Markers + reference

Magnolia

154 species · Magnoliaceae · Magnoliales

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Species 154
Genome length 159–345 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

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

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 383 0.0162 1.00 59.8 yes View details
rps16-trnQ-UUG LSC 1923 0.0078 1.00 68.1 yes View details
petA-psbJ LSC 1175 0.0198 1.00 67.3 yes View details
psbE-petL LSC 1190 0.0114 1.00 67.6 yes View details
ndhF SSC 2226 0.0053 1.00 44.6 yes View details
ndhF-rpl32 SSC 1142 0.0121 1.00 71.2 yes View details
rpl32-trnL-UAG SSC 1205 0.0131 1.00 62.5 yes View details
psaC SSC 246 0.0023 1.00 25.8 yes View details
ycf1 SSC 5595 0.0074 0.99 58.3 yes View details
trnT-GGU-psbD LSC 1448 0.0064 1.00 71.9 yes View details
ndhC-trnV-UAC LSC 1786 0.0069 1.00 70.4 yes View details
atpH-atpI LSC 797 0.0068 1.00 69.0 yes View details
petN-psbM LSC 747 0.0092 1.00 68.4 yes View details
trnS-GCU-trnG-UCC LSC 671 0.0060 1.00 65.9 yes View details
trnE-UUC-trnT-GGU LSC 733 0.0055 1.00 64.4 yes View details
psaJ-rpl33 LSC 431 0.0106 1.00 61.8 yes View details
ycf3-trnS-GGA LSC 434 0.0067 1.00 61.2 yes View details
trnT-UGU-trnL-UAA LSC 777 0.0102 0.99 60.4 yes View details
psbK-psbI LSC 357 0.0089 1.00 60.2 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
trnH-GUG-psbA_p1 trnH-GUG-psbA TCACAATCCACTGCCTTGAG CCTCTAGACCTAGCTGCTGT 450–488 1.000 90.0
trnH-GUG-psbA_p2 trnH-GUG-psbA TCACAATCCACTGCCTTGAG TTCCCTCTAGACCTAGCTGC 453–578 1.000 89.9
trnH-GUG-psbA_p3 trnH-GUG-psbA TCACAATCCACTGCCTTGAG AGCTGCTGTTGAAGTTCCAT 439–477 1.000 88.2
trnH-GUG-psbA_p4 trnH-GUG-psbA CGCATGGTGGATTCACAATC CCTCTAGACCTAGCTGCTGT 462–500 1.000 87.6
trnH-GUG-psbA_p5 trnH-GUG-psbA CGCATGGTGGATTCACAATC TTCCCTCTAGACCTAGCTGC 465–590 1.000 87.6
trnK-UUU_p1 trnK-UUU GTGCTTTCGCGTCTCTCTAA GTTTTGATGGGGTAGGGCAA 2930–2974 0.987 86.9
trnK-UUU_p2 trnK-UUU GTGCTTTCGCGTCTCTCTAA ATGTTTTGATGGGGTAGGGC 2932–2976 0.987 86.1
trnK-UUU_p3 trnK-UUU GTGCTTTCGCGTCTCTCTAA GGGTAGGGCAATCCAATCTC 2921–2965 1.000 85.9
trnK-UUU_p4 trnK-UUU CCAAGCGCACGGATTATCTA GTTTTGATGGGGTAGGGCAA 2863–2907 0.922 82.7
trnK-UUU_p5 trnK-UUU CCAAGCGCACGGATTATCTA ATGTTTTGATGGGGTAGGGC 2865–2909 0.922 82.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAAGAATCCACAGCCGATCA GAGGTTCGAATCCTTCCGTC 1225–2092 1.000 91.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1215–2082 1.000 91.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1213–2080 1.000 91.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AATCCACAGCCGATCATGTC GAGGTTCGAATCCTTCCGTC 1221–2088 1.000 91.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GAATCCACAGCCGATCATGT GAGGTTCGAATCCTTCCGTC 1222–2089 1.000 91.1
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCCAAGATCATTTTTGGGGGA 404–431 1.000 76.8
psbK-psbI_p2 psbK-psbI GCCAAATTACCCGAGGCTTA TCCAAGATCATTTTTGGGGGA 491–518 1.000 76.3
psbK-psbI_p3 psbK-psbI ACCCGAGGCTTATGCTTTTT TCCAAGATCATTTTTGGGGGA 483–510 1.000 75.0
psbK-psbI_p4 psbK-psbI TGGCAAGCTGCTGTAAGTTT TCCAAGATCATTTTTGGGGGA 401–428 1.000 74.8
psbK-psbI_p5 psbK-psbI TTGGCAAGCTGCTGTAAGTT TCCAAGATCATTTTTGGGGGA 402–429 1.000 74.8
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGTCGCTTTAGTCCA AATCAAACCGAAAGACCCCC 774–888 1.000 90.3
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGTCGCTTTAGTCCAC AATCAAACCGAAAGACCCCC 773–887 1.000 90.3
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGTCGCTTTAGTCCA AACCGAAAGACCCCCTAACT 769–883 1.000 88.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGTCGCTTTAGTCCAC AACCGAAAGACCCCCTAACT 768–882 1.000 88.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAATCCGTCGCTTTAGTCCA TCAAACCGAAAGACCCCCTA 772–886 1.000 88.8
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 885–1191 1.000 85.1
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT TTTTTGCAACTTTAGCCGCG 941–1247 1.000 84.4
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT CAAGCGGGATTCAAGCTCTT 906–1212 0.994 84.4
atpH-atpI_p4 atpH-atpI GATACCTTCTACGGCTTGGC TTTTTGCAACTTTAGCCGCG 970–1276 1.000 84.3
atpH-atpI_p5 atpH-atpI CGATACCTTCTACGGCTTGG TTTTTGCAACTTTAGCCGCG 971–1277 1.000 84.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (154)

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

Species Accession Length (bp) Link
Magnolia acuminata MN990595.1 159810 View on NCBI ↗
Magnolia acuminata var. acuminata JX280391.2 159815 View on NCBI ↗
Magnolia albosericea NC_062893.1 159790 View on NCBI ↗
Magnolia amazonica NC_048959.1 159922 View on NCBI ↗
Magnolia amoena NC_062937.1 159987 View on NCBI ↗
Magnolia aromatica NC_037000.1 160062 View on NCBI ↗
Magnolia baillonii NC_048453.1 160107 View on NCBI ↗
Magnolia balansae NC_053860.1 160134 View on NCBI ↗
Magnolia bankardiorum NC_062907.1 159269 View on NCBI ↗
Magnolia bidoupensis MN990624.1 159796 View on NCBI ↗
Magnolia biondii NC_034687.1 160002 View on NCBI ↗
Magnolia borneensis NC_062924.1 160161 View on NCBI ↗
Magnolia buenaventurensis PQ303609.1 159782 View on NCBI ↗
Magnolia campbellii NC_062936.1 160102 View on NCBI ↗
Magnolia carsonii NC_062923.1 160186 View on NCBI ↗
Magnolia cathcartii NC_023234.1 159950 View on NCBI ↗
Magnolia cavaleriei NC_058903.1 159968 View on NCBI ↗
Magnolia cavaleriei var. platypetala NC_062641.1 160112 View on NCBI ↗
Magnolia champaca NC_060724.1 160008 View on NCBI ↗
Magnolia champaca var. champaca MT269873.1 160008 View on NCBI ↗
Magnolia championii NC_062894.1 159828 View on NCBI ↗
Magnolia changhungtana NC_062939.1 160133 View on NCBI ↗
Magnolia chevalieri MN990616.1 160145 View on NCBI ↗
Magnolia chimantensis MN990632.1 159206 View on NCBI ↗
Magnolia coco NC_050980.1 159828 View on NCBI ↗
Magnolia compressa MT682882.1 160074 View on NCBI ↗
Magnolia conifera NC_037001.1 159973 View on NCBI ↗
Magnolia coriacea NC_058758.1 160113 View on NCBI ↗
Magnolia crassipes NC_058270.1 159901 View on NCBI ↗
Magnolia cubensis NC_063084.1 159917 View on NCBI ↗
Magnolia cylindrica NC_062935.1 160074 View on NCBI ↗
Magnolia dawsoniana NC_062928.1 159908 View on NCBI ↗
Magnolia decidua NC_062919.1 160127 View on NCBI ↗
Magnolia denudata NC_056770.1 160090 View on NCBI ↗
Magnolia dixonii NC_048960.1 159884 View on NCBI ↗
Magnolia dodecapetala NC_048992.1 159876 View on NCBI ↗
Magnolia doltsopa NC_058902.1 160054 View on NCBI ↗
Magnolia duclouxii NC_037002.1 160055 View on NCBI ↗
Magnolia elegans NC_062651.1 160110 View on NCBI ↗
Magnolia equatorialis NC_062909.1 159806 View on NCBI ↗
Magnolia ernestii NC_061249.1 159327 View on NCBI ↗
Magnolia ernestii subsp. szechuanica OR946459.1 160147 View on NCBI ↗
Magnolia figlarii NC_058550.1 160043 View on NCBI ↗
Magnolia figo NC_053861.1 160113 View on NCBI ↗
Magnolia figo var. skinneriana MZ297474.1 160088 View on NCBI ↗
Magnolia floribunda NC_062652.1 160030 View on NCBI ↗
Magnolia fordiana NC_058549.1 160074 View on NCBI ↗
Magnolia fordiana var. calcarea PQ246290.1 160067 View on NCBI ↗
Magnolia fordiana var. hainanensis MN306583.1 160157 View on NCBI ↗
Magnolia foveolata NC_062644.1 160082 View on NCBI ↗
Magnolia fraseri NC_062900.1 160028 View on NCBI ↗
Magnolia fraseri subsp. pyramidata NC_023236.1 160025 View on NCBI ↗
Magnolia fujianensis NC_062656.1 160094 View on NCBI ↗
Magnolia fulva NC_062643.1 160022 View on NCBI ↗
Magnolia fulva var. calcicola OR063914.1 160061 View on NCBI ↗
Magnolia fulva var. fulva MT674808.1 160041 View on NCBI ↗
Magnolia garrettii NC_062917.1 160020 View on NCBI ↗
Magnolia gilbertoi NC_048958.1 159630 View on NCBI ↗
Magnolia glaucifolia NC_037003.1 160059 View on NCBI ↗
Magnolia globosa NC_062927.1 159969 View on NCBI ↗
Magnolia grandiflora NC_020318.1 159623 View on NCBI ↗
Magnolia grandis NC_058271.1 160008 View on NCBI ↗
Magnolia griffithii NC_062892.1 160091 View on NCBI ↗
Magnolia guangdongensis NC_060725.1 160142 View on NCBI ↗
Magnolia guangxiensis NC_062645.1 160081 View on NCBI ↗
Magnolia guatapensis NC_086504.1 159356 View on NCBI ↗
Magnolia guatemalensis NC_062922.1 159748 View on NCBI ↗
Magnolia henryi NC_062913.1 159760 View on NCBI ↗
Magnolia hodgsonii NC_062910.1 159687 View on NCBI ↗
Magnolia hookeri NC_053862.1 160035 View on NCBI ↗
Magnolia hookeri var. longirostrata PV239601.1 160076 View on NCBI ↗
Magnolia iltisiana NC_062898.1 159658 View on NCBI ↗
Magnolia insignis NC_035657.1 160117 View on NCBI ↗
Magnolia kachirachirai NC_062903.1 160042 View on NCBI ↗
Magnolia kichuana NC_062905.1 159864 View on NCBI ↗
Magnolia kobus NC_023237.1 159443 View on NCBI ↗
Magnolia kwangsiensis NC_015892.1 159667 View on NCBI ↗
Magnolia kwangtungensis NC_062914.1 160110 View on NCBI ↗
Magnolia lacei NC_058901.1 160066 View on NCBI ↗
Magnolia laevifolia NC_035956.1 160120 View on NCBI ↗
Magnolia lanuginosa NC_062942.1 160088 View on NCBI ↗
Magnolia lenticellata MN990629.1 159290 View on NCBI ↗
Magnolia liliifera NC_062891.1 159736 View on NCBI ↗
Magnolia liliifera var. obovata MT560391.1 159693 View on NCBI ↗
Magnolia lotungensis NC_062929.1 160046 View on NCBI ↗
Magnolia lucida NC_063085.1 160109 View on NCBI ↗
Magnolia macclurei NC_058900.1 159840 View on NCBI ↗
Magnolia macrophylla NC_062933.1 160087 View on NCBI ↗
Magnolia macrophylla var. dealbata NC_023235.1 160002 View on NCBI ↗
Magnolia masticata NC_062653.1 160020 View on NCBI ↗
Magnolia maudiae NC_047409.1 160154 View on NCBI ↗
Magnolia megaphylla NC_037004.1 160077 View on NCBI ↗
Magnolia mercedesiarum NC_062912.1 159896 View on NCBI ↗
Magnolia mexicana NC_062896.1 159787 View on NCBI ↗
Magnolia mindoensis NC_062911.1 159800 View on NCBI ↗
Magnolia montana NC_062654.1 160054 View on NCBI ↗
Magnolia nitida NC_062932.1 160019 View on NCBI ↗
Magnolia obovalifolia NC_058551.1 160073 View on NCBI ↗
Magnolia obovata NC_062934.1 160087 View on NCBI ↗
Magnolia odora NC_023239.1 160070 View on NCBI ↗
Magnolia odoratissima NC_042680.1 159536 View on NCBI ↗
Magnolia ofeliae NC_051512.1 159839 View on NCBI ↗
Magnolia officinalis NC_020316.1 160183 View on NCBI ↗
Magnolia officinalis subsp. biloba NC_020317.1 160105 View on NCBI ↗
Magnolia omeiensis NC_048460.1 160091 View on NCBI ↗
Magnolia opipara NC_062646.1 160169 View on NCBI ↗
Magnolia ovalis NC_062647.1 160123 View on NCBI ↗
Magnolia ovata NC_048993.1 159895 View on NCBI ↗
Magnolia ovoidea NC_062938.1 160112 View on NCBI ↗
Magnolia panamensis NC_062901.1 159721 View on NCBI ↗
Magnolia pastazaensis NC_062906.1 159790 View on NCBI ↗
Magnolia patungensis NC_066227.1 345184 View on NCBI ↗
Magnolia phanerophlebia NC_062904.1 159572 View on NCBI ↗
Magnolia pilocarpa NC_050211.1 160104 View on NCBI ↗
Magnolia poasana NC_062899.1 159732 View on NCBI ↗
Magnolia portoricensis NC_062902.1 159919 View on NCBI ↗
Magnolia praecalva NC_062940.1 160061 View on NCBI ↗
Magnolia praecocissima NC_058268.1 159778 View on NCBI ↗
Magnolia pterocarpa NC_062920.1 159722 View on NCBI ↗
Magnolia rufibarbata NC_062918.1 160092 View on NCBI ↗
Magnolia sargentiana NC_062925.1 160118 View on NCBI ↗
Magnolia schiedeana NC_062931.1 159686 View on NCBI ↗
Magnolia shangsiensis MN990575.1 159682 View on NCBI ↗
Magnolia sharpii NC_062921.1 159730 View on NCBI ↗
Magnolia shiluensis NC_047417.1 160075 View on NCBI ↗
Magnolia siamensis MN990592.1 159796 View on NCBI ↗
Magnolia sieboldii NC_041435.1 160177 View on NCBI ↗
Magnolia sieboldii subsp. sinensis MT682843.1 160146 View on NCBI ↗
Magnolia sinica NC_023241.1 160044 View on NCBI ↗
Magnolia sirindhorniae NC_062609.1 160109 View on NCBI ↗
Magnolia sphaerantha NC_062648.1 160079 View on NCBI ↗
Magnolia splendens NC_062897.1 159926 View on NCBI ↗
Magnolia stellata NC_062926.1 159403 View on NCBI ↗
Magnolia striatifolia NC_062895.1 159686 View on NCBI ↗
Magnolia sumatrae NC_062650.1 160057 View on NCBI ↗
Magnolia sumatrana var. glauca MT682807.1 160101 View on NCBI ↗
Magnolia tarahumara MN990636.1 159787 View on NCBI ↗
Magnolia tripetala NC_024027.1 160037 View on NCBI ↗
Magnolia tsiampacca MN990607.1 160209 View on NCBI ↗
Magnolia utilis NC_062916.1 160066 View on NCBI ↗
Magnolia velutina NC_062649.1 160088 View on NCBI ↗
Magnolia ventii NC_058272.1 159950 View on NCBI ↗
Magnolia virginiana NC_062930.1 159793 View on NCBI ↗
Magnolia viridipetala NC_062642.1 160123 View on NCBI ↗
Magnolia viridula MN990590.1 160060 View on NCBI ↗
Magnolia vrieseana NC_062915.1 160141 View on NCBI ↗
Magnolia wilsonii NC_046054.1 159940 View on NCBI ↗
Magnolia x alba NC_037005.1 160106 View on NCBI ↗
Magnolia x soulangeana NC_058269.1 159778 View on NCBI ↗
Magnolia xanthantha OR946453.1 160166 View on NCBI ↗
Magnolia xinningia NC_088761.1 160082 View on NCBI ↗
Magnolia yarumalensis NC_086503.1 159410 View on NCBI ↗
Magnolia yunnanensis NC_024545.1 160085 View on NCBI ↗
Magnolia zamorana NC_062908.1 159734 View on NCBI ↗