Molecular Organization of 5S Ribosomal DNA and Taxonomic Status of Avenella flexuosa (L.) Drejer (Poaceae)

Ishchenko, O. O.; Mel’nyk, V. M.; Parnikoza, Іvan; Budzhak, Vasyl; Панчук, І. І.; Кунах, В. А.; Волков, Р. А.

doi:10.3103/s0095452720060055

Cited by 8 publications

(4 citation statements)

References 39 publications

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“…Transcriptional regulation of the multigenic 5S rDNA in Arabidopsis has been extensively studied in Sylvette Tourmentes's laboratory (University of Clermont-Ferrand, France), confirming the originally described 5S rRNA internal and external elements involved in regulation of the gene's transcription (reviewed by Layat et al (2012). Later, in Roman Volkov's laboratory, conservation of the putative external promoter elements in the 5S rDNA intergenic spacer (5S IGS) was demonstrated for several families of angiosperms (Volkov et al, 2001(Volkov et al, , 2017Volkov, 2014, 2019;Ishchenko et al, 2018Ishchenko et al, , 2020.…”

Section: Transcriptional Regulation Of Rrna Genesmentioning

confidence: 70%

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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Section: Transcriptional Regulation Of Rrna Genesmentioning

confidence: 70%

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

et al. 2021

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“…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%

“…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%

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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“…Раніше в якості молекулярного маркера для таких досліджень розглядалась нуклеотидна послідовність міжгенного спейсера (intergenic spacer -IGS) генів 5S рРНК (Tynkevich et al, 2015). Цей маркер неодноразово успішно використовувався у філо-генетичних та молекулярно-еволюційних дослідженнях завдяки його високій мінливості (Ishchenko et al, 2020…”

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PHYLOGENETIC RELATIONSHIPS OF UKRAINIAN ACCESSIONS OF LATHYRUS VENETUS (MILL.) WOHLF. AND L. VERNUS (L.) BERNH. BASED ON THE ANALYSIS OF THE psbA-trnH REGION OF THE CHLOROPLAST GENOME

Tynkevich

Derevenko

Chorney

2022

Biolohichni systemy

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The member of the genus Lathyrus, L. venetus is listed in the Red Data Book of Ukraine as a vulnerable species. Estimation of L. venetus abundance is complicated by the prevalence of interspecies hybrids with L. vernus. These hybrid populations are often misidentified as populations of the L. venetus due to their morphological similarity. The study of genetic resources of L. venetus requires the use of molecular markers, both nuclear (to identify hybrid forms) and plastid (to determine the direction of hybridization) localization. One of the most promising chloroplast markers, the IGS region between the psbA and trnH genes, has not yet been sequenced for L. venetus and L. vernus. In this work, we evaluated the possibility of using the psbA-trnH region of the chloroplast genome to identify the parental forms of hybrids between L. venetus and L. vernus. We amplified and sequenced the psbA-trnH IGS for the collected in Ukraine accessions of L. venetus and L. vernus. For comparison, psbA-trnH sequences from the GenBank database were used that represent species from phylogenetically distant sections of the genus Lathyrus, as well as species of the Orobus section closely related to L. venetus and L. vernus. Based on the analysis of alignment of all sequences used, we found that the level of variability of psbA-trnH exceeds that of other chloroplast DNA regions used in phylogenetic studies of the genus Lathyrus. On the phylogenetic tree constructed by us, the genus Lathyrus forms a monophyletic group with high statistical support. The sequences analysis showed significant differences between the psbA-trnH IGS of L. venetus and L. vernus and confirmed the effectiveness of using this region for molecular identification of these species and for determining the direction of hybridization in the hybrid forms.

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Molecular Organization of 5S Ribosomal DNA and Taxonomic Status of Avenella flexuosa (L.) Drejer (Poaceae)

Cited by 8 publications

References 39 publications

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

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

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

PHYLOGENETIC RELATIONSHIPS OF UKRAINIAN ACCESSIONS OF LATHYRUS VENETUS (MILL.) WOHLF. AND L. VERNUS (L.) BERNH. BASED ON THE ANALYSIS OF THE psbA-trnH REGION OF THE CHLOROPLAST GENOME

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