Markers + reference

Rosa

87 species · Rosaceae · Rosales

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Species 87
Genome length 156–157 kb
Candidate markers 266
Primer pairs 90

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 9 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 313 0.0262 0.88 56.1 yes View details
trnK-UUU-rps16 LSC 951 0.0094 0.82 47.6 yes View details
rps16 LSC 1142 0.0094 1.00 50.5 yes View details
rps16-trnQ-UUG LSC 865 0.0149 0.95 62.0 yes View details
trnR-UCU-atpA LSC 528 0.0100 0.97 51.5 yes View details
rpoB-trnC-GCA LSC 1218 0.0108 0.99 50.7 yes View details
trnT-UGU-trnL-UAA LSC 1180 0.0167 0.95 70.2 yes View details
ndhF SSC 2250 0.0049 1.00 37.8 yes View details
ndhA SSC 2348 0.0088 0.98 59.9 yes View details
ycf1 SSC 4539 0.0080 1.00 43.6 yes View details
rpl2-trnH-GUG IRa 63 0.0391 0.92 67.2 no View details
petN-psbM LSC 1282 0.0082 0.99 66.1 yes View details
ndhF-rpl32 SSC 1106 0.0080 0.98 65.4 yes View details
ndhC-trnV-UAC LSC 608 0.0106 0.99 65.0 yes View details
ycf3-trnS-GGA LSC 887 0.0094 0.98 64.5 yes View details
petA-psbJ LSC 962 0.0073 1.00 62.3 yes View details
atpH-atpI LSC 928 0.0063 1.00 62.1 yes View details
accD-psaI LSC 443 0.0117 0.99 61.2 yes View details
psaJ-rpl33 LSC 469 0.0114 0.99 61.0 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 398–476 1.000 90.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 412–490 1.000 90.6
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 411–489 1.000 90.6
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 413–491 1.000 90.6
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 348–426 1.000 90.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAAAAGGCGCTCAACCTACA 912–1213 1.000 90.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CGACGAGAGGGAAGAGATCT 1006–1307 1.000 89.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 GACTCTCCAGAACCTCCCTT AAAAAGGCGCTCAACCTACA 1404–1705 0.851 82.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TTTTCTCGAGCCGTACGAAG 1376–1380 0.057 42.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 GACTCTCCAGAACCTCCCTT TTTTCTCGAGCCGTACGAAG 1869–1874 0.057 42.4
rps16_p1 rps16 AAGTCATCCACACCTTCTTT TGGGTTCCAAACTGAAGGAA 1186–1211 0.414 24.1
rps16_p2 rps16 AGTCATCCACACCTTCTTTT TGGGTTCCAAACTGAAGGAA 1185–1210 0.414 24.1
rps16_p3 rps16 AAGTCATCCACACCTTCTTTT TGGGTTCCAAACTGAAGGAA 1186–1211 0.414 22.9
rps16_p4 rps16 AGTCATCCACACCTTCTTTTT TGGGTTCCAAACTGAAGGAA 1185–1210 0.414 22.9
rps16_p5 rps16 AGTCATCCACACCTTCTTTT ATGGGTTCCAAACTGAAGGA 1186–1211 0.414 22.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 883–938 1.000 90.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GCTACTCGGAGGTTCGAATC 891–946 1.000 89.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 894–949 0.989 89.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 887–942 1.000 89.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GCTACTCGGAGGTTCGAATC 902–957 0.989 88.9
trnR-UCU-atpA_p1 trnR-UCU-atpA ATTGGAGTGAAAAGCGTCCA TGGAACGTTTTCTACTTCAGGA 645–763 1.000 66.0
trnR-UCU-atpA_p2 trnR-UCU-atpA TGGAGTGAAAAGCGTCCATT TGGAACGTTTTCTACTTCAGGA 643–761 1.000 66.0
trnR-UCU-atpA_p3 trnR-UCU-atpA TTGGAGTGAAAAGCGTCCAT TGGAACGTTTTCTACTTCAGGA 644–762 1.000 66.0
trnR-UCU-atpA_p4 trnR-UCU-atpA GGAGTGAAAAGCGTCCATTG TGGAACGTTTTCTACTTCAGGA 642–760 1.000 63.2
trnR-UCU-atpA_p5 trnR-UCU-atpA TGGAGTGAAAAGCGTCCATT TGGAACGTTTTCTACTTCAGGAA 643–761 1.000 63.2
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT GCGAATCCATGGAAGGTCAT 813–1006 1.000 87.7
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT GCGAATCCATGGAAGGTCAT 869–1062 1.000 87.0
atpH-atpI_p3 atpH-atpI AATAACGGAAGCGGCAGAAA GCGAATCCATGGAAGGTCAT 814–1007 1.000 86.5
atpH-atpI_p4 atpH-atpI GCCAATCCAGCAGCAATAAC GCGAATCCATGGAAGGTCAT 828–1021 1.000 86.2
atpH-atpI_p5 atpH-atpI GCAGTACCTTGACCAACTCC GCGAATCCATGGAAGGTCAT 873–1063 0.966 84.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (87)

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

Species Accession Length (bp) Link
Rosa abyssinica PV744412.1 156588 View on NCBI ↗
Rosa anemoniflora NC_083977.1 156578 View on NCBI ↗
Rosa banksiae NC_042194.1 156575 View on NCBI ↗
Rosa banksiae f. lutea NC_079958.1 156537 View on NCBI ↗
Rosa banksiae var. banksiae NC_079959.1 156627 View on NCBI ↗
Rosa banksiae var. normalis NC_079960.1 156555 View on NCBI ↗
Rosa beggeriana NC_079961.1 157139 View on NCBI ↗
Rosa berberifolia NC_045126.1 156886 View on NCBI ↗
Rosa blanda PV744413.1 156672 View on NCBI ↗
Rosa canina NC_047295.1 156501 View on NCBI ↗
Rosa chinensis NC_065867.1 156591 View on NCBI ↗
Rosa chinensis var. chinensis NC_079963.1 156591 View on NCBI ↗
Rosa chinensis var. minima PP976066.1 156591 View on NCBI ↗
Rosa chinensis var. semperflorens NC_079964.1 156603 View on NCBI ↗
Rosa chinensis var. spontanea NC_038102.1 156590 View on NCBI ↗
Rosa clinophylla var. clinophylla OK509171.1 156883 View on NCBI ↗
Rosa cymosa NC_051550.1 156607 View on NCBI ↗
Rosa daishanensis PV744386.1 156508 View on NCBI ↗
Rosa davurica NC_057236.1 156971 View on NCBI ↗
Rosa deqenensis PV744406.1 156664 View on NCBI ↗
Rosa derongensis PV744405.1 156620 View on NCBI ↗
Rosa deseglisei NC_079925.1 156624 View on NCBI ↗
Rosa filipes NC_053856.1 156624 View on NCBI ↗
Rosa foliolosa NC_079926.1 156487 View on NCBI ↗
Rosa forrestiana PV487599.1 156690 View on NCBI ↗
Rosa freitagii PV487598.1 156591 View on NCBI ↗
Rosa fujisanensis PV744391.1 156499 View on NCBI ↗
Rosa glauca NC_079927.1 156573 View on NCBI ↗
Rosa glomerata NC_062462.1 157064 View on NCBI ↗
Rosa graciliflora NC_079934.1 157050 View on NCBI ↗
Rosa hugonis PP976080.1 157214 View on NCBI ↗
Rosa hybrid cultivar NC_044126.1 156989 View on NCBI ↗
Rosa iliensis PV330081.1 157148 View on NCBI ↗
Rosa kwangtungensis PV744375.1 156615 View on NCBI ↗
Rosa laevigata NC_046824.1 156342 View on NCBI ↗
Rosa laevigata var. leiocarpa NC_047418.1 156373 View on NCBI ↗
Rosa lasiosepala NC_071930.1 156581 View on NCBI ↗
Rosa laxa PV330082.1 157346 View on NCBI ↗
Rosa leschenaultiana PV744411.1 156516 View on NCBI ↗
Rosa lichiangensis NC_079928.1 156611 View on NCBI ↗
Rosa longicuspis var. longicuspis PV744392.1 156561 View on NCBI ↗
Rosa longicuspis var. sinowilsonii PV744400.1 156642 View on NCBI ↗
Rosa lucidissima NC_079929.1 156608 View on NCBI ↗
Rosa lucieae var. onoei PV744389.1 156516 View on NCBI ↗
Rosa ludingensis PV744397.1 156589 View on NCBI ↗
Rosa macrophylla NC_079930.1 157225 View on NCBI ↗
Rosa mairei NC_079931.1 157327 View on NCBI ↗
Rosa montana PP541888.1 156653 View on NCBI ↗
Rosa moyesii NC_079932.1 157286 View on NCBI ↗
Rosa multiflora NC_039989.1 156592 View on NCBI ↗
Rosa multiflora var. carnea OQ735286.1 156594 View on NCBI ↗
Rosa multiflora var. cathayensis PV744408.1 156659 View on NCBI ↗
Rosa multiflora var. multiflora PV744385.1 156515 View on NCBI ↗
Rosa murielae NC_079933.1 157056 View on NCBI ↗
Rosa nitida OK539662.1 156487 View on NCBI ↗
Rosa odorata var. erubescens PP976089.1 156652 View on NCBI ↗
Rosa odorata var. odorata NC_079867.1 156664 View on NCBI ↗
Rosa odorata var. pseudindica NC_079868.1 156651 View on NCBI ↗
Rosa omeiensis f. pteracantha OQ992649.1 157052 View on NCBI ↗
Rosa paniculigera PV744390.1 156508 View on NCBI ↗
Rosa praelucens NC_037492.1 157186 View on NCBI ↗
Rosa prattii OK509178.1 156551 View on NCBI ↗
Rosa pricei MK613354.1 156599 View on NCBI ↗
Rosa pricei var. pricei PV744377.1 156599 View on NCBI ↗
Rosa pseudobanksiae NC_079869.1 156560 View on NCBI ↗
Rosa roxburghii f. normalis PP179216.1 156686 View on NCBI ↗
Rosa roxburghii var. hirtula OK509174.1 156582 View on NCBI ↗
Rosa rubus PV744378.1 156521 View on NCBI ↗
Rosa rugosa NC_044094.1 156999 View on NCBI ↗
Rosa rugosa x Rosa sertata NC_062657.1 157120 View on NCBI ↗
Rosa sambucina var. sambucina PV744384.1 156505 View on NCBI ↗
Rosa sempervirens PV744410.1 156574 View on NCBI ↗
Rosa sericea f. glabrescens OQ992651.1 157141 View on NCBI ↗
Rosa sertata NC_066975.1 157150 View on NCBI ↗
Rosa sinobiflora NC_079870.1 157245 View on NCBI ↗
Rosa soulieana NC_079871.1 156619 View on NCBI ↗
Rosa spinosissima NC_079872.1 156998 View on NCBI ↗
Rosa sterilis (nom. nud.) NC_053909.1 156561 View on NCBI ↗
Rosa sterilis var. leioclada (nom. nud.) NC_080356.1 156561 View on NCBI ↗
Rosa sweginzowii NC_080343.1 157233 View on NCBI ↗
Rosa transmorrisonensis NC_065110.1 156507 View on NCBI ↗
Rosa tunquinensis PV744376.1 156594 View on NCBI ↗
Rosa virginiana PP976093.1 157087 View on NCBI ↗
Rosa weisiensis PV744394.1 156538 View on NCBI ↗
Rosa willmottiae NC_088498.1 157277 View on NCBI ↗
Rosa woodsii NC_079924.1 156996 View on NCBI ↗
Rosa x centifolia NC_079962.1 156625 View on NCBI ↗