Molecular Organization of the 25S–18S rDNA IGS of Fagus sylvatica and Quercus suber: A Comparative Analysis

Inácio, Vera; Rocheta, Margarida; Morais-Cecílio, Leonor

doi:10.1371/journal.pone.0098678

Cited by 16 publications

(28 citation statements)

References 103 publications

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“…Similar variation exists among the populations of both diploid progenitor species (Figure S4). As in other plant species (Borisjuk et al ., ; Inacio et al ., ), most IGS variation in Tragopogon originated from length polymorphisms caused by variable numbers of tandem repeats. The IGS containing promoter and regulatory elements are evolving rapidly, hence rDNA variants may be differentially expressed (Lewis et al ., ).…”

Section: Discussionmentioning

confidence: 99%

Interpopulation hybridization generates meiotically stable rDNA epigenetic variants in allotetraploid Tragopogon mirus

et al. 2016

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SUMMARYUniparental silencing of 35S rRNA genes (rDNA), known as nucleolar dominance (ND), is common in interspecific hybrids. Allotetraploid Tragopogon mirus composed of Tragopogon dubius (d) and Tragopogon porrifolius (p) genomes shows highly variable ND. To examine the molecular basis of such variation, we studied the genetic and epigenetic features of rDNA homeologs in several lines derived from recently and independently formed natural populations. Inbred lines derived from T. mirus with a dominant d-rDNA homeolog transmitted this expression pattern over generations, which may explain why it is prevalent among natural populations. In contrast, lines derived from the p-rDNA dominant progenitor were meiotically unstable, frequently switching to co-dominance. Interpopulation crosses between progenitors displaying reciprocal ND resulted in d-rDNA dominance, indicating immediate suppression of p-homeologs in F 1 hybrids. Original p-rDNA dominance was not restored in later generations, even in those segregants that inherited the corresponding parental rDNA genotype, thus indicating the generation of additional p-rDNA and d-rDNA epigenetic variants. Despite preserved intergenic spacer (IGS) structure, they showed altered cytosine methylation and chromatin condensation patterns, and a correlation between expression, hypomethylation of RNA Pol I promoters and chromatin decondensation was apparent. Reversion of such epigenetic variants occurred rarely, resulting in co-dominance maintained in individuals with distinct genotypes. Generally, interpopulation crosses may generate epialleles that are not present in natural populations, underlying epigenetic dynamics in young allopolyploids. We hypothesize that highly expressed variants with distinct IGS features may induce heritable epigenetic reprogramming of the partner rDNA arrays, harmonizing the expression of thousands of genes in allopolyploids.

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Section: Discussionmentioning

confidence: 99%

Interpopulation hybridization generates meiotically stable rDNA epigenetic variants in allotetraploid Tragopogon mirus

et al. 2016

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“…Nevertheless, it contains several highly conserved cis -acting functional elements [ 42 ]. To investigate the IGS sequences for functional elements and domains, we aligned the IGSs from these three species with the transcription intiation regions from of other species, including Poaceae , Cucurbitaceae , Fabaceae , Brassicaceae , Solanaceae , Oleaceae , Fagaceae , and Punicaceae [ 32 , 43 ]. We found a putative TIS ( ) for RNA polymerase I, which was in agreement with reports of TIS in other plants.…”

Section: Resultsmentioning

confidence: 99%

“…sinensis ) in the family Poaceae lacked a typical box [ 44 ]. In contrast to the presence of a -containing sequence in the above plants, sequences lacking adjacent to the TIS were flanked by pyrimidine bases in the families Fagaceae and Punicaceae [ 23 , 43 ]. In addition, a unique AT-rich region that may function as an enhancer of transcription was present upstream of the TIS ( Fig 1 ).…”

Section: Resultsmentioning

confidence: 99%

Comparative genetic analysis of the 45S rDNA intergenic spacers from three Saccharum species

Huang

Fan

et al. 2017

PLoS ONE

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The 45S ribosomal DNA (rDNA) units are separated by an intergenic spacer (IGS) containing the signals for transcription and processing of rRNAs. For the first time, we sequenced and analyzed the entire IGS region from three original species within the genus Saccharum, including S. spontaneum, S. robustum, and S. officinarum in this study. We have compared the IGS organization within three original species of the genus Saccharum. The IGS of these three original species showed similar overall organizations comprised of putative functional elements needed for rRNA gene activity as well as a non-transcribed spacer (NTS), a promoter region, and an external transcribed spacer (ETS). The variability in length of the IGS sequences was assessed at the individual, intraspecies, and interspecies levels of the genus Saccharum, including S. spontaneum, S. robustum, and S. officinarum. The ETS had greater similarity than the NTS across species, but nevertheless exhibited variation in length. Within the IGS of the Saccharum species, base substitutions and copy number variation of sub-repeat were causes of the divergence in IGS sequences. We also identified a significant number of methylation sites. Furthermore, fluorescent in situ hybridization (FISH) co-localization of IGS and pTa71 probes was detected on all representative species of the genus Saccharum tested. Taken together, the results of this study provide a better insight into the structure and organization of the IGS in the genus Saccharum.

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“…Concordantly, 5’-ETS sequences have been previously considered more efficient than traditional ITS1 and ITS2 to study phylogenetic relationships between related species [31, 49]. …”

Section: Discussionmentioning

confidence: 99%

45S rDNA external transcribed spacer organization reveals new phylogenetic relationships in Avena genus

2017

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The genus Avena comprises four distinct genomes organized in diploid (AA or CC), tetraploid (AABB or AACC) and hexaploid species (AACCDD), constituting an interesting model for phylogenetic analysis. The aim of this work was to characterize 45S rDNA intergenic spacer (IGS) variability in distinct species representative of Avena genome diversity–A. strigosa (AA), A. ventricosa (CvCv), A. eriantha (CpCp), A. barbata (AABB), A. murphyi (AACC), A. sativa (AACCDD) and A. sterilis (AACCDD) through the assessment of the 5’ external transcribed spacer (5’-ETS), a promising IGS region for phylogenetic studies poorly studied in Avena genus. In this work, IGS length polymorphisms were detected mainly due to distinct 5’-ETS sequence types resulting from major differences in the number and organization of repeated motifs. Although species with A genome revealed a 5’-ETS organization (A-organization) similar to the one previously described in A. sativa, a distinct organization was unraveled in C genome diploid species (C-organization). Interestingly, such new organization presents a higher similarity with other Poaceae species than A-genome sequences, supporting the hypothesis of C-genome being the ancestral Avena genome. Additionally, polyploid species with both genomes mainly retain the A-genome 5’-ETS organization, confirming the preferential elimination of C-genome sequences in Avena polyploid species. Moreover, 5’-ETS sequences phylogenetic analysis consistently clustered the species studied according to ploidy and genomic constitution supporting the use of ribosomal genes to highlight Avena species evolutive pathways.

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Molecular Organization of the 25S–18S rDNA IGS of Fagus sylvatica and Quercus suber: A Comparative Analysis

Cited by 16 publications

References 103 publications

Interpopulation hybridization generates meiotically stable rDNA epigenetic variants in allotetraploid Tragopogon mirus

Interpopulation hybridization generates meiotically stable rDNA epigenetic variants in allotetraploid Tragopogon mirus

Comparative genetic analysis of the 45S rDNA intergenic spacers from three Saccharum species

45S rDNA external transcribed spacer organization reveals new phylogenetic relationships in Avena genus

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