Markers + reference

Camellia

118 species · Theaceae · Ericales

Back to catalogue

Species 118
Genome length 156–157 kb
Candidate markers 270
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhG SSC 531 0.0038 0.00 28.5 yes View details
ndhB-trnL-CAA IRb 556 0.0000 0.00 22.2 yes View details
trnH-GUG-psbA LSC 387 0.0128 0.99 54.5 yes View details
psbA LSC 1062 0.0015 1.00 56.3 yes View details
rps16 LSC 1123 0.0025 1.00 48.2 yes View details
trnS-GCU-trnR-UCU LSC 1686 0.0039 1.00 59.3 yes View details
petN-psbM LSC 1083 0.0036 1.00 48.7 yes View details
trnE-UUC-psbD LSC 2370 0.0027 1.00 66.5 yes View details
petA-psbJ LSC 1033 0.0023 1.00 61.8 yes View details
clpP LSC 1981 0.0015 1.00 53.0 yes View details
accD-psaI LSC 718 0.0028 1.00 63.1 yes View details
rps16-trnQ-UUG LSC 1613 0.0021 1.00 60.6 yes View details
trnT-UGU-trnL-UAA LSC 1001 0.0023 1.00 60.2 yes View details
psbE-petL LSC 1292 0.0017 1.00 58.5 yes View details
trnK-UUU-rps16 LSC 748 0.0024 1.00 58.2 yes View details
matK-trnK-UUU LSC 717 0.0034 1.00 57.9 yes View details
ycf3-trnS-GGA LSC 877 0.0016 1.00 57.3 yes View details
rpoC2 LSC 4137 0.0012 1.00 56.5 yes View details
trnF-GAA-ndhJ LSC 667 0.0025 1.00 55.5 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ndhG_p1 ndhG TGATTTTGATTTCTAGTTCTGTTCT ACTGGTCAGGTCAACAAAGTC 628–636 0.975 43.2
ndhG_p2 ndhG TGATTTTGATTTCTAGTTCTGTTCT CTGGTCAGGTCAACAAAGTCA 627–635 0.975 43.2
ndhG_p3 ndhG TGATTTTGATTTCTAGTTCTGTTCT TGGTCAGGTCAACAAAGTCA 626–634 0.975 43.2
ndhG_p4 ndhG TGATTTTGATTTCTAGTTCTGTTCT ACTGGTCAGGTCAACAAAGT 628–636 0.975 43.2
ndhG_p5 ndhG AGTTTGATTTTGATTTCTAGTTCTGT ACTGGTCAGGTCAACAAAGTC 632–640 0.975 43.2
ndhB-trnL-CAA_p1 ndhB-trnL-CAA TGCAATTGCTCAGGATACCC GTCTCGCGTGTCTACCATTT 608–623 1.000 83.5
ndhB-trnL-CAA_p2 ndhB-trnL-CAA TGCAATTGCTCAGGATACCC CTCGCGTGTCTACCATTTCA 606–621 1.000 83.5
ndhB-trnL-CAA_p3 ndhB-trnL-CAA TGCAATTGCTCAGGATACCC TACCATTTCACCACCAAGGC 596–611 1.000 82.9
ndhB-trnL-CAA_p4 ndhB-trnL-CAA TGCAATTGCTCAGGATACCC GCGTGTCTACCATTTCACCA 603–618 1.000 82.0
ndhB-trnL-CAA_p5 ndhB-trnL-CAA TGCAATTGCTCAGGATACCC TCTCGCGTGTCTACCATTTC 607–622 1.000 81.4
trnH-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CCGTGCTAACCTTGGTATGG 496–528 0.992 85.4
trnH-GUG-psbA_p2 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC CCGTGCTAACCTTGGTATGG 497–529 0.992 85.2
trnH-GUG-psbA_p3 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT ACCGTGCTAACCTTGGTATG 497–529 0.992 84.9
trnH-GUG-psbA_p4 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC ACCGTGCTAACCTTGGTATG 498–530 0.992 84.7
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 489–521 0.992 83.9
psbA_p1 psbA AGGAACAATAACGCCTTCCT AAATTCGTGTGCTTGGGAGT 1199 0.992 76.2
psbA_p2 psbA GGAACAATAACGCCTTCCTG AAATTCGTGTGCTTGGGAGT 1198 0.992 75.9
psbA_p3 psbA AGGAACAATAACGCCTTCCTG AAATTCGTGTGCTTGGGAGT 1199 0.992 75.3
psbA_p4 psbA GGAACAATAACGCCTTCCTGA AAATTCGTGTGCTTGGGAGT 1198 0.992 75.2
psbA_p5 psbA ACGCCTTCCTGATAGAACAAG AAATTCGTGTGCTTGGGAGT 1189 0.983 75.2
trnK-UUU_p1 trnK-UUU GCCCGTGTCAACCAATATCT TCTGATTGTATCTACACACCCT 2690–2719 1.000 55.6
trnK-UUU_p2 trnK-UUU TGCCCGTGTCAACCAATATC TCTGATTGTATCTACACACCCT 2691–2720 1.000 53.8
trnK-UUU_p3 trnK-UUU GCCCGTGTCAACCAATATCT TCTGATTGTATCTACACACCCTT 2690–2719 1.000 53.3
trnK-UUU_p4 trnK-UUU GCCCGTGTCAACCAATATCT TTCTGATTGTATCTACACACCCT 2691–2720 1.000 53.3
trnK-UUU_p5 trnK-UUU ATGCCCGTGTCAACCAATAT TCTGATTGTATCTACACACCCT 2692–2721 1.000 52.4
matK-trnK-UUU_p1 matK-trnK-UUU CGAAGTCGTGTTGCTGAGAT AACGGTAGAGTACTCGGCTT 790–810 0.992 83.7
matK-trnK-UUU_p2 matK-trnK-UUU CGAAGTCGTGTTGCTGAGAT ACGGTAGAGTACTCGGCTTT 789–809 0.992 83.7
matK-trnK-UUU_p3 matK-trnK-UUU CGAAGTCGTGTTGCTGAGAT GGGTTGCTAACTCAACGGTA 803–823 0.992 81.3
matK-trnK-UUU_p4 matK-trnK-UUU CGAAGTCGTGTTGCTGAGAT TTCGGGTTGCTAACTCAACG 806–826 0.992 81.0
matK-trnK-UUU_p5 matK-trnK-UUU CCATGATCATGAGCAAGTGC ACGGTAGAGTACTCGGCTTT 841–861 0.992 80.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (118)

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

Species Accession Length (bp) Link
Camellia achrysantha NC_057956.1 156658 View on NCBI ↗
Camellia albosericea NC_085496.1 156944 View on NCBI ↗
Camellia amplexicaulis NC_051559.1 157203 View on NCBI ↗
Camellia amplexifolia NC_061610.1 156591 View on NCBI ↗
Camellia anlungensis NC_050354.1 156587 View on NCBI ↗
Camellia anlungensis var. acutiperulata OR360837.1 156636 View on NCBI ↗
Camellia arborescens NC_087763.1 156883 View on NCBI ↗
Camellia atrothea NC_066658.1 157099 View on NCBI ↗
Camellia azalea NC_035574.1 157039 View on NCBI ↗
Camellia bailinshanica NC_080884.1 156943 View on NCBI ↗
Camellia cattienensis PZ180086.1 156357 View on NCBI ↗
Camellia chrysanthoides NC_057957.1 156959 View on NCBI ↗
Camellia chuongtsoensis MT663341.1 156504 View on NCBI ↗
Camellia connata NC_067053.1 156311 View on NCBI ↗
Camellia cordifolia NC_077634.1 156745 View on NCBI ↗
Camellia costei NC_087747.1 156784 View on NCBI ↗
Camellia crapnelliana NC_024541.1 156997 View on NCBI ↗
Camellia crassicolumna NC_087767.1 156973 View on NCBI ↗
Camellia crassicolumna var. multiplex OQ646018.1 156952 View on NCBI ↗
Camellia crispula var. crispula OQ645990.1 157025 View on NCBI ↗
Camellia cuspidata NC_022459.1 156618 View on NCBI ↗
Camellia danzaiensis NC_022460.1 156576 View on NCBI ↗
Camellia delicata PQ539948.1 156879 View on NCBI ↗
Camellia elongata NC_035652.1 156751 View on NCBI ↗
Camellia fangchengensis NC_087769.1 156775 View on NCBI ↗
Camellia fascicularis NC_053896.1 156815 View on NCBI ↗
Camellia flava NC_084240.1 156670 View on NCBI ↗
Camellia flavida NC_068780.1 156935 View on NCBI ↗
Camellia fluviatilis NC_058853.1 157041 View on NCBI ↗
Camellia formosensis NC_065198.1 156986 View on NCBI ↗
Camellia fraterna NC_050388.1 156902 View on NCBI ↗
Camellia fusuiensis NC_084456.1 157025 View on NCBI ↗
Camellia gauchowensis NC_053541.1 157004 View on NCBI ↗
Camellia grandibracteata NC_024659.1 157127 View on NCBI ↗
Camellia granthamiana NC_038181.1 157001 View on NCBI ↗
Camellia grijsii NC_087746.1 156910 View on NCBI ↗
Camellia grijsii var. shensiensis OR353673.1 156739 View on NCBI ↗
Camellia gymnogyna NC_039626.1 156590 View on NCBI ↗
Camellia hamyenensis PZ054906.1 156613 View on NCBI ↗
Camellia huana NC_084455.1 156921 View on NCBI ↗
Camellia huulungensis NC_088067.1 156546 View on NCBI ↗
Camellia impressinervis NC_022461.1 156892 View on NCBI ↗
Camellia irrawadiensis OQ503617.1 156978 View on NCBI ↗
Camellia japonica NC_036830.1 156606 View on NCBI ↗
Camellia kissii NC_053915.1 156961 View on NCBI ↗
Camellia kwangsiensis NC_087765.1 156976 View on NCBI ↗
Camellia kwangsiensis var. kwangnanica OQ646005.1 157011 View on NCBI ↗
Camellia kwangtungensis NC_087768.1 156733 View on NCBI ↗
Camellia lanceoleosa NC_067764.1 157021 View on NCBI ↗
Camellia leptophylla NC_024660.1 157102 View on NCBI ↗
Camellia leyensis OK046127.1 157063 View on NCBI ↗
Camellia liberofilamenta NC_061603.1 156865 View on NCBI ↗
Camellia limonia NC_061599.1 156657 View on NCBI ↗
Camellia lipingensis NC_067613.1 157011 View on NCBI ↗
Camellia longipedicellata NC_065391.1 156669 View on NCBI ↗
Camellia longissima NC_067609.1 157038 View on NCBI ↗
Camellia longzhouensis NC_068781.1 156959 View on NCBI ↗
Camellia lungzhouensis MN579509.2 157110 View on NCBI ↗
Camellia luteoflora NC_082978.1 157172 View on NCBI ↗
Camellia mairei NC_035688.1 156963 View on NCBI ↗
Camellia makuanica NC_087766.1 156359 View on NCBI ↗
Camellia mingii NC_046699.1 156806 View on NCBI ↗
Camellia minima NC_069310.1 156961 View on NCBI ↗
Camellia nitidissima var. nitidissima MT157617.1 156596 View on NCBI ↗
Camellia oblata NC_087751.1 156625 View on NCBI ↗
Camellia obtusifolia NC_068785.1 156892 View on NCBI ↗
Camellia octopetala MN095258.1 156615 View on NCBI ↗
Camellia oleifera NC_023084.1 156971 View on NCBI ↗
Camellia oleifera var. oleifera MZ151355.1 156549 View on NCBI ↗
Camellia parvisepala NC_058924.1 157074 View on NCBI ↗
Camellia paucipetala PQ539951.1 156931 View on NCBI ↗
Camellia perpetua NC_054364.1 156162 View on NCBI ↗
Camellia petelotii NC_024661.1 157121 View on NCBI ↗
Camellia petelotii var. microcarpa NC_061600.1 157046 View on NCBI ↗
Camellia petelotii var. petelotii ON208847.1 156620 View on NCBI ↗
Camellia pilosperma OQ503616.1 156892 View on NCBI ↗
Camellia pingguoensis NC_061051.1 156621 View on NCBI ↗
Camellia piquetiana NC_087752.1 157142 View on NCBI ↗
Camellia pitardii NC_022462.1 156585 View on NCBI ↗
Camellia polyodonta NC_060777.1 156983 View on NCBI ↗
Camellia ptilophylla NC_038198.1 157097 View on NCBI ↗
Camellia pubescens NC_087764.1 156450 View on NCBI ↗
Camellia pubicosta NC_024662.1 157076 View on NCBI ↗
Camellia pubipetala NC_054365.1 156993 View on NCBI ↗
Camellia pyxidiacea NC_070214.1 156677 View on NCBI ↗
Camellia pyxidiacea var. rubituberculata OR413569.1 157045 View on NCBI ↗
Camellia quinquelocularis OQ503555.1 156805 View on NCBI ↗
Camellia reticulata NC_024663.1 156971 View on NCBI ↗
Camellia rhytidophylla NC_050389.1 157073 View on NCBI ↗
Camellia rostrata NC_058254.1 156547 View on NCBI ↗
Camellia rubimuricata NC_082975.1 156631 View on NCBI ↗
Camellia salicifolia NC_087749.1 156580 View on NCBI ↗
Camellia sasanqua NC_041473.1 156544 View on NCBI ↗
Camellia semiserrata var. magnocarpa MZ359672.1 156949 View on NCBI ↗
Camellia sinensis NC_020019.1 157103 View on NCBI ↗
Camellia sinensis var. assamica PX851733.1 157098 View on NCBI ↗
Camellia sinensis var. dehungensis OQ646030.1 157105 View on NCBI ↗
Camellia sinensis var. kucha OQ646011.1 156589 View on NCBI ↗
Camellia sinensis var. lasiocalyx OQ503562.1 157098 View on NCBI ↗
Camellia sinensis var. pubilimba NC_061691.1 157097 View on NCBI ↗
Camellia sinensis var. sinensis PX801050.1 157108 View on NCBI ↗
Camellia suaveolens NC_063576.1 156981 View on NCBI ↗
Camellia synaptica NC_087750.1 156665 View on NCBI ↗
Camellia szechuanensis NC_035651.1 157070 View on NCBI ↗
Camellia tachangensis NC_056149.1 157026 View on NCBI ↗
Camellia tachangensis var. remotiserrata PV992848.1 156883 View on NCBI ↗
Camellia taliensis NC_022264.1 156974 View on NCBI ↗
Camellia tetracocca OK405020.1 157026 View on NCBI ↗
Camellia tianeensis NC_086748.1 156865 View on NCBI ↗
Camellia trichosperma OK181904.1 156605 View on NCBI ↗
Camellia tsaii OQ503552.1 156655 View on NCBI ↗
Camellia vietnamensis NC_060778.1 156999 View on NCBI ↗
Camellia weiningensis MK820035.1 156490 View on NCBI ↗
Camellia xiashiensis NC_061602.1 156865 View on NCBI ↗
Camellia yunnanensis NC_022463.1 156592 View on NCBI ↗
Camellia yunnanensis var. camellioides OQ503551.1 156611 View on NCBI ↗
Camellia zhaiana NC_058253.1 156627 View on NCBI ↗
Camellia zijinica OR567094.1 156927 View on NCBI ↗