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 in Brassicaceae, has been addressed by many studies. Although characterization and applications of ITS2 secondary structures for the members of main Brassicaceae lineages (Lineages I, II, III, and expanded Lineage II) have been studied, the utility of compensatory base change (CBC) species concept has not been the subject of any studies thus far. In the current study, the ITS2 secondary structures of 49 Coluteocarpeae (expanded Lineage II) specimens were investigated to determine relationships among the species. In addition to the utility of the CBC species concept, the availability of hemi-CBC and nonstructural substitutions (NSTs), which are also used for generic and species delimitation, were tested and discussed. A maximum likelihood tree, based on the sequence-structural alignment of the 49 specimens, was constructed to test the different generic assumptions reported by different researchers in the literature. The structural analysis showed that the ITS2 secondary structures of all of the Coluteocarpeae members exhibited a 4-fingered hand model, which was common in the majority of the family members. No CBCs were observed, whereas hemi-CBCs and NSTs were common among the 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 based on the sequence-structural dataset of the ITS2 showed that generic delimitation of Al-Shehbaz was more acceptable due to the fact that Noccaea sensu Al-Shehbaz is monophyletic.

Characterizing nrDNA ITS1, 5.8S and ITS2 secondary structures and their phylogenetic utility in the legume tribe Hedysareae with special reference to Hedysarum

“…However, this does not mean that these organisms are the same species. Moreover, the results didn’t meet Müller et al, [ 34 ], Torres-Suárez [ 55 ], and Ozgişi [ 27 ], determining CBCs useful for generic delimitation. However, they parallel the utility of hCBCs and Nsts to distinguish species reported by Torres-Suárez, [ 55 ] and Karpenko et al, [ 51 ].…”

“…The structure of 4-fingered central loop, UGGU motif near the apex of Helix III (longest Helix), and U-U mismatch in Helix II are considered the characteristics of a conserved ITS2 secondary structure [17]. It keeps excellence in the improvement of the accuracy and robustness of phylogenetic tree reconstruction by the inclusion of secondary structure [18][19][20][21][22][23][24][25][26][27][28] and by comparing the structures [11,[29][30][31].…”

“…Detections about the effectiveness of ITS2 in distinguishing cryptic/pseudo-cryptic species via CBCs [34][35][36], resulting in its frequent use to resolve lower taxonomic affinities of copious primitive eukaryotes, such as diatoms and alveolates [2,[37][38][39][40][41][42][43], fungi [7,44,45], algae [34,[46][47][48]] some cases of terrestrial plants [22,[49][50][51] and zoophytes [52][53][54]. Furthermore, following Torres-Sua ´rez [55], utilizing hemi-CBCs (hCBCs) to assess relationships at the population and species levels and Karpenko et al, [51], using nonstructural substitutions (Nsts) and hCBCs at the species level, Ozgişi [27] applied both for species delimitation.…”

Characterization of Its1 Secondary Structure in Ten Species of Coluteocarpeae (Brassicaceae) and Its Taxonomical Utility

“…Structural characterization of ITS2 and utility of CBC species concept among genus members were tested by Özgişi [24]. But characterization of ITS1 seconder structure of Coluteocarpeae members have not been done, yet.…”