Table 1:
DNA marker | Primer name | Primer sequence 5΄-3΄ | Amplicon length (nt) | Reference |
---|---|---|---|---|
Universal animal DNA barcodes and mini-barcodes | ||||
16S | 16sar-L | TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCGCCTGTTTATCAAAAACAT | 500–600 | Palumbi [41] |
16sar-H | GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCCGGTCTGAACTCAGATCACGT | |||
Mini-16S | 16S-forward | TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGAYAAGACGAGAAGACCC | 250 | Sarri et al. [42] |
16S-reverse | GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGATTGCGCTGTTATTCC | |||
COIa | LepF1_t1 | TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGATTCAACCAATCATAAAGATATTGG | 648c | Modified from Ivanova et al. [21] |
VF1_t1 | TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGTTCTCAACCAACCACAAAGACATTGG | |||
VF1d_t1 | TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGTTCTCAACCAACCACAARGAYATYGG | |||
VF1i_t1 | TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGTTCTCAACCAACCAIAAIGAIATIGG | |||
LepR1_t1 | GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGTAAACTTCTGGATGTCCAAAAAATCA | |||
VR1d_t1 | GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGTAGACTTCTGGGTGGCCRAARAAYCA | |||
VR1_t1 | GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGTAGACTTCTGGGTGGCCAAAGAATCA | |||
VR1i_t1 | GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGTAGACTTCTGGGTGICCIAAIAAICA | |||
Mini-COI | mlCOIintF | TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGGWACWGGWTGAACWGTWTAYCCYCC | 313 | Leray et al. [43], Geller et al. [44] |
jgHCO2198 | GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGTAIACYTCIGGRTGICCRAARAAYCA | |||
cyt b | L14816 | TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCATCCAACATCTCAGCATGATGAAA | 743 | Palumbi [41], Parson et al. [45] |
CB3-H | GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGGCAAATAGGAARTATCATTC | |||
Mini-cyt b | L14816 | TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCATCCAACATCTCAGCATGATGAAA | 357 | Parson et al. [45] |
H15173 | GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCCCTCAGAATGATATTTGTCCTCA | |||
Universal plant DNA barcodes and mini-barcodes | ||||
matK | matK-KIM1R | TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGACCCAGTCCATCTGGAAATCTTGGTTC | 656–889 | Fazekas et al. [46] |
matK-KIM3F | GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCGTACAGTACTTTTGTGTTTACGAG | |||
matK b | matK-390f | TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCGATCTATTCATTCAATATTTC | 656–889 | Cuénoud et al. [47] |
matK-1326r | GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGTCTAGCACACGAAAGTCGAAGT | |||
rbcL | rbcLa-F | TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGATGTCACCACAAACAGAGACTAAAGC | 654 | Levin et al. [48] |
rbcLa-R | GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGTAAAATCAAGTCCACCRCG | Kress and Erickson [49] | ||
rbcL b | rbcL a-F | TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGATGTCACCACAAACAGAGACTAAAGC | 607 | Levin et al. [48] |
rbcLajf634R | GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGAAACGGTCTCTCCAACGCAT | Fazekas et al. [50] | ||
Mini-rbcL | F52 | TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGTTGGATTCAAAGCTGGTGTTA | 140c | Little [14] |
R193 | GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCVGTCCAMACAGTWGTCCATGT | |||
trnL (UAA) | c | TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCGAAATCGGTAGACGCTACG | 767 | Taberlet et al. [51] |
d | GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGGGGATAGAGGGACTTGAAC | |||
trnL (P6 loop) | g | TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGGGCAATCCTGAGCCAA | 10–143c | Taberlet et al. [51] |
h | GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCCATTGAGTCTCTGCACCTATC | |||
ITS2 | S2F | TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGATGCGATACTTGGTGTGAAT | 160–320c | Chen et al. [52] |
S3R | GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACGCTTCTCCAGACTACAAT | |||
psbA-trnHb | psbAf | TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGTTATGCATGAACGTAATGCTC | 264–792 | Sang et al. [53], Tate and Simpson [54] |
trnH2 | GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCGCGCATGGTGGATTCACAATCC |
The shaded text represents the sequence of the Illumina overhang adapters.
aModified COI cocktail primers without M13-tails were used [21].
bThe primers were not included in the final panel of DNA barcodes.
cAmplicon length excluding primers.