Markers + reference

Nymphaea

31 species · Nymphaeaceae · Nymphaeales

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Species 31
Genome length 158–161 kb
Candidate markers 268
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 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
tRNA-His (GUG)-psbA LSC 443 0.0350 0.98 71.6 yes View details
rps16-tRNA-Gln (UUG) LSC 2065 0.0242 0.98 69.8 yes View details
tRNA-Ser (GCU)-tRNA-Gly (UCC) LSC 756 0.0241 0.97 71.2 yes View details
atpF-atpH LSC 382 0.1544 1.00 69.5 yes View details
petA-psbJ LSC 1223 0.0202 0.99 62.5 yes View details
petD-rpoA LSC 424 0.0363 0.98 66.2 yes View details
ndhF SSC 2244 0.0103 1.00 45.8 yes View details
ndhF-rpl32 SSC 1140 0.0308 0.97 68.1 yes View details
ycf1 SSC 5931 0.0233 0.99 59.8 yes View details
rpl2-tRNA-His (GUG) IRa 35 0.0213 0.99 71.6 no View details
tRNA-Glu (UUC)-tRNA-Thr (GGU) LSC 564 0.0231 0.96 68.6 yes View details
tRNA-Lys (UUU)-rps16 LSC 803 0.0144 0.99 67.9 yes View details
ndhC-tRNA-Val (UAC) LSC 1933 0.0205 0.99 66.8 yes View details
tRNA-Leu (UAA)-tRNA-Phe (GAA) LSC 381 0.0268 1.00 66.2 yes View details
petN-psbM LSC 1337 0.0202 0.94 65.9 yes View details
rpoB-tRNA-Cys (GCA) LSC 1306 0.0164 0.96 65.7 yes View details
psbI-tRNA-Ser (GCU) LSC 177 0.0369 1.00 64.9 yes View details
ccsA-ndhD SSC 365 0.0315 0.96 64.8 yes View details
atpH-atpI LSC 1301 0.0195 0.99 63.5 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
tRNA-His (GUG)-psbA_p1 tRNA-His (GUG)-psbA AATCCACTTGGCTACATCCG GTCGAAGCTCCATCCACAAA 471–523 1.000 87.8
tRNA-His (GUG)-psbA_p2 tRNA-His (GUG)-psbA AATCCACTTGGCTACATCCG CGTGCTAACCTTGGTATGGA 540–592 1.000 83.9
tRNA-His (GUG)-psbA_p3 tRNA-His (GUG)-psbA AATCCACTTGGCTACATCCG TCGTGCTAACCTTGGTATGG 541–593 1.000 83.9
tRNA-His (GUG)-psbA_p4 tRNA-His (GUG)-psbA AATCCACTTGGCTACATCCG TCGAAGCTCCATCCACAAAT 470–522 1.000 83.0
tRNA-His (GUG)-psbA_p5 tRNA-His (GUG)-psbA AATCCACTTGGCTACATCCG CGAAGCTCCATCCACAAATG 469–521 1.000 82.6
tRNA-Lys (UUU)-rps16_p1 tRNA-Lys (UUU)-rps16 CCGATGGTATGGACGAATCC AAAAAGGAGCTCAACCCACG 969–1060 0.968 81.4
tRNA-Lys (UUU)-rps16_p2 tRNA-Lys (UUU)-rps16 ACGAATCCGCTTCATCCAAA AAAAAGGAGCTCAACCCACG 957–1048 0.968 81.3
tRNA-Lys (UUU)-rps16_p3 tRNA-Lys (UUU)-rps16 CCGATGGTATGGACGAATCC TGAAAAAGGAGCTCAACCCA 971–1062 0.968 80.9
tRNA-Lys (UUU)-rps16_p4 tRNA-Lys (UUU)-rps16 AAAGCCGAGTACTCTACCGT AAAAAGGAGCTCAACCCACG 911–1002 0.968 80.9
tRNA-Lys (UUU)-rps16_p5 tRNA-Lys (UUU)-rps16 AAGCCGAGTACTCTACCGTT AAAAAGGAGCTCAACCCACG 910–1001 0.968 80.9
rps16-tRNA-Gln (UUG)_p1 rps16-tRNA-Gln (UUG) GTCATTCAAGTCGCACGTTG ACGGGTTTTGGTCCTGTTAC 1177–2179 1.000 90.9
rps16-tRNA-Gln (UUG)_p2 rps16-tRNA-Gln (UUG) GTTGCCTTCTACCACATCGT ACGGGTTTTGGTCCTGTTAC 1161–2163 1.000 90.7
rps16-tRNA-Gln (UUG)_p3 rps16-tRNA-Gln (UUG) ACGTTGCCTTCTACCACATC ACGGGTTTTGGTCCTGTTAC 1163–2165 1.000 90.6
rps16-tRNA-Gln (UUG)_p4 rps16-tRNA-Gln (UUG) AATCCACAGCCGATCATGTC ACGGGTTTTGGTCCTGTTAC 1194–2196 0.968 89.4
rps16-tRNA-Gln (UUG)_p5 rps16-tRNA-Gln (UUG) AATCCACAGCCGATCATGTC GAGGTTCGAATCCTTCCGTC 1171–2173 0.968 89.1
psbI-tRNA-Ser (GCU)_p1 psbI-tRNA-Ser (GCU) TGTCTAATGACCCAGGACGT GCTATTCGTACCGAGGGTTC 253–284 1.000 87.4
psbI-tRNA-Ser (GCU)_p2 psbI-tRNA-Ser (GCU) TGTCTAATGACCCAGGACGT GGGTTCGAATCCCTCTCTCT 239–270 1.000 86.7
psbI-tRNA-Ser (GCU)_p3 psbI-tRNA-Ser (GCU) TGTCTAATGACCCAGGACGT AGCTATTCGTACCGAGGGTT 254–285 1.000 86.6
psbI-tRNA-Ser (GCU)_p4 psbI-tRNA-Ser (GCU) TGTCTAATGACCCAGGACGT GTGGACTAAAGCGGCAGATT 290–321 1.000 85.3
psbI-tRNA-Ser (GCU)_p5 psbI-tRNA-Ser (GCU) TGTCTAATGACCCAGGACGT TGGACTAAAGCGGCAGATTG 289–320 1.000 85.3
tRNA-Ser (GCU)-tRNA-Gly (UCC)_p1 tRNA-Ser (GCU)-tRNA-Gly (UCC) GGAAACGGAGAGAGAGGGAT TGTATCAAACCGAAAGAACCCT 837–939 0.806 62.0
tRNA-Ser (GCU)-tRNA-Gly (UCC)_p2 tRNA-Ser (GCU)-tRNA-Gly (UCC) AATCTGCCGCTTTAGTCCAC TGTATCAAACCGAAAGAACCCT 778–880 0.806 62.0
tRNA-Ser (GCU)-tRNA-Gly (UCC)_p3 tRNA-Ser (GCU)-tRNA-Gly (UCC) CAATCTGCCGCTTTAGTCCA TGTATCAAACCGAAAGAACCCT 779–881 0.806 62.0
tRNA-Ser (GCU)-tRNA-Gly (UCC)_p4 tRNA-Ser (GCU)-tRNA-Gly (UCC) AGATTAGCAATCTGCCGCTT TGTATCAAACCGAAAGAACCCT 786–888 0.806 61.4
tRNA-Ser (GCU)-tRNA-Gly (UCC)_p5 tRNA-Ser (GCU)-tRNA-Gly (UCC) CGGAGAGAGAGGGATTCGAA TGTATCAAACCGAAAGAACCCT 832–934 0.806 61.2
atpF-atpH_p1 atpF-atpH TAAAGTGCAGCTGGTTGGTT AATTTACGGACTGGTCGTGG 623–677 1.000 90.8
atpF-atpH_p2 atpF-atpH GATCTCTGGAGGGCTCTTCT AATTTACGGACTGGTCGTGG 1111–1159 1.000 90.6
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG AATTTACGGACTGGTCGTGG 496–550 1.000 90.3
atpF-atpH_p4 atpF-atpH TACACAACTCGCACACACTC AATTTACGGACTGGTCGTGG 586–640 1.000 90.1
atpF-atpH_p5 atpF-atpH GCCTACCCTCTCTTCTCTGT AATTTACGGACTGGTCGTGG 1169–1219 1.000 90.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (31)

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

Species Accession Length (bp) Link
Nymphaea alba NC_006050.1 159930 View on NCBI ↗
Nymphaea alba subsp. alba MK040444.1 159925 View on NCBI ↗
Nymphaea amazonum NC_056818.1 159186 View on NCBI ↗
Nymphaea ampla NC_035680.2 159861 View on NCBI ↗
Nymphaea atrans NC_060672.1 160929 View on NCBI ↗
Nymphaea capensis NC_040167.1 159998 View on NCBI ↗
Nymphaea cf. capensis MG-2022 MW057740.1 159809 View on NCBI ↗
Nymphaea colorata NC_057562.1 159842 View on NCBI ↗
Nymphaea conardii NC_056819.1 159257 View on NCBI ↗
Nymphaea dimorpha NC_063734.1 159917 View on NCBI ↗
Nymphaea gigantea NC_057568.1 160179 View on NCBI ↗
Nymphaea glandulifera NC_056820.1 159093 View on NCBI ↗
Nymphaea gracilis NC_056821.1 159797 View on NCBI ↗
Nymphaea heudelotii NC_056822.1 159850 View on NCBI ↗
Nymphaea hybrid cultivar MW644616.1 159968 View on NCBI ↗
Nymphaea immutabilis NC_056823.1 160042 View on NCBI ↗
Nymphaea jamesoniana NC_031826.2 158963 View on NCBI ↗
Nymphaea lasiophylla NC_063733.1 158991 View on NCBI ↗
Nymphaea lotus NC_041238.1 159311 View on NCBI ↗
Nymphaea mexicana NC_024542.1 159962 View on NCBI ↗
Nymphaea micrantha NC_057566.1 159900 View on NCBI ↗
Nymphaea nouchali NC_059865.1 159978 View on NCBI ↗
Nymphaea odorata NC_057567.1 159968 View on NCBI ↗
Nymphaea potamophila NC_057564.1 159232 View on NCBI ↗
Nymphaea pubescens NC_072673.1 159707 View on NCBI ↗
Nymphaea rubra NC_057563.1 159322 View on NCBI ↗
Nymphaea rudgeana NC_056824.1 159220 View on NCBI ↗
Nymphaea tenerinervia NC_056825.1 158290 View on NCBI ↗
Nymphaea tetragona NC_057565.1 159956 View on NCBI ↗
Nymphaea thermarum NC_056953.1 159849 View on NCBI ↗
Nymphaea x daubenyana NC_063735.1 159707 View on NCBI ↗