Markers + reference

Pyrenaria

11 species · Theaceae · Ericales

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Species 11
Genome length 157–157 kb
Candidate markers 273
Primer pairs 95

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 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnE-UUC-trnT-GGU LSC 776 0.0053 1.00 46.8 yes View details
rpl16 LSC 1426 0.0039 1.00 43.9 yes View details
rps3 LSC 657 0.0055 1.00 36.1 yes View details
ndhF SSC 2247 0.0063 1.00 41.7 yes View details
ndhF-rpl32 SSC 685 0.0087 0.99 47.2 yes View details
rpl32-trnL-UAG SSC 923 0.0072 1.00 52.7 yes View details
rps15-ycf1 SSC 390 0.0058 0.98 26.8 yes View details
ycf1 SSC 5616 0.0053 1.00 43.9 yes View details
trnH-GUG-psbA LSC 382 0.0084 1.00 60.8 yes View details
trnT-UGU-trnL-UAA LSC 1007 0.0033 1.00 60.4 yes View details
rps16-trnQ-UUG LSC 1622 0.0043 1.00 56.2 yes View details
rpoB-trnC-GCA LSC 1237 0.0042 1.00 53.2 yes View details
accD-psaI LSC 704 0.0050 1.00 53.1 yes View details
matK LSC 1500 0.0044 1.00 52.9 yes View details
ndhA SSC 2195 0.0018 0.99 52.7 yes View details
psaA-ycf3 LSC 770 0.0024 0.99 51.9 yes View details
trnS-GGA-rps4 LSC 292 0.0093 1.00 51.5 yes View details
atpH-atpI LSC 1106 0.0028 1.00 51.3 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CCGTGCTAACCTTGGTATGG 485–508 1.000 81.7
trnH-GUG-psbA_p2 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC CCGTGCTAACCTTGGTATGG 486–509 1.000 81.4
trnH-GUG-psbA_p3 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT ACCGTGCTAACCTTGGTATG 486–509 1.000 81.2
trnH-GUG-psbA_p4 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC ACCGTGCTAACCTTGGTATG 487–510 1.000 81.0
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 478–501 1.000 80.1
trnK-UUU_p1 trnK-UUU GCCCGTGTCAACCAATATCT TCTCCGTCCATAGGTTTGGT 2949–2959 1.000 80.2
trnK-UUU_p2 trnK-UUU TGCCCGTGTCAACCAATATC TCTCCGTCCATAGGTTTGGT 2950–2960 1.000 78.5
trnK-UUU_p3 trnK-UUU ATATGCCCGTGTCAACCAAT TCTCCGTCCATAGGTTTGGT 2953–2963 1.000 77.0
trnK-UUU_p4 trnK-UUU ATGCCCGTGTCAACCAATAT TCTCCGTCCATAGGTTTGGT 2951–2961 1.000 77.0
trnK-UUU_p5 trnK-UUU GCCCGTGTCAACCAATATCT CTCCGTCCATAGGTTTGGTT 2948–2958 1.000 74.4
matK_p1 matK GGGATAATTTCGATTTACACGGT TGTTTTGACCGTATCGCACT 1610–1616 1.000 47.7
matK_p2 matK GGGATAATTTCGATTTACACGGTC TGTTTTGACCGTATCGCACT 1610–1616 1.000 47.5
matK_p3 matK AGGGATAATTTCGATTTACACGG TGTTTTGACCGTATCGCACT 1611–1617 1.000 45.6
matK_p4 matK AGGGATAATTTCGATTTACACGGT TGTTTTGACCGTATCGCACT 1611–1617 1.000 45.1
matK_p5 matK GGGATAATTTCGATTTACACGGT CCTTGTTTTGACCGTATCGC 1613–1619 1.000 44.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 1704–1712 1.000 80.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1687–1695 1.000 79.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG TAGAAACGAAAATGGGGCGT 1764–1772 1.000 79.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1705–1713 1.000 79.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAGAAACGAAAATGGGGCGT 1747–1755 1.000 78.9
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 1187–1194 1.000 77.0
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT TTTTTGCAACTTTAGCCGCG 1243–1250 1.000 76.3
atpH-atpI_p3 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTTGCAACTTTAGCCGCG 1188–1195 1.000 75.8
atpH-atpI_p4 atpH-atpI GCAGTACCTTGACCAACTCC TTTTTGCAACTTTAGCCGCG 1247–1254 1.000 75.7
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC TTTTTGCAACTTTAGCCGCG 1202–1209 1.000 75.5
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CTTCATTTCCATCCCGTAGCA CCAGATTTGAACCGGGGAAA 1311–1322 1.000 72.4
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TTCATTTCCATCCCGTAGCA CCAGATTTGAACCGGGGAAA 1310–1321 1.000 72.3
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TTCCTTCATTTCCATCCCGT CCAGATTTGAACCGGGGAAA 1314–1325 1.000 71.5
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AGTTCTTCCGTCAAGCTTTGA CCAGATTTGAACCGGGGAAA 1393–1404 1.000 71.4
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TCATTTCCATCCCGTAGCAT CCAGATTTGAACCGGGGAAA 1309–1320 1.000 70.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (11)

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

Species Accession Length (bp) Link
Pyrenaria diospyricarpa NC_035704.1 157102 View on NCBI ↗
Pyrenaria hirta var. cordatula KY406785.1 156907 View on NCBI ↗
Pyrenaria hirta var. hirta KY406771.1 156892 View on NCBI ↗
Pyrenaria jonquieriana subsp. multisepala KY406772.1 156858 View on NCBI ↗
Pyrenaria khasiana NC_035644.1 157065 View on NCBI ↗
Pyrenaria menglaensis NC_035639.1 157122 View on NCBI ↗
Pyrenaria microcarpa NC_035686.1 156864 View on NCBI ↗
Pyrenaria oblongicarpa NC_035694.1 156732 View on NCBI ↗
Pyrenaria pingpienensis NC_035642.1 156926 View on NCBI ↗
Pyrenaria spectabilis NC_035687.1 156912 View on NCBI ↗
Pyrenaria spectabilis var. greeniae KY406753.1 156933 View on NCBI ↗