Markers + reference

Gynostemma

12 species · Cucurbitaceae · Cucurbitales

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Species 12
Genome length 158–159 kb
Candidate markers 272
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 392 0.0951 0.96 76.5 yes View details
trnk-UUU-rps16 LSC 1122 0.0367 0.98 76.9 yes View details
trnS-GCU-trnG-UCC LSC 623 0.0306 0.98 70.0 yes View details
trnR-UCU-atpA LSC 310 0.0944 0.99 78.0 yes View details
atpH-atpI LSC 1145 0.0317 0.99 71.2 yes View details
rpoB-trnC-GCA LSC 1173 0.0342 1.00 75.7 yes View details
petA-psbJ LSC 1061 0.0344 1.00 78.3 yes View details
rpl32-trnL-UAG SSC 1307 0.0297 1.00 75.5 yes View details
ccsA-ndhD SSC 285 0.0697 1.00 69.7 yes View details
psaA-ycf3 LSC 759 0.0228 0.99 74.1 yes View details
ndhF-rpl32 SSC 607 0.0242 1.00 71.3 yes View details
trnT-UGU-trnL-UAA LSC 1010 0.0209 0.99 71.2 yes View details
trnL-UAA-trnF-GAA LSC 352 0.0220 1.00 70.1 yes View details
rpl2-trnH-GUG IRa 81 0.0872 0.81 69.7 no View details
atpA-atpF LSC 62 0.0412 1.00 69.6 yes View details
psbC-trnS-UGA LSC 231 0.0475 1.00 69.4 yes View details
ndhC-trnV-UAC LSC 828 0.0241 0.98 68.4 yes View details
trnT-GGU-psbD LSC 1563 0.0122 0.99 62.0 yes View details
psbH-petB LSC 127 0.0236 0.98 61.7 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 TTCCCTCTAGACCTAGCTGC 306–494 0.833 83.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 320–508 0.833 83.7
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 319–507 0.833 83.7
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 321–509 0.833 83.7
trnH-GUG-psbA_p5 trnH-GUG-psbA CGCATGGTGGATTCACAATC TTCCCTCTAGACCTAGCTGC 335–523 0.833 80.9
trnk-UUU-rps16_p1 trnk-UUU-rps16 CCGCACTTAAAAGCCGAGTA ACGGAACTTCACCTTAATCA 1087–1229 1.000 60.1
trnk-UUU-rps16_p2 trnk-UUU-rps16 CCGCACTTAAAAGCCGAGTA ACGGAACTTCACCTTAATCAA 1087–1229 1.000 59.0
trnk-UUU-rps16_p3 trnk-UUU-rps16 GTGTAAAAGATGCTAGCCGC ACGGAACTTCACCTTAATCA 1103–1245 1.000 56.5
trnk-UUU-rps16_p4 trnk-UUU-rps16 CGCACTTAAAAGCCGAGTAC ACGGAACTTCACCTTAATCA 1086–1228 1.000 56.1
trnk-UUU-rps16_p5 trnk-UUU-rps16 CCGCACTTAAAAGCCGAGTA GTTTTTACGGAACTTCACCT 1093–1235 1.000 55.9
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGGCGCTTTA TACCACTAAACTATACCCGC 619–717 1.000 58.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGGCGCTTTA TTACCACTAAACTATACCCGC 620–718 1.000 56.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TACCACTAAACTATACCCGC 668–766 1.000 56.7
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TTACCACTAAACTATACCCGC 669–767 1.000 55.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ATTAGCAATCCGGCGCTTTA TTTACCACTAAACTATACCCGC 621–719 1.000 55.2
trnR-UCU-atpA_p1 trnR-UCU-atpA TTCAAATCCTGTTGGACGCA TCCACCAAGATATTCACCGC 410–769 1.000 89.2
trnR-UCU-atpA_p2 trnR-UCU-atpA TTCAAATCCTGTTGGACGCA CCACCAAGATATTCACCGCT 409–768 1.000 89.1
trnR-UCU-atpA_p3 trnR-UCU-atpA TTCAAATCCTGTTGGACGCA TGAAGCAGAAGCCCTTTTGA 390–749 1.000 88.9
trnR-UCU-atpA_p4 trnR-UCU-atpA TTCAAATCCTGTTGGACGCA ATTCACCGCTGAAGCAGAAG 399–758 1.000 87.4
trnR-UCU-atpA_p5 trnR-UCU-atpA GTTCAAATCCTGTTGGACGC TCCACCAAGATATTCACCGC 411–770 1.000 86.7
atpA-atpF_p1 atpA-atpF ACTTGAAGTACGGTACCGGT ATTGGCATGTTTGGGACGAT 204–209 1.000 80.4
atpA-atpF_p2 atpA-atpF TTGCTCAATACGTTCACGGA ATTGGCATGTTTGGGACGAT 157–162 1.000 80.3
atpA-atpF_p3 atpA-atpF TGCTCAATACGTTCACGGAT ATTGGCATGTTTGGGACGAT 156–161 1.000 78.5
atpA-atpF_p4 atpA-atpF ACTTGAAGTACGGTACCGGT TATTGGCATGTTTGGGACGA 205–210 1.000 77.6
atpA-atpF_p5 atpA-atpF TTGCTCAATACGTTCACGGA TATTGGCATGTTTGGGACGA 158–163 1.000 77.5
atpH-atpI_p1 atpH-atpI GATCCCTTCTACAGCTTGGC TGTTTCGAATTGGTCAGGGG 1281–1718 1.000 89.5
atpH-atpI_p2 atpH-atpI GATCCCTTCTACAGCTTGGC ACCATTCCTACTGACGGTCA 1412–1849 1.000 89.4
atpH-atpI_p3 atpH-atpI GATCCCTTCTACAGCTTGGC AGCAAAACTCAGATTGGCGA 1352–1789 1.000 89.3
atpH-atpI_p4 atpH-atpI AACAGAAGCGGCAGAAATCA ACCATTCCTACTGACGGTCA 1325–1762 1.000 89.2
atpH-atpI_p5 atpH-atpI GATCCCTTCTACAGCTTGGC GGTTTCCAAGTACATGCCCA 1505–1942 1.000 88.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (12)

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

Species Accession Length (bp) Link
Gynostemma burmanicum (nom. inval.) NC_036141.1 157687 View on NCBI ↗
Gynostemma cardiospermum NC_035959.1 159042 View on NCBI ↗
Gynostemma caulopterum NC_036135.1 157937 View on NCBI ↗
Gynostemma compressum NC_037179.1 157960 View on NCBI ↗
Gynostemma guangxiense NC_068908.1 157785 View on NCBI ↗
Gynostemma laxiflorum NC_036134.1 158273 View on NCBI ↗
Gynostemma laxum NC_073103.1 157787 View on NCBI ↗
Gynostemma longipes NC_036140.1 157601 View on NCBI ↗
Gynostemma pentagynum NC_036136.1 157791 View on NCBI ↗
Gynostemma pubescens NC_036142.1 157666 View on NCBI ↗
Gynostemma simplicifolium NC_073104.1 157840 View on NCBI ↗
Gynostemma yixingense NC_053537.1 157910 View on NCBI ↗