Testing the utility of matK and ITS DNA regions for discrimination of Allium species

Molecular phylogenetic analysis of the genus Allium L. has been mainly based on the nucleotide sequences of ITS region. In 2009 matK and rbcL were accepted as a two-locus DNA barcode to classify plant species by the Consortium for the Barcode of Life (CBOL) Plant Working Group. MatK region has been chosen as a DNA barcode because of its effective species discrimination power, high quality sequence recovery and easy experimental procedures. Integration of matK sequences into Allium phylogeny could improve phylogenetic reconstruction of this genus. This study was carried out to test usability of nucleotide sequences of matK for discrimination of Allium species and to compare topology of the phylogenetic trees based on matK and ITS analyses. Phylogenetic relationships among the Allium species based on both ITS and matK analyses were in agreement with the previous studies. In addition, topology of phylogenetic trees based on ITS and matK analyses were very similar. However, neither ITS nor matK analyses discriminated some closely related Allium species. Although the ITS region has been successfully used for phylogenetic analysis of the genus Allium, we can suggest to use matK region as an additional tool for phylogenetic analysis in Allium because characterization of the nucleotide sequences of matK region was easier to recover and more cost effective than those of ITS region.