Table 1.
Molecular markers routinely used for DNA barcoding studies
| Organism | Region | Marker | Gene description | References |
|---|---|---|---|---|
| Animals | Mitochondrion | 12S | 12S ribosomal RNA | (Kocher et al. 1989; Olmstead 1996) |
| 16S | 16S ribosomal RNA | (Palumbi 1991) | ||
| atp6 | ATP synthase F0 subunit 6 | (Haag et al. 2009; Trigo et al. 2008) | ||
| COI | Cytochrome c oxidase subunit I | (Hebert et al. 2003a, 2003b) | ||
| cytb | Cytochrome b | (Hardman 2004; Kocher et al. 1989; Maxfield et al. 2012; Tchaicka et al. 2007) | ||
| D-loop | Mitochondrial displacement loop region | (Hoelzel et al. 1991) | ||
| ND1 | NADH dehydrogenase subunit 1 | (Thacker 2003) | ||
| ND2 | NADH dehydrogenase subunit 2 | (Thacker 2003) | ||
| Nucleus | 28S | 28S ribosomal RNA | (Saux et al. 2004) | |
| ITS | Internal transcribed spacer | (Smith et al. 2008) | ||
| Rag1 | Recombination activating 1 | (López et al. 2004) | ||
| Rag2 | Recombination activating 2 | (Hardman 2004) | ||
| WG | Wingless | (Fagan-Jeffries et al. 2018) | ||
| Plants | Nucleus | ITS | Internal transcribed spacer | (Chen et al. 2005; Michelangeli et al. 2004) |
| ITS2 | The 2nd internal transcribed spacer | (Moorhouse-Gann et al. 2018) | ||
| Plastid | atpF-atpH | Non-coding atpF-atpH intergenic spacer region | (Marcelo et al. 2010; Reginato and Michelangeli 2016) | |
| matK | Maturase K | (Fazekas et al. 2008; Parveen et al. 2012) | ||
| psbK-psbI | Non-coding psbK-psbI intergenic spacer region | (Marcelo et al. 2010) | ||
| rbcL | Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit | (Fazekas et al. 2008; Parveen et al. 2012) | ||
| rpoB | RNA polymerase beta subunit | (Fazekas et al. 2008; Parveen et al. 2012) | ||
| rpoC1 | RNA polymerase beta’ subunit | (Parveen et al. 2012) | ||
| rps16 | Ribosomal protein S16 | (Oxelman et al. 1997) | ||
| trnC-rpoB | Non-coding trnC-rpoB intergenic spacer region | (Ohsako and Ohnishi 2000) | ||
| trnH-psbA | Non-coding trnH-psbA intergenic spacer region | (Tate and Simpson 2003) | ||
| trnL (UAA) | tRNA trnL intron | (Chen et al. 2005; Taberlet et al. 2007) | ||
| trnL (UAA)-trnF (GAA) | tRNA trnL-trnF intergenic spacer region | (Sang et al. 1997) | ||
| trnK (UUU) | tRNA trnK intron | (Ohsako and Ohnishi 2000) | ||
| ycf1 | Translocon at the inner envelope membrane of chloroplasts 214 | (Dong et al. 2014) | ||
| ycf5 | Cytochrome c biogenesis protein CcsA | (Kress and Erickson 2007) | ||
| Fungi | Mitochondrion | atp6 | ATP synthase F0 subunit 6 | (Vialle et al. 2009) |
| COI | Cytochrome c oxidase subunit I | (Pino-Bodas et al. 2013; Vialle et al. 2009) | ||
| CO3 | Cytochrome c oxidase III | (Vialle et al. 2009) | ||
| nad6 | NADH dehydrogenase subunit 6 | (Vialle et al. 2009) | ||
| Nucleus | LSU | large ribosomal subunit gene D1/D2 domains | (Eberhardt 2012; Robert et al. 2011) | |
| ACT | Actin | (Carbone and Kohn 1999) | ||
| TUB | β-tubulin | (Glass and Donaldson 1995) | ||
| CAL | Calmodulin | (Carbone and Kohn 1999) | ||
| EF1-α | Translation elongation factor 1-alpha | (Pino-Bodas et al. 2013) | ||
| H3 | Histone H3 | (Crous et al. 2006) | ||
| ITS | internal transcribed spacer | (Vialle et al. 2009) | ||
| rpb2 | DNA-directed RNA polymerase II subunit | (Pino-Bodas et al. 2013) | ||
| Bacteria | Nucleoid | 16S | 16S ribosomal RNA | (Lane 1991; Sundquist et al. 2007) |
| chaperonin-60 | 60 kDa chaperonin | (Brousseau et al. 2001) | ||
| rpoB | RNA polymerase beta subunit | (Adékambi et al. 2009) | ||
| ITS | Internal transcribed spacer | (Benga et al. 2020; Soltan Dallal et al. 2019) | ||
| Archaea | Nucleoid | 16S | 16S ribosomal RNA | (Bates et al. 2011) |