Markers + reference

Chrysanthemum

10 species · Asteraceae · Asterales

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Species 10
Genome length 151–151 kb
Candidate markers 268
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnC-GCA LSC 731 0.0050 1.00 52.7 yes View details
petN-psbM LSC 532 0.0087 0.99 60.5 yes View details
trnR-UCU-trnT-GGU LSC 1183 0.0022 0.99 47.6 yes View details
psaA-ycf3 LSC 737 0.0043 1.00 65.3 yes View details
psbE-petL LSC 1264 0.0035 1.00 63.9 yes View details
rpl2 IRb 1490 0.0004 1.00 46.1 no View details
ycf1 SSC 3111 0.0037 1.00 59.4 yes View details
ndhD SSC 1503 0.0017 1.00 39.4 yes View details
trnL-UAG-rpl32 SSC 875 0.0050 0.99 61.0 yes View details
rpl32-ndhF SSC 993 0.0046 1.00 65.5 yes View details
ndhF SSC 2226 0.0009 1.00 38.0 yes View details
ycf1 IRa 576 0.0037 1.00 37.9 no View details
rpl2 IRa 1490 0.0271 1.00 60.3 yes View details
rpl2-trnH-GUG IRa 123 0.1455 0.54 66.8 no View details
psaC-ndhD SSC 114 0.0380 0.99 66.1 yes View details
ndhC-trnV-UAC LSC 1147 0.0033 1.00 58.2 yes View details
ycf1-rps15 SSC 2298 0.0029 1.00 57.2 yes View details
trnE-UUC-rpoB LSC 865 0.0037 1.00 56.9 yes View details
rpl14-rpl16 LSC 118 0.0080 0.97 56.6 yes View details
cplP LSC 1996 0.0017 1.00 56.2 yes View details
ycf3-trnS-GGA LSC 830 0.0020 0.99 55.6 yes View details
rpoC2 LSC 4152 0.0017 1.00 55.4 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
trnK-UUU_p1 trnK-UUU GGGCGTGTCAACCAATATCT TCTGATTGTATCTACATACCCCT 2754–2783 1.000 42.1
trnK-UUU_p2 trnK-UUU TGGGCGTGTCAACCAATATC TCTGATTGTATCTACATACCCCT 2755–2784 1.000 42.1
trnK-UUU_p3 trnK-UUU GGGCGTGTCAACCAATATCT TCTGATTGTATCTACATACCCCTT 2754–2783 1.000 42.1
trnK-UUU_p4 trnK-UUU GGGCGTGTCAACCAATATCT TTCTGATTGTATCTACATACCCCT 2755–2784 1.000 42.1
trnK-UUU_p5 trnK-UUU ATGGGCGTGTCAACCAATAT TCTGATTGTATCTACATACCCCT 2756–2785 1.000 42.1
trnS-GCU-trnC-GCA_p1 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA CCGGATTTGAACTGGGGAAA 882–903 1.000 79.2
trnS-GCU-trnC-GCA_p2 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA AAAAGGATTTGCAGTCCCCC 864–885 1.000 77.0
trnS-GCU-trnC-GCA_p3 trnS-GCU-trnC-GCA CTTTCGTCCACTCAGCCATC CCGGATTTGAACTGGGGAAA 818–839 1.000 75.4
trnS-GCU-trnC-GCA_p4 trnS-GCU-trnC-GCA AACGGAAAGAGAGGGATTCG CCGGATTTGAACTGGGGAAA 883–904 1.000 75.0
trnS-GCU-trnC-GCA_p5 trnS-GCU-trnC-GCA CTTTCGTCCACTCAGCCATC AAAAGGATTTGCAGTCCCCC 800–821 1.000 73.3
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTT 691–697 1.000 62.0
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTTT 691–697 1.000 60.3
petN-psbM_p3 petN-psbM ATAGTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATTT 692–698 1.000 56.0
petN-psbM_p4 petN-psbM CTCGCTTGGGCTGCTTTAAT TGCTACTGCACTGTTCATTT 683–689 1.000 56.0
petN-psbM_p5 petN-psbM TGGGCTGCTTTAATGGTAGTC TGCTACTGCACTGTTCATTT 677–683 1.000 55.2
trnE-UUC-rpoB_p1 trnE-UUC-rpoB GGGACTTGAACCCTCGTTTT AGTTCTTCTGTCAAACCCTGA 998–1012 1.000 64.4
trnE-UUC-rpoB_p2 trnE-UUC-rpoB TAACCACTGGACCATAGGGG AGTTCTTCTGTCAAACCCTGA 957–971 1.000 63.8
trnE-UUC-rpoB_p3 trnE-UUC-rpoB CCCTCGTTTTCTCCGTGAAA AGTTCTTCTGTCAAACCCTGA 988–1002 1.000 63.6
trnE-UUC-rpoB_p4 trnE-UUC-rpoB TTGAACCCTCGTTTTCTCCG AGTTCTTCTGTCAAACCCTGA 993–1007 1.000 63.6
trnE-UUC-rpoB_p5 trnE-UUC-rpoB GGGACTTGAACCCTCGTTTT TCAAACCCTGATCAATGAACCT 988–1002 1.000 63.0
rpoC2_p1 rpoC2 TTTAGTGCTGAACTGGGACC CATTAGCGCGATCTGATCCA 194 1.000 76.6
rpoC2_p2 rpoC2 TTTAGTGCTGAACTGGGACC ACATTAGCGCGATCTGATCC 195 1.000 76.6
rpoC2_p3 rpoC2 TAGTGCTGAACTGGGACCAA CATTAGCGCGATCTGATCCA 192 1.000 76.5
rpoC2_p4 rpoC2 TTAGTGCTGAACTGGGACCA CATTAGCGCGATCTGATCCA 193 1.000 76.5
rpoC2_p5 rpoC2 TAGTGCTGAACTGGGACCAA ACATTAGCGCGATCTGATCC 193 1.000 76.5
trnR-UCU-trnT-GGU_p1 trnR-UCU-trnT-GGU AGAAGACCTCTGTCCTATCCA TACGCCTTACCGTGGGATTA 1245–1260 1.000 63.4
trnR-UCU-trnT-GGU_p2 trnR-UCU-trnT-GGU AGAAGACCTCTGTCCTATCCA GCCTTACCGTGGGATTACTC 1242–1257 1.000 63.3
trnR-UCU-trnT-GGU_p3 trnR-UCU-trnT-GGU AGAAGACCTCTGTCCTATCCA ATTTGAACCGAGGGCTTACG 1261–1276 1.000 63.0
trnR-UCU-trnT-GGU_p4 trnR-UCU-trnT-GGU AGGTTTAGAAGACCTCTGTCCT TACGCCTTACCGTGGGATTA 1251–1266 1.000 62.7
trnR-UCU-trnT-GGU_p5 trnR-UCU-trnT-GGU AGGTTTAGAAGACCTCTGTCCT GCCTTACCGTGGGATTACTC 1248–1263 1.000 62.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Chrysanthemum boreale NC_037388.1 151012 View on NCBI ↗
Chrysanthemum chanetii NC_064343.1 151393 View on NCBI ↗
Chrysanthemum dichrum NC_064344.1 151371 View on NCBI ↗
Chrysanthemum indicum NC_020320.1 150972 View on NCBI ↗
Chrysanthemum indicum var. aromaticum MW924116.1 151017 View on NCBI ↗
Chrysanthemum indicum var. edule MH339741.1 151262 View on NCBI ↗
Chrysanthemum lavandulifolium NC_057202.1 151085 View on NCBI ↗
Chrysanthemum vestitum NC_057203.1 151012 View on NCBI ↗
Chrysanthemum x morifolium NC_020092.1 151033 View on NCBI ↗
Chrysanthemum zawadzkii NC_056150.1 151034 View on NCBI ↗