Structural characterization of ITS2 and CBC species concept applications in the tribe Coluteocarpeae (Brassicaceae)

Abstract

The taxonomic utility of internal transcribed spacer 2 (ITS2) secondary structures in different plant groups, as well as inBrassicaceae, has been addressed by many studies. Although characterization and applications of ITS2 secondary structures for themembers of main Brassicaceae lineages (Lineages I, II, III, and expanded Lineage II) have been studied, the utility of compensatory basechange (CBC) species concept has not been the subject of any studies thus far. In the current study, the ITS2 secondary structures of49 Coluteocarpeae (expanded Lineage II) specimens were investigated to determine relationships among the species. In addition to theutility of the CBC species concept, the availability of hemi-CBC and nonstructural substitutions (NSTs), which are also used for genericand species delimitation, were tested and discussed. A maximum likelihood tree, based on the sequence-structural alignment of the 49specimens, was constructed to test the different generic assumptions reported by different researchers in the literature. The structuralanalysis showed that the ITS2 secondary structures of all of the Coluteocarpeae members exhibited a 4-fingered hand model, whichwas common in the majority of the family members. No CBCs were observed, whereas hemi-CBCs and NSTs were common amongthe tribe members. Although hemi-CBCs and NSTs were useful for distinguishing most of the Coluteocarpeae species (Noccaea aptera(Velen.) F.K. Mey., Noccaea aghrica (P.H. Davis & Kit Tan) M. Fırat & Özüdoğru, Noccaea fendleri (A.Gray) Holub subsp. glauca (A.Nelson) Al-Shehbaz & M. Koch, Noccaea griffithiana (Boiss.) F.K. Mey., Noccaea rubescens (Schott & Kotschy ex Boiss.) F.K. Mey., etc.),they were not effective for delimitating some problematic species, such as members of Thlaspiceras F.K. Mey. A phylogenetic tree basedon the sequence-structural dataset of the ITS2 showed that generic delimitation of Al-Shehbaz was more acceptable due to the fact thatNoccaea sensu Al-Shehbaz is monophyletic.