl2 LSC 1554 0.0501 1.00 76.0 yes View details
rps4-trnL-UAA LSC 623 0.0649 1.00 75.8 yes View details
clpP-psbB LSC 470 0.0553 0.99 75.8 yes View details
trnC-GCA-trnG-GCC LSC 505 0.0883 0.97 75.7 yes View details
petN-trnC-GCA LSC 473 0.0581 0.97 75.5 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
matK_p1 matK AAGCAAGCCGTTGATAAGCT GTGAAACCCGAGCTAGGAAG 1797 0.200 46.5
matK_p2 matK AAGCAAGCCGTTGATAAGCT AGGTAGCTCAATCAACAGCG 2310 0.200 46.5
matK_p3 matK GAAGCAAGCCGTTGATAAGC GTGAAACCCGAGCTAGGAAG 1798 0.200 46.5
matK_p4 matK GCAAGCCGTTGATAAGCTTC GTGAAACCCGAGCTAGGAAG 1795 0.200 46.5
matK_p5 matK GCAAGCCGTTGATAAGCTTC AGGTAGCTCAATCAACAGCG 2308 0.200 46.4
matK-chlB_p1 matK-chlB TTTCTGTTTCCGAAGCCGAA TTGGAGATACGATAGCCCGT 2782–2843 1.000 91.2
matK-chlB_p2 matK-chlB TTCTGTTTCCGAAGCCGAAA TTGGAGATACGATAGCCCGT 2781–2842 0.900 87.1
matK-chlB_p3 matK-chlB TTTTCTGTTTCCGAAGCCGA TTGGAGATACGATAGCCCGT 2783–2844 0.600 74.8
matK-chlB_p4 matK-chlB TTCTGTTTCCGAAGCCGAAA ACACGACACTAAGGGGGTAA 2601 0.200 47.5
matK-chlB_p5 matK-chlB TTTCTGTTTCCGAAGCCGAA ACACGACACTAAGGGGGTAA 2602 0.200 47.5
trnS-GCU-ycf12_p1 trnS-GCU-ycf12 CCGACGCTTTAAACCTCTCA TCGGCTAGATGTTCCAAACG 809–810 0.200 47.5
trnS-GCU-ycf12_p2 trnS-GCU-ycf12 GGGAGAGAGAGGGATTCGAA TCGGCTAGATGTTCCAAACG 866–867 0.200 47.5
trnS-GCU-ycf12_p3 trnS-GCU-ycf12 AAGGGAGAGAGAGGGATTCG TCGGCTAGATGTTCCAAACG 868–869 0.200 47.4
trnS-GCU-ycf12_p4 trnS-GCU-ycf12 TGCCTCAATTGTCTCGTCAG TCGGCTAGATGTTCCAAACG 929–930 0.200 47.4
trnS-GCU-ycf12_p5 trnS-GCU-ycf12 CCGACGCTTTAAACCTCTCA CGAAGTACAAGAGTGACGGG 1025–1026 0.200 47.3
trnG-UCC_p1 trnG-UCC CGTTTGGAACATCTAGCCGA ACACTGCAGGAGAAGTAGGT 1386 0.200 47.9
trnG-UCC_p2 trnG-UCC CGTTTGGAACATCTAGCCGA ATTAGCTAGGGGTCAGCGAT 1660 0.200 47.9
trnG-UCC_p3 trnG-UCC CGTAACGGCCACTATTTCCA ACACTGCAGGAGAAGTAGGT 1800–1801 0.200 47.9
trnG-UCC_p4 trnG-UCC CGTAACGGCCACTATTTCCA ATTAGCTAGGGGTCAGCGAT 2074–2075 0.200 47.8
trnG-UCC_p5 trnG-UCC ACGTAACGGCCACTATTTCC ACACTGCAGGAGAAGTAGGT 1801–1802 0.200 47.8
atpH-atpI_p1 atpH-atpI TCCCTCCTGGAAAGTTTTGC GAATACCGTTCCTGGGTTCC 1795–1827 1.000 90.0
atpH-atpI_p2 atpH-atpI TTCTGGCTGTCTCGCAATAC GAATACCGTTCCTGGGTTCC 1332–1366 1.000 90.0
atpH-atpI_p3 atpH-atpI TCCCTCCTGGAAAGTTTTGC AGGGATTTAACGAGGACCCA 1828–1860 1.000 89.9
atpH-atpI_p4 atpH-atpI TCCCTCCTGGAAAGTTTTGC GGTAGTAGCTGTCCTCGTCT 1466–1498 0.900 86.4
atpH-atpI_p5 atpH-atpI TCCCTCCTGGAAAGTTTTGC TGGGGGAAGAAGAATACCGT 1818–1838 0.400 63.6
rpoB-trnD-GUC_p1 rpoB-trnD-GUC CAAGTTCTGGTAGTACGGGC GGTGCTCTAACCGATTGAACT 723–743 1.000 81.7
rpoB-trnD-GUC_p2 rpoB-trnD-GUC GCAAGTTCTGGTAGTACGGG GGTGCTCTAACCGATTGAACT 724–744 1.000 81.7
rpoB-trnD-GUC_p3 rpoB-trnD-GUC CAAGTTCTGGTAGTACGGGC GGATTGACGGGTCTCGAAC 766–786 1.000 81.4
rpoB-trnD-GUC_p4 rpoB-trnD-GUC GCAAGTTCTGGTAGTACGGG GGATTGACGGGTCTCGAAC 767–787 1.000 81.4
rpoB-trnD-GUC_p5 rpoB-trnD-GUC AGTTCTGGTAGTACGGGCAT GGTGCTCTAACCGATTGAACT 721–741 1.000 80.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Pyrrosia adnascens NC_080934.1 154753 View on NCBI ↗
Pyrrosia angustissima MT210543.1 157507 View on NCBI ↗
Pyrrosia assimilis MN617019.1 154964 View on NCBI ↗
Pyrrosia bonii NC_040226.1 158174 View on NCBI ↗
Pyrrosia drakeana MT210542.1 158132 View on NCBI ↗
Pyrrosia hastata NC_080935.1 154766 View on NCBI ↗
Pyrrosia lingua MN885668.1 160568 View on NCBI ↗
Pyrrosia petiolosa MN885667.1 163026 View on NCBI ↗
Pyrrosia sheareri MN885669.1 158165 View on NCBI ↗
Pyrrosia subfurfuracea NC_047436.1 158201 View on NCBI ↗