Targeted Enrichment of rRNA Gene Tandem Arrays for Ultra-Long Sequencing by Selective Restriction Endonuclease Digestion

McKinlay, Anastasia; Fultz, Dalen; Wang, Zhen; Pikaard, Craig S.

doi:10.3389/fpls.2021.656049

Cited by 6 publications

(4 citation statements)

References 34 publications

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“…There is some evidence that both the chromosomal position and/or the presence of the control elements that are located within rDNA units may be responsible for the preferential expression of rDNA via ND ( Chandrasekhara et al, 2016 ; Mohannath et al, 2016 ). Thus, using the new whole-genome sequencing strategies that permit a closer look at the complete rDNA units ( McKinlay et al, 2021 ) may significantly improve our understanding of the rDNA evolution and behavior in allopolyploids.…”

Section: Discussionmentioning

confidence: 99%

To Be or Not to Be Expressed: The First Evidence of a Nucleolar Dominance Tissue-Specificity in Brachypodium hybridum

et al. 2021

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Nucleolar dominance (ND) is an epigenetic, developmentally regulated phenomenon that describes the selective inactivation of 35S rDNA loci derived from one progenitor of a hybrid or allopolyploid. The presence of ND was documented in an allotetraploid grass, Brachypodium hybridum (genome composition DDSS), which is a polyphyletic species that arose from crosses between two putative ancestors that resembled the modern B. distachyon (DD) and B. stacei (SS). In this work, we investigated the developmental stability of ND in B. hybridum genotype 3-7-2 and compared it with the reference genotype ABR113. We addressed the question of whether the ND is established in generative tissues such as pollen mother cells (PMC). We examined condensation of rDNA chromatin by fluorescence in situ hybridization employing state-of-art confocal microscopy. The transcription of rDNA homeologs was determined by reverse-transcription cleaved amplified polymorphic sequence analysis. In ABR113, the ND was stable in all tissues analyzed (primary and adventitious root, leaf, and spikes). In contrast, the 3-7-2 individuals showed a strong upregulation of the S-genome units in adventitious roots but not in other tissues. Microscopic analysis of the 3-7-2 PMCs revealed extensive decondensation of the D-genome loci and their association with the nucleolus in meiosis. As opposed, the S-genome loci were always highly condensed and localized outside the nucleolus. These results indicate that genotype-specific loss of ND in B. hybridum occurs probably after fertilization during developmental processes. This finding supports our view that B. hybridum is an attractive model to study ND in grasses.

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Section: Discussionmentioning

confidence: 99%

To Be or Not to Be Expressed: The First Evidence of a Nucleolar Dominance Tissue-Specificity in Brachypodium hybridum

et al. 2021

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“…In order to address these questions, it will be essential to improve methodical approaches used for scoring rDNA variation within and across the arrays establishing clearly defined, biologically relevant threshold values, e.g., specific number of variations, SNPs per DNA sequence length. MinION technology, generating >200 kb reads, appears to be a suitable method for long-scale analyses of rDNA arrangement and unit structure (McKinlay et al 2021 ), as was applied to the latest human T2T genome assembly including rDNA assembly (Nurk et al 2022 ). However, its per-base error rate is still high (5–15%) (Istace et al 2017 ) preventing unambiguous base calling.…”

Section: Discussionmentioning

confidence: 99%

Intragenomic rDNA variation - the product of concerted evolution, mutation, or something in between?

et al. 2023

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The classical model of concerted evolution states that hundreds to thousands of ribosomal DNA (rDNA) units undergo homogenization, making the multiple copies of the individual units more uniform across the genome than would be expected given mutation frequencies and gene redundancy. While the universality of this over 50-year-old model has been confirmed in a range of organisms, advanced high throughput sequencing techniques have also revealed that rDNA homogenization in many organisms is partial and, in rare cases, even apparently failing. The potential underpinning processes leading to unexpected intragenomic variation have been discussed in a number of studies, but a comprehensive understanding remains to be determined. In this work, we summarize information on variation or polymorphisms in rDNAs across a wide range of taxa amongst animals, fungi, plants, and protists. We discuss the definition and description of concerted evolution and describe whether incomplete concerted evolution of rDNAs predominantly affects coding or non-coding regions of rDNA units and if it leads to the formation of pseudogenes or not. We also discuss the factors contributing to rDNA variation, such as interspecific hybridization, meiotic cycles, rDNA expression status, genome size, and the activity of effector genes involved in genetic recombination, epigenetic modifications, and DNA editing. Finally, we argue that a combination of approaches is needed to target genetic and epigenetic phenomena influencing incomplete concerted evolution, to give a comprehensive understanding of the evolution and functional consequences of intragenomic variation in rDNA.

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“…Figure 4 and 9). Available target enrichment of major rDNA and other repeats for long read sequencing (McKinlay et al, 2021) could provide further insight into formation of complex repeat structures involving rDNA.…”

Section: Discussionmentioning

confidence: 99%

The role of repetitive DNA in re-patterning of major rDNA clusters in Lepidoptera

Dalíková

Provazníková

Provazník

et al. 2022

Preprint

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Genes for major ribosomal RNAs (rDNA) are present in multiple copies organized in tandem arrays. Number and position of rDNA loci can change dynamically and their re-patterning is presumably driven by repetitive sequences. We explored a peculiar rDNA organization in several representatives of Lepidoptera with either extremely large or numerous rDNA clusters. We combined molecular cytogenetics with analyses of second and third generation sequencing data to show that rDNA spreads as a transcription unit and reveal association between rDNA and various repeats. Furthermore, we performed comparative long read analyses between the species with derived rDNA distribution and moths with a single rDNA locus, which is considered ancestral. Our results suggest that satellite arrays, rather than mobile elements, facilitate homology-mediated spread of rDNA via either integration of extrachromosomal rDNA circles or ectopic recombination. The latter arguably better explains preferential spread of rDNA into terminal regions of lepidopteran chromosomes as efficiency of ectopic recombination depends on proximity of homologous sequences to telomeres.

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Targeted Enrichment of rRNA Gene Tandem Arrays for Ultra-Long Sequencing by Selective Restriction Endonuclease Digestion

Cited by 6 publications

References 34 publications

To Be or Not to Be Expressed: The First Evidence of a Nucleolar Dominance Tissue-Specificity in Brachypodium hybridum

To Be or Not to Be Expressed: The First Evidence of a Nucleolar Dominance Tissue-Specificity in Brachypodium hybridum

Intragenomic rDNA variation - the product of concerted evolution, mutation, or something in between?

The role of repetitive DNA in re-patterning of major rDNA clusters in Lepidoptera

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