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. 2023 Apr 12;18(4):e0283847.
doi: 10.1371/journal.pone.0283847. eCollection 2023.

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

Haniyeh Nafisi  1 , Akram Kaveh  1 , Shahrokh Kazempour-Osaloo  1
Affiliations

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

Haniyeh Nafisi et al. PLoS One. .

Abstract

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.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. ITS1 sequence-structure Maximum-Likelihood tree calculated with R including a representative subset of 204 sequence-structure pairs from Hedysarum and its affiliated genera.
Bootstrap support values from 1000 pseudo-replicates greater than 50% mapped at the internodes.
Fig 2
Fig 2. ITS2 sequence-structure Maximum-Likelihood tree calculated with R including a representative subset of 204 sequence-structure pairs from Hedysarum and its affiliated genera.
Bootstrap support values from 1000 pseudo-replicates greater than 50% mapped at the internodes. The blue blocks represent conserved motifs.
Fig 3
Fig 3. Olsen layout of ITS1 100% conserved consensus secondary structure of A. H. sect. Multicaulia subsect. Crinifera (clade C). B. H. sect. stracheya (clade S). C. H. sect. Multicaulia subsect. Multicaulia (clade M) and d. H. sect. Hedysarum (clade H).
The blocks represent a conserved motif.
Fig 4
Fig 4. Olsen layout of 5.8S region 100% conserved consensus secondary structure.
Fig 5
Fig 5. ITS2 consensus secondary structure scheme, with 100% conserved positions through the tribe.
Fig 6
Fig 6. ITS2 Consensus secondary structure of H. sect. Hedysarum (clade H).
Yellow flashes 100% conserved regions in the section.
Fig 7
Fig 7. ITS2 Consensus secondary structure of H. sect. Stracheya (clade S).
Yellow flashes 100% conserved regions in the section.
Fig 8
Fig 8. ITS2 Consensus secondary structure of H. sect. Multicaulia Subsect. Crinifera (clade C).
Yellow flashes 100% conserved regions in the section.
Fig 9
Fig 9. ITS2 Consensus secondary structure of H. sect. Multicaulia Subsect. Multicaulia (clade M).
Yellow flashes 100% conserved regions in the section.
See this image and copyright information in PMC

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