Highly variable YCF1 useful for evaluating plant phylogeny at low taxonomic levels.

Twelve genera scanned to find highly variable regions of the chloroplast genome.Twenty-three loci were selected, the most variable were intergenic regions ycf1-a, trnK, rpl32-trnL, and trnH-psbA, followed by trnSUGA-trnGUCC, petA-psbJ, rps16-trnQ, ndhC-trnV, ycf1-b, ndhF, rpoB-trnC, psbE-petL, and rbcL-accD. Three loci, trnSUGA-trnGUCC, trnT-psbD, and trnW-psaJ, showed very high nucleotide diversity. The chloroplast genome is often used to determine plant phylogeny but becomes difficult in closely related species. Finding regions with more variability allows lower level taxonomy. The ycf1 region was found to have the most variability among the regions looked at. To solve phylogenetic problems at the species level,regions with very high evolutionary rates are needed. Greater availability of such regions will increase the ability to resolve such identification problems.

Reference:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3325284/?tool=pmcentrez

Wenpan Dong,^1,2 Jing Liu,^1,3 Jing Yu,^1,3 Ling Wang,² and Shiliang Zhou^1*