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

Kurtuluş Özgişi

doi:10.3906/bot-1911-4

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. Firat & Ozudogru, 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.

Highlights

The tribe Coluteocarpeae is the most taxonomically complex group among the 52 Brassicaceae tribes in terms of generic delimitation of the tribe members
Edger et al (2014) indicated that solely using ITS1 and internal transcribed spacer 2 (ITS2) is insufficient for delimitation taxonomic groups due to the lack of sufficient signals; some studies (Müller et al, 2007; Coleman, 2009) have reported that there was a positive correlation between the presence of a compensatory base change (CBC) in the ITS2 secondary structure and sexual incompatibility
The utility of hemi-CBCs and nonstructural substitutions (NSTs) to distinguish species has been reported in some studies (Torres-Suárez, 2014; Karpenko et al, 2018)

Summary

Introduction

The tribe Coluteocarpeae is the most taxonomically complex group among the 52 Brassicaceae tribes in terms of generic delimitation of the tribe members (https:// brassibase.cos.uni-heidelberg.de/, accessed 27 August 2019). Schulz (1936) placed members of Thlaspi under the subtribe Thlaspidinae, which was one of the 13 subtribes of the tribe Lepidieae. Many molecular studies (Mummenhoff and Hurka, 1995; Mummenhoff et al, 2001, 2004) have been performed to clarify the tribal boundaries of the family. These studies showed that the assumptions of the Schulz (1936) were artificial, and using this character for classification resulted in unrelated genera (i.e. Aethionema W.T. Aiton, Isatis L., Thlaspi L., Iberis L.) being grouped together under the tribe Lepidieae

Methods

Results

Conclusion