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Table 2 in Molecular phylogenetic data and seed coat anatomy resolve the generic position of some critical Chenopodioideae (Chenopodiaceae - Amaranthaceae) with reduced perianth segments
Description
Table 2. Primers and cycler programmes used for the molecular analysis.
| Marker | Primer sequences and combination | Reference | Cycler programmer |
|---|---|---|---|
| ITS | ITS5 5'-GGA AGT AAA AGT CGT AAC AAG G-3' | White et al. (1990) | 95 °C for 5 min, 33 cycles of amplification (95 °C for 15 s, 55 °C for 30 s, 72 °C for 40 s), 72 °C for 5 min |
| ITS4 5'-TCC TCC GCT TAT TGA TAT GC-3' | |||
| rbcL (partial) | rbcLaF 5'- ATG TCA CCA CAA ACA GAG ACT AAA GC-3' | Levin et al. (2003) | 95 °C for 5 min, 35 cycles of amplification (95 °C for 10 s, 55 °C for 30 s, 72 °C for 40 s), 72 °C for 5 min |
| rbcLaR 5'-GTA AAA TCA AGT CCA CCR CG-3' | Kress et al. (2009) | ||
| atpB-rbcL spacer | atpB-rbcL F 5'-GAA GTA GTA GGA TTG ATT CTC-3' | Golenberg et al. (1993) | 95 °C for 5 min, 35 cycles of amplification (95 °C for 20 s, 56 °C for 30 s, 72 °C for 60 s), 95 °C for 20 s, 56 °C for 80 s, 72 °C for 8 min |
| atpB-rbcL R 5'-CAA CAC TTG CTT TAG TCT CTG-3' | |||
| trnL-F | Tab C 5'-CGA AAT CGG TAG ACG CTA CG-3' | Taberlet et al. (1991) | 95 °C for 5 min, 35 cycles of amplification (95 C for 1 min, 50 °C - 65 °C (increasing in 0.3 C per cycle) for 1 min, 72 °C for 4 min), 72 °C for 5 min |
| Tab D 5'-GGG GAT AGA GGG ACT TGA AC-3' | |||
| Tab E 5'- GGT TCA AGT CCC TCT ATC CCC-3' | |||
| Tab F 5'ATI' TGA ACT GGT GAC ACG AG 3' |
Notes
Published as part of Sukhorukov, Alexander P., Nilova, Maya V., Krinitsina, Anastasiya A., Maxim A. Zaika,, Erst, Andrey S. & Shepherd, Kelly A., 2018, Molecular phylogenetic data and seed coat anatomy resolve the generic position of some critical Chenopodioideae (Chenopodiaceae - Amaranthaceae) with reduced perianth segments, pp. 103 in PhytoKeys 109 on page 103, DOI: 10.3897/phytokeys.109.28956, http://zenodo.org/record/1476320
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References
- White, TJ, Bruns, T, Lee, S, Taylor, J, 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis, MA, Gelfand, DH, Sninsky, JJ, White, TJ, Eds., PCR Protocols: a guide to methods and applications. Academic Press, New York: 315 - 322, DOI: https://doi.org/10.1016/B978-0-12-372180-8.50042-1
- Levin, RA, Wagner, WL, Hoch, PC, Nepokroeff, M, Pires, JC, Zimmer, EA, Sytsma, KJ, 2003. Family level relationships of Onagraceae based on chloroplast rbcL and ndhF data. American Journal of Botany 90 (1): 107 - 115, DOI: https://doi.org/10.3732/ajb.90.1.107
- Kress, WJ, Erickson, DL, Jones, FA, Swenson, NG, Perez, R, Sanjur, O, Bermingham, E, 2009. Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama. Proceedings of the National Academy of Sciences of the United States of America 106 (44): 18621 - 18626, DOI: https://doi.org/10.1073/pnas.0909820106
- Golenberg, EM, Clegg, MT, Durbin, M, Doebley, J, Ma, DP, 1993. Evolution of a noncoding region of the chloroplast genome. Molecular Phylogenetics and Evolution 2: 52 - 64, DOI: https://doi.org/10.1006/mpev.1993.1006
- Taberlet, P, Gielly, L, Pautou, G, Bouvet, J, 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology 17 (5): 1105 - 1109, DOI: https://doi.org/10.1007/BF00037152