Markers + reference

Citrus

35 species · Rutaceae · Sapindales

Back to catalogue

Species 35
Genome length 160–161 kb
Candidate markers 276
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 276 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH_gug-psbA LSC 432 0.0108 0.98 52.4 yes View details
trnR_ucu-atpA LSC 253 0.0178 0.91 47.2 yes View details
petN-psbM LSC 1280 0.0093 0.99 56.8 yes View details
psbM-trnD_guc LSC 1204 0.0076 0.99 56.1 yes View details
ndhJ LSC 477 0.0032 1.00 43.9 yes View details
petA-psbJ LSC 1097 0.0073 0.99 57.1 yes View details
rpl22 LSC 492 0.0154 0.99 47.8 yes View details
ycf1 IRb 1092 0.0017 1.00 31.7 no View details
ndhF-rpl32 SSC 1025 0.0093 1.00 54.0 yes View details
rpl32-trnL_uag SSC 1114 0.0130 0.99 56.8 yes View details
ccsA-ndhD SSC 338 0.0202 0.93 48.0 yes View details
ycf1 SSC 5493 0.0066 1.00 48.9 yes View details
rpl22 IRa 242 0.0029 1.00 32.0 no View details
ndhK-ndhC LSC 64 0.0146 1.00 60.1 yes View details
rpl22-trnH_gug LSC 30 0.1755 0.37 60.0 no View details
ndhE-ndhG SSC 277 0.0183 1.00 59.9 yes View details
rpl14-rpl16 LSC 146 0.0177 0.92 58.9 yes View details
trnT_ugu-trnL_uaa LSC 1060 0.0080 1.00 57.6 yes View details
trnG_gcc-trnfM_cau LSC 187 0.0121 0.99 57.1 yes View details
accD-psaI LSC 769 0.0077 0.99 56.6 yes View details
petL-petG LSC 194 0.0178 0.99 56.3 yes View details
rps16-trnQ_uug LSC 1292 0.0073 1.00 55.9 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 95 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 438–519 0.943 85.7
trnH_gug-psbA_p2 trnH_gug-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 452–533 0.943 85.5
trnH_gug-psbA_p3 trnH_gug-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 451–532 0.943 85.5
trnH_gug-psbA_p4 trnH_gug-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 453–534 0.943 85.5
trnH_gug-psbA_p5 trnH_gug-psbA CGCATGGTGGATTCACAATC TTCCCTCTAGACCTAGCTGC 467–548 0.943 82.7
rps16-trnQ_uug_p1 rps16-trnQ_uug CAGCGGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 878–1428 1.000 86.6
rps16-trnQ_uug_p2 rps16-trnQ_uug GCGGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 876–1426 1.000 86.6
rps16-trnQ_uug_p3 rps16-trnQ_uug CAGCGGATCATGTCCTTCAA CGAAATTGAAATGGGGCGTC 937–1487 1.000 86.4
rps16-trnQ_uug_p4 rps16-trnQ_uug CAGCGGATCATGTCCTTCAA GAAATTGAAATGGGGCGTCG 936–1486 1.000 86.4
rps16-trnQ_uug_p5 rps16-trnQ_uug GCGGATCATGTCCTTCAAGT GAAATTGAAATGGGGCGTCG 934–1484 1.000 86.4
trnR_ucu-atpA_p1 trnR_ucu-atpA AGCCTTCCAAGCTAACGATG CTCTCACGGTGGAAGAACAG 769–806 1.000 86.6
trnR_ucu-atpA_p2 trnR_ucu-atpA AGCCTTCCAAGCTAACGATG CGAAGCTTATCCCGGAGATG 1200–1237 1.000 84.4
trnR_ucu-atpA_p3 trnR_ucu-atpA AGCCTTCCAAGCTAACGATG ATCCCTCCAAACAAGCACAG 1264–1301 1.000 84.0
trnR_ucu-atpA_p4 trnR_ucu-atpA AGCCTTCCAAGCTAACGATG GATCCCTCCAAACAAGCACA 1265–1302 1.000 84.0
trnR_ucu-atpA_p5 trnR_ucu-atpA AGCCTTCCAAGCTAACGATG TGATCCCTCCAAACAAGCAC 1266–1303 1.000 83.9
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT CGTTCTAGTTCCTACTGCGT 1199–1515 1.000 79.3
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT AGTTCCTACTGCGTTTTTGC 1193–1509 1.000 78.1
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT GTTCCTACTGCGTTTTTGCT 1192–1508 1.000 78.1
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT CGTTCTAGTTCCTACTGCGT 1138–1454 1.000 77.7
petN-psbM_p5 petN-psbM TAGTAAGTCTCGCTTGGGCT TCGTTCTAGTTCCTACTGCG 1200–1516 1.000 77.0
psbM-trnD_guc_p1 psbM-trnD_guc ACGCAGTAGGAACTAGAACG TTCAATTGGTCAGAGCACCG 1299–1361 1.000 74.4
psbM-trnD_guc_p2 psbM-trnD_guc AGCAAAAACGCAGTAGGAAC TTCAATTGGTCAGAGCACCG 1306–1368 1.000 73.3
psbM-trnD_guc_p3 psbM-trnD_guc GCAAAAACGCAGTAGGAACT TTCAATTGGTCAGAGCACCG 1305–1367 1.000 73.3
psbM-trnD_guc_p4 psbM-trnD_guc CGCAGTAGGAACTAGAACGA TTCAATTGGTCAGAGCACCG 1298–1360 1.000 72.2
psbM-trnD_guc_p5 psbM-trnD_guc AACGCAGTAGGAACTAGAACG TTCAATTGGTCAGAGCACCG 1300–1362 1.000 72.1
trnG_gcc-trnfM_cau_p1 trnG_gcc-trnfM_cau TCTTTGCCAAGGAGAAGACG CTTGAGGTCACGGGTTCAAA 215–316 1.000 85.9
trnG_gcc-trnfM_cau_p2 trnG_gcc-trnfM_cau TCTTTGCCAAGGAGAAGACG GGGTAGAGCAGTTTGGTAGC 251–352 1.000 85.6
trnG_gcc-trnfM_cau_p3 trnG_gcc-trnfM_cau TCTTTGCCAAGGAGAAGACG CCAGTCCTTCTCTTCATCGC 272–373 1.000 85.0
trnG_gcc-trnfM_cau_p4 trnG_gcc-trnfM_cau TCTTTGCCAAGGAGAAGACG TGAGGTCACGGGTTCAAATC 213–314 1.000 84.8
trnG_gcc-trnfM_cau_p5 trnG_gcc-trnfM_cau TCTTTGCCAAGGAGAAGACG TAGCTCGCAAGGCTCATAAC 235–336 1.000 84.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (35)

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

Species Accession Length (bp) Link
Citrus australasica NC_058999.1 160335 View on NCBI ↗
Citrus australis NC_065752.1 160413 View on NCBI ↗
Citrus benikoji NC_079953.1 160699 View on NCBI ↗
Citrus cavaleriei NC_053572.1 160996 View on NCBI ↗
Citrus depressa NC_031894.1 160120 View on NCBI ↗
Citrus erythrosa MW722946.1 160120 View on NCBI ↗
Citrus glauca LC794891.1 160450 View on NCBI ↗
Citrus hindsii NC_053690.1 160145 View on NCBI ↗
Citrus indica NC_065753.1 160312 View on NCBI ↗
Citrus jambhiri NC_065754.1 160210 View on NCBI ↗
Citrus japonica NC_053733.1 160229 View on NCBI ↗
Citrus japonica var. margarita NC_072621.1 160230 View on NCBI ↗
Citrus junos NC_064135.1 160612 View on NCBI ↗
Citrus keraji NC_064136.1 160121 View on NCBI ↗
Citrus latipes LC794892.1 160145 View on NCBI ↗
Citrus limonia NC_065755.1 160723 View on NCBI ↗
Citrus madurensis NC_064137.1 160229 View on NCBI ↗
Citrus mangshanensis NC_064138.1 160262 View on NCBI ↗
Citrus maxima NC_034290.1 160133 View on NCBI ↗
Citrus micrantha NC_065667.1 159928 View on NCBI ↗
Citrus natsudaidai NC_079954.1 160185 View on NCBI ↗
Citrus nobilis NC_065756.1 160700 View on NCBI ↗
Citrus oto NC_064139.1 160127 View on NCBI ↗
Citrus platymamma NC_030194.1 160121 View on NCBI ↗
Citrus reticulata NC_034671.1 160100 View on NCBI ↗
Citrus sinensis NC_008334.1 160129 View on NCBI ↗
Citrus tachibana NC_064140.1 160600 View on NCBI ↗
Citrus tangerina NC_065757.1 160699 View on NCBI ↗
Citrus tarogayo NC_064141.1 160121 View on NCBI ↗
Citrus unshiu x Citrus sinensis NC_079821.1 160699 View on NCBI ↗
(Citrus unshiu x Citrus sinensis) x Citrus reticulata NC_079822.1 160699 View on NCBI ↗
Citrus x clementina NC_059803.1 160702 View on NCBI ↗
Citrus x latifolia NC_079825.1 160141 View on NCBI ↗
Citrus x paradisi NC_063672.1 160186 View on NCBI ↗
Citrus x tangelo NC_079952.1 160183 View on NCBI ↗