Remarkable variation of ribosomal DNA organization and copy number in gnetophytes, a distinct lineage of gymnosperms

Wang, Wencai; Wan, Tao; Becher, Hannes; Kuderová, Alena; Leitch, Ilia J.; Garcia, Sònia; Leitch, Andrew R.; Kovařı́k, Aleš

doi:10.1093/aob/mcy172

Cited by 17 publications

(25 citation statements)

References 83 publications

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“…In other eukaryotic organisms (e.g., plants and animals), rDNA CNV has been shown to have a strong positive correlation with genome size, independent of size contributions from rDNA cassettes (Prokopowich et al, 2003;Wencai et al, 2018). Conversely, investigation into this correlation for bacteria has shown no such relationship (Fogel, Collins, Li, & Brunk, 1999).…”

Section: Discussionmentioning

confidence: 99%

Genome‐based estimates of fungal rDNA copy number variation across phylogenetic scales and ecological lifestyles

et al. 2019

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Ribosomal DNA (rDNA) copy number variation (CNV) has major physiological implications for all organisms, but how it varies for fungi, an ecologically ubiquitous and important group of microorganisms, has yet to be systemically investigated. Here, we examine rDNA CNV using an in silico read depth approach for 91 fungal taxa with sequenced genomes and assess copy number conservation across phylogenetic scales and ecological lifestyles. rDNA copy number varied considerably across fungi, ranging from an estimated 14 to 1,442 copies (mean = 113, median = 82), and copy number similarity was inversely correlated with phylogenetic distance. No correlations were found between rDNA CNV and fungal trophic mode, ecological guild or genome size. Taken together, these results show that like other microorganisms, fungi exhibit substantial variation in rDNA copy number, which is linked to their phylogeny in a scale‐dependent manner.

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Section: Discussionmentioning

confidence: 99%

Genome‐based estimates of fungal rDNA copy number variation across phylogenetic scales and ecological lifestyles

et al. 2019

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“…Although this prolongs computation times (typically 5-6 hours on the MetaCentrum ELIXIR computer clusters) we were able to reconstruct 5S rDNA units in the large (50 GB) Fritillaria imperialis genome (Zonneveld, 2010) although, in this case, the number of reads in the cluster was too low, preventing graph analysis. High coverages may also help to reveal rare 5S rDNA variants and pseudogenes that are frequent in gymnosperms (Wang et al, 2016;Wang et al, 2019) while they rarely occur in angiosperms. In interspecific comparisons, the usage of a standard fraction of genome (0.1-1.0%) is recommended to prevent biases in interspecific comparisons.…”

Section: In Silico Identification Of 5s Rdna Repeatsmentioning

confidence: 99%

The Utility of Graph Clustering of 5S Ribosomal DNA Homoeologs in Plant Allopolyploids, Homoploid Hybrids, and Cryptic Introgressants

et al. 2020

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Introduction: Ribosomal DNA (rDNA) loci have been widely used for identification of allopolyploids and hybrids, although few of these studies employed high-throughput sequencing data. Here we use graph clustering implemented in the RepeatExplorer (RE) pipeline to analyze homoeologous 5S rDNA arrays at the genomic level searching for hybridogenic origin of species. Data were obtained from more than 80 plant species, including several well-defined allopolyploids and homoploid hybrids of different evolutionary ages and from widely dispersed taxonomic groups.Results: (i) Diploids show simple circular-shaped graphs of their 5S rDNA clusters. In contrast, most allopolyploids and other interspecific hybrids exhibit more complex graphs composed of two or more interconnected loops representing intergenic spacers (IGS). (ii) There was a relationship between graph complexity and locus numbers. (iii) The sequences and lengths of the 5S rDNA units reconstituted in silico from k-mers were congruent with those experimentally determined. (iv) Three-genomic comparative cluster analysis of reads from allopolyploids and progenitor diploids allowed identification of homoeologous 5S rRNA gene families even in relatively ancient (c. 1 Myr) Gossypium and Brachypodium allopolyploids which already exhibit uniparental partial loss of rDNA repeats. (v) Finally, species harboring introgressed genomes exhibit exceptionally complex graph structures. Conclusion:We found that the cluster graph shapes and graph parameters (k-mer coverage scores and connected component index) well-reflect the organization and intragenomic homogeneity of 5S rDNA repeats. We propose that the analysis of 5S rDNA cluster graphs computed by the RE pipeline together with the cytogenetic analysis might be a reliable approach for the determination of the hybrid or allopolyploid plant species parentage and may also be useful for detecting historical introgression events.

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“…The adaptive value of the wide-spread or deep evolutionary invention of silencing supernumerary copies is not known, but may have something to do with facile transcriptional regulation or with stability of the large repeat gene array (Kobayashi 2008;Peng and Karpen 2008;Ianni et al 2017;Paredes et al 2018). That many gene copies are silenced can hide considerable sequence variation (Kim et al 2018;Parks et al 2018), since not all copies of the rDNA need be perfect if potentially toxic mutant rDNA are preferentially inactivated (Eickbush et al 2008;Guerrero and Maggert 2011;Larson et al 2012;Wang et al 2018). Polymorphisms in the intergenic "non-transcribed" spacer, in the regions corresponding to mature rRNAs, in the presence or absence of interrupting retrotransposable elements (Eickbush et al 1997;Eickbush and Eickbush 2003), can all be hidden by silencing, or may contribute to the choice of which copies are silenced (Guerrero and Maggert 2011).…”

Section: The Ribosomal Dnamentioning

confidence: 99%

The peculiar genetics of the ribosomal DNA blurs the boundaries of transgenerational epigenetic inheritance

Bughio

Maggert

2018

Chromosome Res

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Our goal is to draw a line-hypothetical in its totality but experimentally supported at each individual step-connecting the ribosomal DNA and the phenomenon of transgenerational epigenetic inheritance of induced phenotypes. The reasonableness of this hypothesis is offset by its implication, that many (or most) (or all) of the cases of induced-and-inherited phenotypes that are seen to persist for generations are instead unmapped induced polymorphisms in the ribosomal DNA, and thus are the consequence of the peculiar and enduringly-fascinating genetics of the highly-transcribed repeat DNA structure at that locus.

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Remarkable variation of ribosomal DNA organization and copy number in gnetophytes, a distinct lineage of gymnosperms

Cited by 17 publications

References 83 publications

Genome‐based estimates of fungal rDNA copy number variation across phylogenetic scales and ecological lifestyles

Genome‐based estimates of fungal rDNA copy number variation across phylogenetic scales and ecological lifestyles

The Utility of Graph Clustering of 5S Ribosomal DNA Homoeologs in Plant Allopolyploids, Homoploid Hybrids, and Cryptic Introgressants

The peculiar genetics of the ribosomal DNA blurs the boundaries of transgenerational epigenetic inheritance

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