Markers + reference

Rhodiola

50 species · Crassulaceae · Saxifragales

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Species 50
Genome length 151–152 kb
Candidate markers 273
Primer pairs 100

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 9 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0051 1.00 46.1 yes View details
trnS-GCU-trnG-GCC LSC 633 0.0200 0.99 70.3 yes View details
rpoB-trnC-GCA LSC 1001 0.0210 1.00 75.6 yes View details
trnC-GCA-petN LSC 834 0.0137 1.00 71.7 yes View details
trnD-GUC-trnY-GUA LSC 300 0.0251 1.00 64.7 yes View details
petA-psbJ LSC 1009 0.0151 0.99 72.6 yes View details
psbE-petL LSC 1059 0.0141 0.98 82.3 yes View details
ndhF SSC 2217 0.0110 0.99 58.2 yes View details
ndhF-rpl32 SSC 581 0.0177 1.00 74.7 yes View details
ccsA-ndhD SSC 270 0.0305 0.97 66.6 yes View details
rps15-ycf1 SSC 5535 0.0113 1.00 61.0 yes View details
lhbA-trnG-UCC LSC 595 0.0110 0.96 75.1 yes View details
trnH-GUG-psbA LSC 252 0.0426 0.96 74.1 yes View details
trnT-UGU-trnL-UAA LSC 405 0.0117 1.00 72.6 yes View details
matK-trnK-UUU LSC 702 0.0121 1.00 72.1 yes View details
trnE-UUC-trnT-GGU LSC 842 0.0128 1.00 69.4 yes View details
ycf4-cemA LSC 600 0.0096 1.00 68.8 yes View details
rps16-trnQ-UUG LSC 698 0.0113 1.00 67.2 yes View details
accD-psaI LSC 547 0.0061 1.00 66.6 yes View details
trnT-GGU-psbD LSC 688 0.0116 0.98 66.4 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 100 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 CCTCTAGACCTAGCTGCTGT 227–341 1.000 90.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 241–355 1.000 90.4
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 240–354 1.000 90.4
trnH-GUG-psbA_p4 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 230–344 1.000 90.4
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 242–356 0.980 89.6
psbA_p1 psbA ACTCGTATAGACTAATACCGAAGT ATTTGGTTGCTTGGGAGTCC 1136–1139 0.940 41.4
psbA_p2 psbA AACTCGTATAGACTAATACCGAAGT ATTTGGTTGCTTGGGAGTCC 1137–1140 0.940 41.4
psbA_p3 psbA ACTCGTATAGACTAATACCGAAGTT ATTTGGTTGCTTGGGAGTCC 1136–1139 0.940 41.4
psbA_p4 psbA ACTCGTATAGACTAATACCGAAG ATTTGGTTGCTTGGGAGTCC 1136–1139 0.940 41.4
psbA_p5 psbA CTCGTATAGACTAATACCGAAGT ATTTGGTTGCTTGGGAGTCC 1135–1138 0.940 41.4
matK-trnK-UUU_p1 matK-trnK-UUU CGGACCTATGATCATGAGCA AACGGTAGAGTACTCGGCTT 823–853 0.980 79.3
matK-trnK-UUU_p2 matK-trnK-UUU CGGACCTATGATCATGAGCA ACGGTAGAGTACTCGGCTTT 822–852 0.980 79.3
matK-trnK-UUU_p3 matK-trnK-UUU ACGGACCTATGATCATGAGC AACGGTAGAGTACTCGGCTT 824–854 0.980 79.2
matK-trnK-UUU_p4 matK-trnK-UUU ACGGACCTATGATCATGAGC ACGGTAGAGTACTCGGCTTT 823–853 0.980 79.2
matK-trnK-UUU_p5 matK-trnK-UUU CGGACCTATGATCATGAGCA TTTTGGCTTGGGGTTGCTAA 846–876 0.980 79.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 769–1593 1.000 85.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 780–1604 1.000 85.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTATGCGGAGGTTCGAATCC 776–1600 1.000 84.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTATGCGGAGGTTCGAATCC 787–1611 1.000 84.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCACAGCTGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 790–1614 1.000 83.8
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA TACCACTAAACTATACCCGC 600–703 1.000 59.9
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC TACCACTAAACTATACCCGC 599–702 1.000 59.9
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC GCTCGTACAACGGATTAGCA TACCACTAAACTATACCCGC 618–721 1.000 59.2
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCTCACTTTTACCACT 614–717 1.000 59.1
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCTCACTTTTACCACT 613–716 1.000 59.1
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AGTTCTTCCGTCAAGCCATG CCGGATTTGAACTGGGGAAA 1110–1200 1.000 89.9
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GTTCTTCCGTCAAGCCATGA CCGGATTTGAACTGGGGAAA 1109–1199 1.000 89.8
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AGTTCTTCCGTCAAGCCATG AGTCTTGTGTTGATCAGGCG 1134–1224 1.000 88.9
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AGTTCTTCCGTCAAGCCATG GTCTTGTGTTGATCAGGCGA 1133–1223 1.000 88.9
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AGTTCTTCCGTCAAGCCATG TCTTGTGTTGATCAGGCGAC 1132–1222 1.000 88.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (50)

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

Species Accession Length (bp) Link
Rhodiola alsia PP975596.1 150819 View on NCBI ↗
Rhodiola alterna PP965695.1 151472 View on NCBI ↗
Rhodiola amabilis PZ229033.1 151548 View on NCBI ↗
Rhodiola angusta PP965696.1 151854 View on NCBI ↗
Rhodiola atuntsuensis PP965697.1 150968 View on NCBI ↗
Rhodiola bupleuroides NC_060674.1 151250 View on NCBI ↗
Rhodiola calliantha NC_060675.1 151307 View on NCBI ↗
Rhodiola chrysanthemifolia NC_085687.1 151544 View on NCBI ↗
Rhodiola chrysanthemifolia subsp. sacra NC_052735.1 150941 View on NCBI ↗
Rhodiola crenulata NC_050881.1 151912 View on NCBI ↗
Rhodiola cretinii subsp. sinoalpina PP262148.1 151855 View on NCBI ↗
Rhodiola discolor PP965698.1 151021 View on NCBI ↗
Rhodiola dumulosa NC_063628.1 150920 View on NCBI ↗
Rhodiola fastigiata PP262134.1 151010 View on NCBI ↗
Rhodiola forrestii PP975597.1 151682 View on NCBI ↗
Rhodiola gelida NC_063786.1 151832 View on NCBI ↗
Rhodiola henryi NC_060676.1 151739 View on NCBI ↗
Rhodiola heterodonta PP965699.1 151646 View on NCBI ↗
Rhodiola himalensis NC_060677.1 150879 View on NCBI ↗
Rhodiola hobsonii MN794325.1 150641 View on NCBI ↗
Rhodiola humilis MN794326.1 150779 View on NCBI ↗
Rhodiola integrifolia MN794327.1 151452 View on NCBI ↗
Rhodiola juparensis NC_082109.1 151073 View on NCBI ↗
Rhodiola kirilowii NC_052736.1 150905 View on NCBI ↗
Rhodiola liciae NC_060678.1 151577 View on NCBI ↗
Rhodiola litwinowii PP262149.1 151687 View on NCBI ↗
Rhodiola macrocarpa NC_060679.1 151310 View on NCBI ↗
Rhodiola nobilis PP975600.1 151862 View on NCBI ↗
Rhodiola ovatisepala MN794328.1 151073 View on NCBI ↗
Rhodiola prainii MN794329.1 151594 View on NCBI ↗
Rhodiola primuloides PP965694.1 151208 View on NCBI ↗
Rhodiola purpureoviridis PP975601.1 151784 View on NCBI ↗
Rhodiola quadrifida NC_060680.1 150773 View on NCBI ↗
Rhodiola renii PP975602.1 151714 View on NCBI ↗
Rhodiola rhodantha MN794330.1 151061 View on NCBI ↗
Rhodiola rosea NC_041671.1 151348 View on NCBI ↗
Rhodiola sachalinensis PP262147.1 151882 View on NCBI ↗
Rhodiola semenovii PP975608.1 151666 View on NCBI ↗
Rhodiola serrata PP975609.1 151689 View on NCBI ↗
Rhodiola sexifolia NC_052737.1 151605 View on NCBI ↗
Rhodiola sinuata NC_060681.1 151349 View on NCBI ↗
Rhodiola smithii PP234588.1 150597 View on NCBI ↗
Rhodiola stapfii NC_060682.1 151380 View on NCBI ↗
Rhodiola subopposita NC_063629.1 151916 View on NCBI ↗
Rhodiola tangutica NC_060605.1 151707 View on NCBI ↗
Rhodiola tibetica PP965701.1 151644 View on NCBI ↗
Rhodiola tieghemii PP262133.1 151350 View on NCBI ↗
Rhodiola wallichiana NC_060683.1 151358 View on NCBI ↗
Rhodiola wallichiana var. cholaensis PP262153.1 151606 View on NCBI ↗
Rhodiola yunnanensis PP262155.1 151286 View on NCBI ↗