New Insight into Taxonomy of European Mountain Pines, Complex, Based on Complete Chloroplast Genomes Sequencing.

The complex is a large group of closely related mountain pines, which are an important component of the ecosystems of the most important mountain ranges, such as the Alps, Carpathians and Pyrenees. The phylogenetic relationships between taxa in this complex have been under discussion for many years. Despite the use of many different approaches, they still need to be clarified and supplemented with new data, especially those obtained with high-throughput methods. Therefore, in this study, the complete sequences of the chloroplast genomes of the three most recognized members of the complex, i.e., , and , were sequenced and analyzed to gain new insight into their phylogenetic relationships. Comparative analysis of their complete chloroplast genome sequences revealed several mutational hotspots potentially useful for the genetic identification of taxa from the complex. Phylogenetic inference based on sixteen complete chloroplast genomes of different coniferous representatives showed that pines from the complex form one distinct monophyletic group. The results obtained in this study provide new and valuable omics data for further research within the European mountain pine complex. They also indicate which regions may be useful in the search for diagnostic DNA markers for the members of complex and set the baseline in the conservation of genetic resources of its endangered taxa.