This is a confusing question. The molecular phylogenetic literature on plants surely must have many papers that discuss the relative utility of various genes with evolutionary rates suitable for your project. The choice depends entirely on the organisms you study and approximately when you think the various OTUS may have separated: e.g. 40 mya and 4 mya would require different markers.
So many thanks for your answer. I agree with you that each project need different markers to shed further light on the true status of taxa. However, in the case of too closely related taxa, various markers won't guide us to the answer. We can not use conservative genes (e.g., chloroplastic genes). Thereby, i need a marker with higher level of evolution, a marker better than ITS. What is the solution?
I am working on plant specimen. It doesn’t have any difference wether i work with nuclear or mitochondrial gene. I only interested in finding a marker with higher level of evolution than that of ITS.