Markers + reference

Hosta

13 species · Asparagaceae · Asparagales

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Species 13
Genome length 156–157 kb
Candidate markers 272
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

15 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0018 1.00 31.0 yes View details
trnK-UUU-rps16 LSC 530 0.0068 1.00 51.8 yes View details
ndhC-trnV-UAC LSC 1605 0.0018 1.00 52.6 yes View details
rbcL-accD LSC 737 0.0014 1.00 32.8 yes View details
psbE-petL LSC 1220 0.0025 1.00 50.0 yes View details
rpl16 LSC 1393 0.0035 1.00 50.0 yes View details
rps3 LSC 663 0.0016 1.00 46.2 yes View details
rps19 IRb 280 0.0005 1.00 37.8 no View details
ycf1 IRb 927 0.0002 1.00 29.4 no View details
rpl32-trnL-UAG SSC 662 0.0137 1.00 62.3 yes View details
ccsA SSC 969 0.0008 1.00 34.4 yes View details
ndhA SSC 2188 0.0023 1.00 51.0 yes View details
rps15-ycf1 SSC 409 0.0056 1.00 47.6 yes View details
ycf1 SSC 5319 0.0016 1.00 46.5 yes View details
rps19 IRa 279 0.0017 1.00 34.0 yes View details
ccsA-ndhD SSC 216 0.0262 0.99 67.2 yes View details
rps19-psbA IRa 187 0.0553 0.93 65.2 no View details
ycf4-cemA LSC 857 0.0018 1.00 58.7 yes View details
trnT-GGU-psbD LSC 1091 0.0021 1.00 58.1 yes View details
petA-psbJ LSC 1114 0.0014 1.00 54.8 yes View details
trnT-UGU-trnL-UAA LSC 906 0.0021 0.99 53.6 yes View details
ndhF-rpl32 SSC 954 0.0034 1.00 53.5 yes View details
atpH-atpI LSC 498 0.0015 1.00 50.0 yes View details
psbA-trnK-UUU LSC 240 0.0080 0.99 49.8 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
psbA_p1 psbA GGGTATAGCTCCCTCAACGA GTGCTTGGGAGTCCTTGAAA 1156 0.923 75.1
psbA_p2 psbA GGGTATAGCTCCCTCAACGA GTTTGGGGAGGGGTCTTTTT 1441–1443 0.923 74.8
psbA_p3 psbA GGGTATAGCTCCCTCAACGA GTATGTGTGCTTGGGAGTCC 1162 0.923 73.3
psbA_p4 psbA TGGGTATAGCTCCCTCAACG GTGCTTGGGAGTCCTTGAAA 1157 0.923 72.8
psbA_p5 psbA GGGTATAGCTCCCTCAACGA TATGTGTGCTTGGGAGTCCT 1161 0.923 72.6
psbA-trnK-UUU_p1 psbA-trnK-UUU TAAAGACGGTTTTCGGTGCT GTTTGGGGAGGGGTCTTTTT 414–416 1.000 78.8
psbA-trnK-UUU_p2 psbA-trnK-UUU GCTTGTACTTTCGCGTCTCT GTTTGGGGAGGGGTCTTTTT 364–366 1.000 78.6
psbA-trnK-UUU_p3 psbA-trnK-UUU GTAAAGACGGTTTTCGGTGC GTTTGGGGAGGGGTCTTTTT 415–417 1.000 78.3
psbA-trnK-UUU_p4 psbA-trnK-UUU CCCCACAGGCTTGTACTTTC GTTTGGGGAGGGGTCTTTTT 372–374 1.000 77.2
psbA-trnK-UUU_p5 psbA-trnK-UUU TAAAGACGGTTTTCGGTGCT TTTGGGGAGGGGTCTTTTTC 413–415 1.000 76.5
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAA ACAAGGGAATCAATCATTCGT 618–1393 1.000 53.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC ACAAGGGAATCAATCATTCGT 593–1368 1.000 51.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 TAGTCGCACTTAAAAGCCGA ACAAGGGAATCAATCATTCGT 619–1394 1.000 49.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 GCCGAATACTCTACCGTTGA ACAAGGGAATCAATCATTCGT 604–1379 1.000 48.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGCCGAATACTCTACCGTTG ACAAGGGAATCAATCATTCGT 605–1380 1.000 48.0
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT ATAGGGGAATCCATGGAGGG 546–563 1.000 82.5
atpH-atpI_p2 atpH-atpI CGCAATACCTTCTACGGCTT ATAGGGGAATCCATGGAGGG 634–651 1.000 81.8
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 571–588 1.000 81.8
atpH-atpI_p4 atpH-atpI TACCTTGACCAACTCCAGGT ATAGGGGAATCCATGGAGGG 602–619 1.000 81.6
atpH-atpI_p5 atpH-atpI CGCAATACCTTCTACGGCTT TTTTGCAACTTTAGCTGCGG 659–676 1.000 81.2
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG CGGACCAACCTACAAAAACG 941–1253 1.000 78.9
trnT-GGU-psbD_p2 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GCCGGACCAACCTACAAAAA 943–1255 1.000 78.9
trnT-GGU-psbD_p3 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA CGGACCAACCTACAAAAACG 944–1256 1.000 78.8
trnT-GGU-psbD_p4 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GAAAGAGCAATAGGCCGGAC 956–1268 1.000 78.7
trnT-GGU-psbD_p5 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA GCCGGACCAACCTACAAAAA 946–1258 1.000 78.7
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 929–956 1.000 82.5
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACAATCAAGTCCGTAGCGTC 950–977 1.000 82.5
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 937–964 1.000 82.0
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 961–988 1.000 81.6
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACAATCAAGTCCGTAGCGTC 982–1009 1.000 81.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (13)

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

Species Accession Length (bp) Link
Hosta capitata NC_045519.1 156416 View on NCBI ↗
Hosta clausa NC_046896.1 156624 View on NCBI ↗
Hosta clausa var. ensata MW044628.1 156630 View on NCBI ↗
Hosta clausa var. geumgangensis OL628765.1 156567 View on NCBI ↗
Hosta jonesii NC_046897.1 156708 View on NCBI ↗
Hosta minor NC_035999.1 156674 View on NCBI ↗
Hosta plantaginea NC_053555.1 157091 View on NCBI ↗
Hosta sieboldiana NC_060662.1 156576 View on NCBI ↗
Hosta tsushimensis NC_060664.1 156714 View on NCBI ↗
Hosta tsushimensis var. tibae NC_060663.1 156626 View on NCBI ↗
Hosta ventricosa NC_032706.1 156577 View on NCBI ↗
Hosta venusta NC_046895.1 156676 View on NCBI ↗
Hosta yingeri NC_039976.1 156756 View on NCBI ↗