PCR internals - Selection and Drift

You like to know what else to expect from PCR than ideal results ? In this report the terms PCR Selection and PCR Drift are explained. This is particularly interesting when you work with imperfect single copy regions or elements of incomplete concerted evolution (e.g. the internal transcribed spacer, ITS, ETS and NTS).

Wagner, A. et al., 1994. Surveys of Gene Families Using Polymerase Chain Reaction: PCR Selection and PCR Drift. Syst. Biol, 43(2), pp.250–261.  

Available at: http://www.jstor.org/stable/2413465.

Review: High Levels of Genetic Diversity within One Population of Rheum tanguticum on the Qinghai-Tibet Plateau have Implications for Germplasm Conservation

Ma, X., Xie, C., Guan, M., Xu, X., Miki, E., Takeda, O., … Chen, S. (2014). High Levels of Genetic Diversity within One Population of Rheum tanguticum on the Qinghai-Tibet Plateau have Implications for Germplasm Conservation. Pharmaceutical Crops, (5), 1–8.

Summary

The authors analyzed the ITS region of 29 Rheum tanguticum samples collected from respective plants at the Baihe pasture of Zoige in the Sichuan Province of China. The ITS region was amplified using primer ITS5 and ITS4 (White 1990). Direct sequencing failed due to multiple ITS types. Consequently the PCR products were introduced into a vector and amplified by DH5alpha E. coli. Five clones of each sample were then sequenced resulting in 105 ITS sequences of R. tanguticum and 40 sequences of fungal origin (27.6 %). Three of the sequences (KF514611, KF514546 and KF514613) were not included in further analyses because of a 90 bp deletion at the start of the ITS region. The remaining 102 sequences were used to calculate a genetic distance matrix (K2P) and construct a Neighbor Joining Tree.

Results

to be continued...

ITS Sequence Data from Rheum

As of today, NCBIs Nucleotide Database contains ITS sequence data connected to the following publication:

• Sanchez, A., Schuster, T. M., & Kron, K. A. (2009). A Large-Scale Phylogeny of Polygonaceae Based on Molecular Data. International Journal of Plant Sciences, 170(8), 1044–1055. doi:10.1086/605121

• Chen, S., Yao, H., Han, J., Liu, C., Song, J., Shi, L., … Leon, C. (2010). Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLoS ONE, 5(1), 1–8. doi:10.1371/journal.pone.0008613

• Tian, X., Luo, J., Wang, A., Mao, K., & Liu, J. (2011). On the origin of the woody buckwheat Fagopyrum tibeticum (=Parapteropyrum tibeticum) in the Qinghai-Tibetan Plateau. Molecular Phylogenetics and Evolution, 61(2), 515–520. doi:10.1016/j.ympev.2011.07.001

• Yurtseva, O. V, Levina, M. S., Severova, E. E., & Troitsky, A. V. (2012). Morphology and taxonomy of Polygonum cognatum Meisn ., P . alpestre C . A . Mey . and allied taxa from Central Asia and the Caucasus ( Polygonaceae ), 19, 141–180.

• Ma, X., Xie, C., Guan, M., Xu, X., Miki, E., Takeda, O., … Chen, S. (2014). High Levels of Genetic Diversity within One Population of Rheum tanguticum on the Qinghai-Tibet Plateau have Implications for Germplasm Conservation, 1–8.

• Wan, D., Sun, Y., Zhang, X., Bai, X., Wang, J., Wang, A., & Milne, R. (2014). Multiple ITS copies reveal extensive hybridization within Rheum (polygonaceae), a genus that has undergone rapid radiation. PLoS ONE, 9(2), 37–39. doi:10.1371/journal.pone.0089769