Markers + reference

Actinidia

45 species · Actinidiaceae · Ericales

Back to catalogue

Species 45
Genome length 156–158 kb
Candidate markers 268
Primer pairs 90

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
trnG (UCC)-trnR (UCU) LSC 342 0.0269 0.97 69.0 yes View details
petN-psbM LSC 728 0.0174 1.00 78.9 yes View details
trnT (UGU)-trnL (UAA) LSC 628 0.0193 1.00 70.9 yes View details
trnF (GAA)-ndhJ LSC 709 0.0143 0.98 64.5 yes View details
accD LSC 834 0.0148 0.95 62.7 yes View details
petA-psbJ LSC 937 0.0172 1.00 77.8 yes View details
rps12-psbB LSC 3011 0.0379 0.85 68.6 yes View details
ndhF-rpl32 SSC 974 0.0145 0.99 69.4 yes View details
accD-psaI LSC 614 0.0134 0.99 74.4 yes View details
ndhC-trnV (UAC) LSC 1184 0.0120 0.99 71.3 yes View details
rps16-trnQ (UUG) LSC 1408 0.0124 0.99 71.0 yes View details
trnC (GCA)-petN LSC 783 0.0125 0.94 69.4 yes View details
atpH-atpI LSC 1084 0.0077 1.00 68.4 yes View details
trnE (UUC)-trnT (GGU) LSC 796 0.0081 0.99 67.3 yes View details
trnS (GCU)-trnG (UCC) LSC 663 0.0077 1.00 67.1 yes View details
rpoB-trnC (GCA) LSC 1252 0.0076 0.99 66.4 yes View details
psbE-petL LSC 1312 0.0082 0.99 65.6 yes View details
atpB-rbcL LSC 763 0.0054 0.99 65.2 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ (UUG)_p1 rps16-trnQ (UUG) AACGGATCGTGTCCTTCAAG GAAATTGAAATGGGGCGTGG 1455–1616 1.000 91.2
rps16-trnQ (UUG)_p2 rps16-trnQ (UUG) AAGTCGCACGTTGCTTTCTA GAAATTGAAATGGGGCGTGG 1438–1599 1.000 90.7
rps16-trnQ (UUG)_p3 rps16-trnQ (UUG) CAACGGATCGTGTCCTTCAA GAAATTGAAATGGGGCGTGG 1456–1617 1.000 90.1
rps16-trnQ (UUG)_p4 rps16-trnQ (UUG) GGATCGTGTCCTTCAAGTCG GAAATTGAAATGGGGCGTGG 1452–1613 1.000 88.9
rps16-trnQ (UUG)_p5 rps16-trnQ (UUG) CGGATCGTGTCCTTCAAGTC GAAATTGAAATGGGGCGTGG 1453–1614 1.000 88.8
trnS (GCU)-trnG (UCC)_p1 trnS (GCU)-trnG (UCC) ATTAGCAATCCGCCGCTTTA TGAATTCAACCGAAAGACCCT 619–793 0.978 76.1
trnS (GCU)-trnG (UCC)_p2 trnS (GCU)-trnG (UCC) AGGAAACGGAAAGAGAGGGA TGAATTCAACCGAAAGACCCT 673–847 0.978 75.8
trnS (GCU)-trnG (UCC)_p3 trnS (GCU)-trnG (UCC) ACGGAAAGAGAGGGATTCGA TGAATTCAACCGAAAGACCCT 668–842 0.978 74.8
trnS (GCU)-trnG (UCC)_p4 trnS (GCU)-trnG (UCC) AGGAAACGGAAAGAGAGGGA GCACGAATCACACTTTTACCA 630–804 1.000 73.5
trnS (GCU)-trnG (UCC)_p5 trnS (GCU)-trnG (UCC) GCTTTAGTCCACTCAGCCAT TGAATTCAACCGAAAGACCCT 605–779 0.978 73.2
trnG (UCC)-trnR (UCU)_p1 trnG (UCC)-trnR (UCU) AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 422–486 1.000 75.3
trnG (UCC)-trnR (UCU)_p2 trnG (UCC)-trnR (UCU) CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 425–489 1.000 75.1
trnG (UCC)-trnR (UCU)_p3 trnG (UCC)-trnR (UCU) AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 428–492 1.000 74.7
trnG (UCC)-trnR (UCU)_p4 trnG (UCC)-trnR (UCU) CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 431–495 1.000 74.5
trnG (UCC)-trnR (UCU)_p5 trnG (UCC)-trnR (UCU) CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 426–490 1.000 72.9
atpH-atpI_p1 atpH-atpI AACAGAAGCGGCAGAAATCA TTTTTGCAACTTTAGCCGCG 1164–1248 1.000 82.6
atpH-atpI_p2 atpH-atpI GCCAATCCAGCAGCAATAAC TTTTTGCAACTTTAGCCGCG 1181–1265 1.000 81.6
atpH-atpI_p3 atpH-atpI CAGCAGCAATAACAGAAGCG TTTTTGCAACTTTAGCCGCG 1174–1258 0.978 81.0
atpH-atpI_p4 atpH-atpI AACAGAAGCGGCAGAAATCA CCGCGGCTTATATAGGTGAA 1149–1233 1.000 80.9
atpH-atpI_p5 atpH-atpI AGTACCCTGACCAACTCCAG TTTTTGCAACTTTAGCCGCG 1224–1308 1.000 80.3
rpoB-trnC (GCA)_p1 rpoB-trnC (GCA) CGTCAAGCCCTGATCAATGA GTCTTTTGTTGATCAGGCGC 1308–1438 1.000 89.2
rpoB-trnC (GCA)_p2 rpoB-trnC (GCA) CGTCAAGCCCTGATCAATGA AAAAGGATTTGCAGTCCCCC 1267–1397 1.000 86.7
rpoB-trnC (GCA)_p3 rpoB-trnC (GCA) AAAGTTCTTCCGTCAAGCCC GTCTTTTGTTGATCAGGCGC 1318–1448 1.000 86.2
rpoB-trnC (GCA)_p4 rpoB-trnC (GCA) TTCTTTTTCATCCCGGAGCA GTCTTTTGTTGATCAGGCGC 1233–1363 1.000 85.0
rpoB-trnC (GCA)_p5 rpoB-trnC (GCA) AAAGTTCTTCCGTCAAGCCC AAAAGGATTTGCAGTCCCCC 1277–1407 1.000 83.7
trnC (GCA)-petN_p1 trnC (GCA)-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 817–867 1.000 87.9
trnC (GCA)-petN_p2 trnC (GCA)-petN GGGGGACTGCAAATCCTTTT AGAGTCCACTTCTTCCCCAT 878–928 1.000 86.3
trnC (GCA)-petN_p3 trnC (GCA)-petN TATCCATTTGGCGACATGGC AGCCCAAGCGAGACTTACTA 850–900 1.000 85.3
trnC (GCA)-petN_p4 trnC (GCA)-petN TATCCATTTGGCGACATGGC AGAGTCCACTTCTTCCCCAT 911–961 1.000 83.7
trnC (GCA)-petN_p5 trnC (GCA)-petN AGTTCAAATCTGGGTGGCG AGCCCAAGCGAGACTTACTA 792–842 1.000 82.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (45)

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

Species Accession Length (bp) Link
Actinidia arguta var. hypoleuca OM949906.1 157500 View on NCBI ↗
Actinidia callosa var. discolor OM949888.1 156330 View on NCBI ↗
Actinidia chengkouensis OM949912.1 156893 View on NCBI ↗
Actinidia chinensis NC_026690.1 156346 View on NCBI ↗
Actinidia chrysantha OM949890.1 156828 View on NCBI ↗
Actinidia cylindrica OM949905.1 156440 View on NCBI ↗
Actinidia farinosa OM949917.1 156413 View on NCBI ↗
Actinidia fasciculoides OM949913.1 155755 View on NCBI ↗
Actinidia fortunatii OM949932.1 155789 View on NCBI ↗
Actinidia fulvicoma NC_051888.1 157339 View on NCBI ↗
Actinidia glaucocallosa OM949892.1 157070 View on NCBI ↗
Actinidia glaucophylla OM949889.1 156488 View on NCBI ↗
Actinidia grandiflora OM949914.1 156389 View on NCBI ↗
Actinidia henryi OM949904.1 156319 View on NCBI ↗
Actinidia holotricha OM949927.1 156508 View on NCBI ↗
Actinidia hubeiensis OM949937.1 156283 View on NCBI ↗
Actinidia indochinensis OM949936.1 156830 View on NCBI ↗
Actinidia laevissima OM949921.1 155992 View on NCBI ↗
Actinidia liangguangensis OM949922.1 156084 View on NCBI ↗
Actinidia linguiensis OM949924.1 156170 View on NCBI ↗
Actinidia longicarpa OM949907.1 157243 View on NCBI ↗
Actinidia macrosperma NC_051887.1 156231 View on NCBI ↗
Actinidia melanandra OM949901.1 157805 View on NCBI ↗
Actinidia melliana OM949926.1 156651 View on NCBI ↗
Actinidia obovata OM949915.1 156922 View on NCBI ↗
Actinidia persicina OM949916.1 156424 View on NCBI ↗
Actinidia pilosula OM949918.1 157281 View on NCBI ↗
Actinidia polygama NC_031186.1 156583 View on NCBI ↗
Actinidia rongshuiensis OM949928.1 157173 View on NCBI ↗
Actinidia rubricaulis var. coriacea OM949903.1 156741 View on NCBI ↗
Actinidia rubus NC_053769.1 156573 View on NCBI ↗
Actinidia rudis OM949911.1 155612 View on NCBI ↗
Actinidia rufa NC_039973.1 156543 View on NCBI ↗
Actinidia rufotricha OM949919.1 155538 View on NCBI ↗
Actinidia sabiifolia OM949895.1 157275 View on NCBI ↗
Actinidia setosa NC_051881.1 156728 View on NCBI ↗
Actinidia sorbifolia OM949885.1 156245 View on NCBI ↗
Actinidia styracifolia OM949908.1 157022 View on NCBI ↗
Actinidia suberifolia OM949909.1 156922 View on NCBI ↗
Actinidia trichogyna PX754132.1 156507 View on NCBI ↗
Actinidia umbelloides OM949929.1 155813 View on NCBI ↗
Actinidia valvata NC_050357.1 156548 View on NCBI ↗
Actinidia venosa NC_069068.1 156544 View on NCBI ↗
Actinidia vitifolia OM949884.1 156230 View on NCBI ↗
Actinidia zhejiangensis OM949935.1 156967 View on NCBI ↗