Markers + reference

Pyrus

31 species · Rosaceae · Rosales

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Species 31
Genome length 159–170 kb
Candidate markers 267
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
MW450_pgt001-psbA LSC 265 0.0164 0.97 54.6 no View details
rps16 LSC 1176 0.0030 0.99 58.5 no View details
rps16-MW450_pgt003 LSC 908 0.0075 0.94 61.1 no View details
MW450_pgt006-atpA LSC 837 0.0137 0.74 61.9 yes View details
rpoB-MW450_pgt007 LSC 1215 0.0029 1.00 43.8 yes View details
MW450_pgt018-MW450_pgt019 LSC 1219 0.0053 1.00 58.4 yes View details
ndhC-MW450_pgt021 LSC 1503 0.0097 0.97 64.0 yes View details
rpl16 LSC 1408 0.0029 1.00 39.1 yes View details
ndhF-rpl32 SSC 1061 0.0060 0.99 68.0 yes View details
rps19-MW450_pgt001 LSC 10222 0.0328 0.02 31.7 no View details
petA-psbJ LSC 992 0.0015 1.00 56.6 yes View details
petG-MW450_pgt022 LSC 124 0.0093 1.00 54.1 yes View details
MW450_pgt011-psbD LSC 1410 0.0014 1.00 53.4 yes View details
MW450_pgt002-rps16 LSC 956 0.0045 1.00 51.8 no View details
psbM-MW450_pgt008 LSC 1228 0.0029 1.00 50.2 yes View details
MW450_pgt012-MW450_pgt013 LSC 357 0.0032 1.00 50.0 yes View details
atpH-atpI LSC 1176 0.0020 0.99 49.9 yes View details
psaA-pafI LSC 707 0.0011 1.00 48.9 yes View details
accD-psaI LSC 583 0.0021 1.00 48.9 yes View details
petN-psbM LSC 1216 0.0033 0.98 48.3 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
MW450_pgt006-atpA_p1 MW450_pgt006-atpA TGGAATGAAAAGCGTCCATTG AGACATTTACCGACGAAGCG 531–1006 1.000 75.1
MW450_pgt006-atpA_p2 MW450_pgt006-atpA GGAATGAAAAGCGTCCATTGT AGACATTTACCGACGAAGCG 530–1005 1.000 75.1
MW450_pgt006-atpA_p3 MW450_pgt006-atpA GGTTCAAATCCTATTGGACGC AGACATTTACCGACGAAGCG 470–945 1.000 74.7
MW450_pgt006-atpA_p4 MW450_pgt006-atpA TGGATAGGACAGAGGTCTTCT AGACATTTACCGACGAAGCG 505–980 1.000 71.5
MW450_pgt006-atpA_p5 MW450_pgt006-atpA TGGAATGAAAAGCGTCCATT AGACATTTACCGACGAAGCG 531–1006 1.000 71.1
atpH-atpI_p1 atpH-atpI AATAGAAGCAAGCCCGACAG GCGAATCCATGGAAGGTCAT 1257–1283 1.000 81.1
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT GCGAATCCATGGAAGGTCAT 1223–1249 1.000 81.1
atpH-atpI_p3 atpH-atpI AATAGAAGCAAGCCCGACAG TTTTTGCAACCTTAGCTGCG 1287–1313 1.000 80.2
atpH-atpI_p4 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACCTTAGCTGCG 1253–1279 1.000 80.2
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA GCGAATCCATGGAAGGTCAT 1224–1250 1.000 79.9
rpoB-MW450_pgt007_p1 rpoB-MW450_pgt007 TAAGCCCTGCTCAATGAACC CCGGATTTGAACTGGGGAAA 1358–1373 1.000 79.9
rpoB-MW450_pgt007_p2 rpoB-MW450_pgt007 TAAGCCCTGCTCAATGAACC AAAAGGATTTGCAGTCCCCC 1340–1355 1.000 77.7
rpoB-MW450_pgt007_p3 rpoB-MW450_pgt007 TATTGCCTCATTTCCACCCC CCGGATTTGAACTGGGGAAA 1292–1307 1.000 77.4
rpoB-MW450_pgt007_p4 rpoB-MW450_pgt007 CTCTGTTAAGCCCTGCTCAA CCGGATTTGAACTGGGGAAA 1364–1379 1.000 77.1
rpoB-MW450_pgt007_p5 rpoB-MW450_pgt007 GTTCCTCTGTTAAGCCCTGC CCGGATTTGAACTGGGGAAA 1368–1383 1.000 76.5
petN-psbM_p1 petN-psbM AGTAAATCTCGCTTGGGCTG AAAACAGTCAGCCAAGGTGA 1299–1324 1.000 78.7
petN-psbM_p2 petN-psbM AGTATGGGGAAGGAGTGGAC AAAACAGTCAGCCAAGGTGA 1242–1267 1.000 78.1
petN-psbM_p3 petN-psbM GTATGGGGAAGGAGTGGACT AAAACAGTCAGCCAAGGTGA 1241–1266 1.000 78.1
petN-psbM_p4 petN-psbM TATGGGGAAGGAGTGGACTC AAAACAGTCAGCCAAGGTGA 1240–1265 1.000 77.6
petN-psbM_p5 petN-psbM GGGGAAGGAGTGGACTCTAG AAAACAGTCAGCCAAGGTGA 1237–1262 1.000 77.3
psbM-MW450_pgt008_p1 psbM-MW450_pgt008 TCACCTTGGCTGACTGTTTT TTCAATTGGTCAGAGCACCG 1391–1418 1.000 74.2
psbM-MW450_pgt008_p2 psbM-MW450_pgt008 AATCACCTTGGCTGACTGTT TTCAATTGGTCAGAGCACCG 1393–1420 1.000 72.4
psbM-MW450_pgt008_p3 psbM-MW450_pgt008 ATCACCTTGGCTGACTGTTT TTCAATTGGTCAGAGCACCG 1392–1419 1.000 72.4
psbM-MW450_pgt008_p4 psbM-MW450_pgt008 TCACCTTGGCTGACTGTTTT GTTCAATTGGTCAGAGCACC 1392–1419 1.000 70.0
psbM-MW450_pgt008_p5 psbM-MW450_pgt008 ATCACCTTGGCTGACTGTTTT TTCAATTGGTCAGAGCACCG 1392–1419 1.000 69.3
MW450_pgt011-psbD_p1 MW450_pgt011-psbD GTGGTAGAGTAACGCCATGG GGCCAGACCAACCTACAAAA 1575–1713 1.000 82.9
MW450_pgt011-psbD_p2 MW450_pgt011-psbD TCAGTGGTAGAGTAACGCCA GGCCAGACCAACCTACAAAA 1578–1716 1.000 82.7
MW450_pgt011-psbD_p3 MW450_pgt011-psbD GTGGTAGAGTAACGCCATGG TAGGCCAGACCAACCTACAA 1577–1715 1.000 82.7
MW450_pgt011-psbD_p4 MW450_pgt011-psbD GTGGTAGAGTAACGCCATGG ACCTACAAAAACGAAGCGGT 1565–1703 1.000 82.7
MW450_pgt011-psbD_p5 MW450_pgt011-psbD TCAGTGGTAGAGTAACGCCA TAGGCCAGACCAACCTACAA 1580–1718 1.000 82.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (31)

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

Species Accession Length (bp) Link
Pyrus calleryana NC_062432.1 169965 View on NCBI ↗
Pyrus communis NC_045336.1 160171 View on NCBI ↗
Pyrus communis subsp. caucasica NC_061917.1 159707 View on NCBI ↗
Pyrus cordata OR995437.1 159179 View on NCBI ↗
Pyrus cossonii OR995438.1 159880 View on NCBI ↗
Pyrus demetrii NC_061933.1 159939 View on NCBI ↗
Pyrus dimorphophylla OR995439.1 159493 View on NCBI ↗
Pyrus elaeagrifolia OR995440.1 160003 View on NCBI ↗
Pyrus elata NC_061557.1 159979 View on NCBI ↗
Pyrus georgica NC_061558.1 159870 View on NCBI ↗
Pyrus hondoensis OR995445.1 159448 View on NCBI ↗
Pyrus hopeiensis OR995446.1 159572 View on NCBI ↗
Pyrus korshinskyi OR995448.1 160148 View on NCBI ↗
Pyrus mamorensis OR995449.1 160112 View on NCBI ↗
Pyrus neoserrulata OR995467.1 159832 View on NCBI ↗
Pyrus pashia NC_034909.1 160153 View on NCBI ↗
Pyrus phaeocarpa NC_085573.1 160097 View on NCBI ↗
Pyrus pseudopashia OR995457.1 159679 View on NCBI ↗
Pyrus pyraster NC_061934.1 159440 View on NCBI ↗
Pyrus pyrifolia NC_015996.1 159922 View on NCBI ↗
Pyrus regelii OR995462.1 160125 View on NCBI ↗
Pyrus sachokiana OR995464.1 160017 View on NCBI ↗
Pyrus salicifolia NC_061935.1 159962 View on NCBI ↗
Pyrus spinosa OR995469.1 159867 View on NCBI ↗
Pyrus syriaca OR995444.1 159813 View on NCBI ↗
Pyrus takhtadzhianii OR995472.1 159816 View on NCBI ↗
Pyrus turcomanica NC_061559.1 159871 View on NCBI ↗
Pyrus ussuriensis NC_041461.1 160157 View on NCBI ↗
Pyrus ussuriensis var. aromatica OR995428.1 159862 View on NCBI ↗
Pyrus x nivalis OR995451.1 159890 View on NCBI ↗
Pyrus xerophila OR995477.1 159429 View on NCBI ↗