The characterisation and taxonomic utility of ITS2 in Tenthredopsis Costa, 1859 (Tenthredinidae: Hymenoptera) with some new records from Turkey

Budak, Mahir; Güler, Murat; Korkmaz, Ertan Mahir; Örgen, Sevda Hastaoğlu; Basibuyuk, Hasan H.

doi:10.1016/j.bse.2016.03.008

Cited by 4 publications

(9 citation statements)

References 35 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The ITS2 structures in the database for eukaryotes display a common core structure (Ankenbrand et al, 2015). However, in the previous study of the same family (Budak et al, 2016), the ITS2 structures showed numerous branching. Despite diverged nucleotide sequences of ITS2 for studied taxon, secondary structures displayed a similar pattern.…”

Section: Resultsmentioning

confidence: 88%

“…The intra-specific length variation of ITS2 was found mostly in D. puncticollis (619-624 bp). The length variation of ITS2 in all studied animals was ranged between 100 and 2052 bp (Budak et al, 2016).…”

Section: Resultsmentioning

confidence: 96%

“…Cytochrome oxidase subunit I (COI) and internal transcribed spacers 2 (ITS2) genes have been preferred as molecular markers in many studies. Also, ITS2 has conserved primer sequences across many different taxa (Schulmeister, 2003;Prous et al, 2011;Kearse et al, 2012;Leppänen et al, 2012;Budak et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Characterization and taxonomic utility of ITS2 in Dolerus Panzer, 1801 (Hymenoptera: Tenthredinidae)

Gülmez¹,

Budak²,

Korkmaz³

et al. 2022

Turkish Journal of Entomology

Self Cite

View full text Add to dashboard Cite

show abstract

Section: Resultsmentioning

confidence: 88%

Section: Resultsmentioning

confidence: 96%

See 1 more Smart Citation

Characterization and taxonomic utility of ITS2 in Dolerus Panzer, 1801 (Hymenoptera: Tenthredinidae)

Gülmez¹,

Budak²,

Korkmaz³

et al. 2022

Turkish Journal of Entomology

Self Cite

View full text Add to dashboard Cite

show abstract

“…The only difference in the structure among the tribe members occurred in Helix IV. The length polymorphism and structural difference of Helix IV were considered the result of RNA strand slippage events occurring in Helix III and are common among most eukaryotes (Mullineux and Hausner, 2009;Budak et al, 2016). Since it has a common shape, the ITS2 secondary structure is not a useful tool to distinguish tribe members.…”

Section: Discussionmentioning

confidence: 99%

“…Taxa differing by the CBCs (even by just 1 CBC) in the conserved pairing positions of the ITS2 secondary structure were experimentally observed to be completely incapable of intercrossing (Coleman and Vacquier, 2002). Since this finding referred to the biological species concept, CBCs have been used as a species delimitation tool by many researchers (Müller et al, 2007;Mullineux and Hausner, 2009;Budak et al, 2016;Saha et al, 2017;Karpenko et al, 2018). Furthermore, CBCs in the ITS2 secondary structure and hemi-CBCs, which involve changes on only 1 side of the nucleotide pair, have also been used to assess relationships at the population and species level (Torres-Suárez, 2014).…”

Section: Introductionmentioning

confidence: 99%

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

Özgi̇şi¹

2020

Turk J Bot

View full text Add to dashboard Cite

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.

show abstract

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

2023

View full text Add to dashboard Cite

This is the first study to systematically evaluate rRNA secondary structures of Hedysareae with an emphasis on Hedysarum. ITS2 and 5.8S regions of the genus shared a common secondary structure with a four-fingered central loop, whereas ITS1 possessed five distinct structures. The secondary structural features of the two regions provided advantageous data for clades, species groups, and closely related species. Hemi-CBCs were mostly observed in the reconstruction of species groups, and Nsts, mostly between closely related species. The investigations showed that ITS1 varied more than ITS2 in length, GC content, and most of the diversity indices within the tribe. Maximum likelihood analyses of the synchronized sequence-structure tree of ITS1 were performed. The accuracy and phylogenetic signals of ITS1 were higher than ITS2. The similar GC content, and no CBC, in both spacers, fortified the close relationship of CEGO and H. sections Stracheya and Hedysarum clades in the synchronized sequence-structure tree topology of ITS1. In both regions, no inter-generic CBCs were detected inside the CEGO clade and the inter-sectional level of Hedysarum. But, in the ITS2 region, a CBC was detected between H. section Multicaulia, and Taverniera versus H. sections Hedysarum, and Stracheya. The lowest inter-sectional genetic distance and structural features were found between H. sect. Hedysarum and H. sect. Stracheya clades in the ITS2 region.

show abstract

The characterisation and taxonomic utility of ITS2 in Tenthredopsis Costa, 1859 (Tenthredinidae: Hymenoptera) with some new records from Turkey

Cited by 4 publications

References 35 publications

Characterization and taxonomic utility of ITS2 in Dolerus Panzer, 1801 (Hymenoptera: Tenthredinidae)

Characterization and taxonomic utility of ITS2 in Dolerus Panzer, 1801 (Hymenoptera: Tenthredinidae)

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

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

Contact Info

Product

Resources

About