Application of 5S Ribosomal DNA for Molecular Taxonomy of Subtribe Loliinae (Poaceae)

Ishchenko, O. O.; Bednarska, Iryna; Панчук, І. І.

doi:10.3103/s0095452721010096

Cited by 12 publications

(7 citation statements)

References 48 publications

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“…These signals include the TATATA motif (so-called TATA-box), GC-dinucleotide, and C nucleotide in positions-28,-13, and-1 bp, respectively. Similar sequences were also found in other plants ( Tynkevich and Volkov, 2014 ; Tynkevich et al, 2015 ; Ishchenko et al, 2018 , 2021 ). In representatives of the Solanum genus, as well as in Quercus ( Tynkevich and Volkov, 2019 ) and Rosa ( Tynkevich and Volkov, 2014 ), the TATA-box has a length of 7 bp and begins in position-30.…”

Section: Discussionsupporting

confidence: 81%

“…Comparative sequence analysis revealed that the most conservative regions of the IGS in Solanum species are the 7- and 40-bp-long fragments at the 5′ and 3′ ends ( Figure 5 ). The evolutionary conservation of these regions has already been observed in other plants ( Hemleben and Werts, 1988 ; Crisp et al, 1999 ; Tynkevich and Volkov, 2019 ; Ishchenko et al, 2020 , 2021 ), and a possible reason for this seems to be their involvement in the transcription of 5S rDNA by RNA polymerase III (Pol III).…”

Section: Discussionmentioning

confidence: 87%

“…However, incongruence of results obtained by application of different markers is a well-known problem. Respectively, other genomic regions, particularly the 5S rDNA IGS, can additionally be used to clarify the phylogeny of lower-ranking taxa ( Blöch et al, 2009 ; Tynkevich and Volkov, 2019 ; Cardoni et al, 2021 ; Ishchenko et al, 2021 ), including sect. Petota of the Solanum genus ( Volkov et al, 2001 ).…”

Section: Discussionmentioning

confidence: 99%

“…Especially, a significant sequence divergence was found for spatially distant 5S rDNA variants that are located in different loci of the same chromosome set ( Cronn et al, 1996 ; Vozárová et al, 2021 ) and for different parent loci in genomes of hybrid origin ( Fulnecek et al, 2002 ; Matyasek et al, 2002 ), while repeats from the same locus appeared to be highly homogenized. Accordingly, 5S rDNA became an attractive focus for investigation of molecular evolution of repeated sequences, identification of hybrids, and phylogenetic studies on angiosperms ( Blöch et al, 2009 ; Baum et al, 2012 ; Simeone et al, 2018 ; Tynkevich and Volkov, 2019 ; Ishchenko et al, 2020 , 2021 ; Cardoni et al, 2021 ; Vozárová et al, 2021 ). However, 5S rDNA is still poorly characterized in many important plant groups such as the Solanum L. genus.…”

Section: Introductionmentioning

confidence: 99%

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5S Ribosomal DNA of Genus Solanum: Molecular Organization, Evolution, and Taxonomy

et al. 2022

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The Solanum genus, being one of the largest among high plants, is distributed worldwide and comprises about 1,200 species. The genus includes numerous agronomically important species such as Solanum tuberosum (potato), Solanum lycopersicum (tomato), and Solanum melongena (eggplant) as well as medical and ornamental plants. The huge Solanum genus is a convenient model for research in the field of molecular evolution and structural and functional genomics. Clear knowledge of evolutionary relationships in the Solanum genus is required to increase the effectiveness of breeding programs, but the phylogeny of the genus is still not fully understood. The rapidly evolving intergenic spacer region (IGS) of 5S rDNA has been successfully used for inferring interspecific relationships in several groups of angiosperms. Here, combining cloning and sequencing with bioinformatic analysis of genomic data available in the SRA database, we evaluate the molecular organization and diversity of IGS for 184 accessions, representing 137 species of the Solanum genus. It was found that the main mechanisms of IGS molecular evolution was step-wise accumulation of single base substitution or short indels, and that long indels and multiple base substitutions, which arose repeatedly during evolution, were mostly not conserved and eliminated. The reason for this negative selection seems to be association between indels/multiple base substitutions and pseudogenization of 5S rDNA. Comparison of IGS sequences allowed us to reconstruct the phylogeny of the Solanum genus. The obtained dendrograms are mainly congruent with published data: same major and minor clades were found. However, relationships between these clades and position of some species (S. cochoae, S. clivorum, S. macrocarpon, and S. spirale) were different from those of previous results and require further clarification. Our results show that 5S IGS represents a convenient molecular marker for phylogenetic studies on the Solanum genus. In particular, the simultaneous presence of several structural variants of rDNA in the genome enables the detection of reticular evolution, especially in the largest and economically most important sect. Petota. The origin of several polyploid species should be reconsidered.

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Section: Discussionsupporting

confidence: 81%

Section: Discussionmentioning

confidence: 87%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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5S Ribosomal DNA of Genus Solanum: Molecular Organization, Evolution, and Taxonomy

et al. 2022

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“…Similarly, the 5S IGS appeared very useful for clarifying phylogenetic relationships at low taxonomic levels (Röser et al, 2001;Volkov et al, 2001;Denk and Grimm, 2010;Tynkevich and Volkov, 2019;Ishchenko et al, 2021) and for identification of interspecific hybrids (Garcia et al, 2020). This contrasts with the really strongly conserved sequences of the mature 5S, 5.8 S, 18S, and 25S rRNA coding regions.…”

Section: Molecular Evolution Of Rdna Locimentioning

confidence: 99%

Personal Perspectives on Plant Ribosomal RNA Genes Research: From Precursor-rRNA to Molecular Evolution

et al. 2021

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The history of rDNA research started almost 90 years ago when the geneticist, Barbara McClintock observed that in interphase nuclei of maize the nucleolus was formed in association with a specific region normally located near the end of a chromosome, which she called the nucleolar organizer region (NOR). Cytologists in the twentieth century recognized the nucleolus as a common structure in all eukaryotic cells, using both light and electron microscopy and biochemical and genetic studies identified ribosomes as the subcellular sites of protein synthesis. In the mid- to late 1960s, the synthesis of nuclear-encoded rRNA was the only system in multicellular organisms where transcripts of known function could be isolated, and their synthesis and processing could be studied. Cytogenetic observations of NOR regions with altered structure in plant interspecific hybrids and detailed knowledge of structure and function of rDNA were prerequisites for studies of nucleolar dominance, epistatic interactions of rDNA loci, and epigenetic silencing. In this article, we focus on the early rDNA research in plants, performed mainly at the dawn of molecular biology in the 60 to 80-ties of the last century which presented a prequel to the modern genomic era. We discuss – from a personal view – the topics such as synthesis of rRNA precursor (35S pre-rRNA in plants), processing, and the organization of 35S and 5S rDNA. Cloning and sequencing led to the observation that the transcribed and processed regions of the rRNA genes vary enormously, even between populations and species, in comparison with the more conserved regions coding for the mature rRNAs. Epigenetic phenomena and the impact of hybridization and allopolyploidy on rDNA expression and homogenization are discussed. This historical view of scientific progress and achievements sets the scene for the other articles highlighting the immense progress in rDNA research published in this special issue of Frontiers in Plant Science on “Molecular organization, evolution, and function of ribosomal DNA.”

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Molecular Organization and Polymorphism of 5S rDNA in Carpathian Bees

Cherevatov

Волков

2021

Cytol. Genet.

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Application of 5S Ribosomal DNA for Molecular Taxonomy of Subtribe Loliinae (Poaceae)

Cited by 12 publications

References 48 publications

5S Ribosomal DNA of Genus Solanum: Molecular Organization, Evolution, and Taxonomy

5S Ribosomal DNA of Genus Solanum: Molecular Organization, Evolution, and Taxonomy

Personal Perspectives on Plant Ribosomal RNA Genes Research: From Precursor-rRNA to Molecular Evolution

Molecular Organization and Polymorphism of 5S rDNA in Carpathian Bees

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