Markers + reference

Geum

7 species · Rosaceae · Rosales

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Species 7
Genome length 155–156 kb
Candidate markers 269
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0042 1.00 34.1 yes View details
trnK-UUU-rps16 LSC 1032 0.0275 0.98 69.8 yes View details
rps16-trnQ-UUG LSC 846 0.0297 0.98 67.0 yes View details
trnS-GCU-trnG-UCC LSC 643 0.0308 0.98 75.9 yes View details
trnR-UCU-atpA LSC 630 0.0351 0.98 71.6 yes View details
petN-psbM LSC 1214 0.0271 0.99 67.1 yes View details
psbM-trnD-GUC LSC 1033 0.0233 0.96 63.3 yes View details
psbZ-trnG-GCC LSC 438 0.0432 0.98 73.6 yes View details
petA-psbJ LSC 1100 0.0272 0.99 61.5 yes View details
ndhF SSC 2250 0.0170 1.00 55.0 yes View details
ndhA SSC 2296 0.0141 0.99 50.2 yes View details
rpl2-trnH-GUG IRa 74 0.0941 0.86 72.1 no View details
accD-psaI LSC 445 0.0304 0.98 67.6 yes View details
rps15-ycf1 SSC 413 0.0354 0.96 67.4 yes View details
trnD-GUC-trnY-GUA LSC 448 0.0299 0.99 64.7 yes View details
psbI-trnS-GCU LSC 167 0.0516 1.00 64.4 yes View details
ndhF-rpl32 SSC 1087 0.0239 0.98 64.3 yes View details
trnT-UGU-trnL-UAA LSC 724 0.0240 0.98 63.9 yes View details
trnH-GUG-psbA LSC 218 0.0581 0.90 63.4 yes View details
trnP-UGG-psaJ LSC 422 0.0221 0.96 63.4 yes View details
psbE-petL LSC 1223 0.0179 0.99 62.2 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG AGCTGCTGTTGAAGTTCCAT 240–273 1.000 88.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA AGCTGCTGTTGAAGTTCCAT 254–287 1.000 88.7
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC AGCTGCTGTTGAAGTTCCAT 253–286 1.000 88.7
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC AGCTGCTGTTGAAGTTCCAT 255–288 1.000 88.7
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCTGCTGTTGAAGTTCCATC 239–272 1.000 86.0
psbA_p1 psbA GATCCACTTGGCTACATCCG AACATCGATATCGGCGGATG 1438–1471 1.000 84.4
psbA_p2 psbA GATCCACTTGGCTACATCCG CATCGATATCGGCGGATGTT 1436–1469 1.000 84.4
psbA_p3 psbA CAATCCACTGCCTTGATCCA AACATCGATATCGGCGGATG 1452–1485 1.000 84.3
psbA_p4 psbA CAATCCACTGCCTTGATCCA CATCGATATCGGCGGATGTT 1450–1483 1.000 84.3
psbA_p5 psbA AATCCACTGCCTTGATCCAC CATCGATATCGGCGGATGTT 1449–1482 1.000 84.3
trnK-UUU_p1 trnK-UUU AACATCCGCCGATATCGATG TTTGATGGCGTTGTGCTAGT 2830–2913 0.857 78.3
trnK-UUU_p2 trnK-UUU CATCCGCCGATATCGATGTT TTTGATGGCGTTGTGCTAGT 2828–2911 0.857 78.3
trnK-UUU_p3 trnK-UUU CCCAAGCACACAAACTCTCT TTTGATGGCGTTGTGCTAGT 2937–2985 0.714 70.7
trnK-UUU_p4 trnK-UUU CTCCCAAGCACACAAACTCT TTTGATGGCGTTGTGCTAGT 2939–2987 0.714 70.7
trnK-UUU_p5 trnK-UUU TCCCAAGCACACAAACTCTC TTTGATGGCGTTGTGCTAGT 2938–2986 0.714 70.6
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGGCAGGGGTTTTTAAGGAA 1104–1195 1.000 87.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGGCAGGGGTTTTTAAGGAA 1103–1194 1.000 87.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAGGGCAGGGGTTTTTAAGG 1106–1197 1.000 87.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAGGGCAGGGGTTTTTAAGG 1105–1196 1.000 87.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GGGCAGGGGTTTTTAAGGAA 1113–1204 1.000 86.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CTCCACAGCTGATCATGTCC GAGGTTCGAATCCTTCCGTC 942–1014 1.000 88.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 919–991 1.000 87.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 930–1002 1.000 87.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCACAGCTGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 940–1012 1.000 85.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCCACAGCTGATCATGTCCT GAGGTTCGAATCCTTCCGTC 941–1013 1.000 85.2
psbI-trnS-GCU_p1 psbI-trnS-GCU TCTTGTACAACCGCGACAAA TGGACTAAAGCGTCGGATTG 480–489 1.000 85.5
psbI-trnS-GCU_p2 psbI-trnS-GCU TTCTTGTACAACCGCGACAA TGGACTAAAGCGTCGGATTG 481–490 1.000 85.5
psbI-trnS-GCU_p3 psbI-trnS-GCU TCTTGTACAACCGCGACAAA GTGGACTAAAGCGTCGGATT 481–490 1.000 85.5
psbI-trnS-GCU_p4 psbI-trnS-GCU TTCTTGTACAACCGCGACAA GTGGACTAAAGCGTCGGATT 482–491 1.000 85.5
psbI-trnS-GCU_p5 psbI-trnS-GCU TCTTGTACAACCGCGACAAA CAATTGGGAGGAGAGATGGC 504–513 1.000 85.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Geum elatum var. elatum PX414092.1 156114 View on NCBI ↗
Geum elatum var. humile PX414095.1 156121 View on NCBI ↗
Geum henryi PX414096.1 155175 View on NCBI ↗
Geum japonicum NC_077561.1 156042 View on NCBI ↗
Geum japonicum var. chinense PX414098.1 156007 View on NCBI ↗
Geum macrophyllum NC_053765.1 155940 View on NCBI ↗
Geum rivale PP336754.1 156064 View on NCBI ↗