ArticleFrontiers in plant science2020
The Utility of Graph Clustering of 5S Ribosomal DNA Homoeologs in Plant Allopolyploids, Homoploid Hybrids, and Cryptic Introgressants.
Article in Frontiers in plant science, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Pruning the Tree: Comparing OTUs and ASVs in High-Throughput Sequencing of 5S-IGS Nuclear Ribosomal DNA in Phylogenetic Studies.Ecology and evolution · 2025Article
- Divergent landscapes and evolutionary trajectories of 5S rDNA and Cassandra retroelement in Saccharinae.BMC plant biology · 2025Article
- Does time matter? Intraspecific diversity of ribosomal RNA genes in lineages of the allopolyploid model grass Brachypodium hybridum with different evolutionary ages.BMC plant biology · 2024Article
- First insight into the genomes of the Pulmonaria officinalis group (Boraginaceae) provided by repeatome analysis and comparative karyotyping.BMC plant biology · 2024Article
- Uniparental silencing of 5S rRNA genes in plant allopolyploids - insights from Cardamine (Brassicaceae).The Plant journal : for cell and molecular biology · 2024Article
- The Dynamic Interplay Between Ribosomal DNA and Transposable Elements: A Perspective From Genomics and Cytogenetics.Molecular biology and evolution · 2024Article
- Genomic and cytogenetic analyses reveal satellite repeat signature in allotetraploid okra (Abelmoschus esculentus).BMC plant biology · 2024Article
- Expansions and contractions of repetitive DNA elements reveal contrasting evolutionary responses to the polyploid genome shock hypothesis inFrontiers in plant science · 2024Article
- Ancient hybridization and repetitive element proliferation in the evolutionary history of the monocot genusFrontiers in plant science · 2024Article
- Intragenomic rDNA variation - the product of concerted evolution, mutation, or something in between?Heredity · 2023Review
- Comparative Cytogenetic of the 36-Chromosomes Genera ofPlants (Basel, Switzerland) · 2023Article
- Investigating the Origin and Evolution of PolyploidPlants (Basel, Switzerland) · 2023Article
- Analysis of 5S rDNA Genomic Organization Through the RepeatExplorer2 Pipeline: A Simplified Protocol.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Phylogenomics and Systematics of Overlooked Mesoamerican and South American Polyploid Broad-LeavedPlants (Basel, Switzerland) · 2022Article
- Genome diploidization associates with cladogenesis, trait disparity, and plastid gene evolution.Plant physiology · 2022Article
- Complex Scenarios of Reticulation, Polyploidization, and Species Diversity within Annual Pansies of Subsect.Plants (Basel, Switzerland) · 2022Article
- A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae.GigaScience · 2022Article
- Molecular and Cytogenetic Analysis of rDNA Evolution in Crepis Sensu Lato.International journal of molecular sciences · 2022Article
- 5S-IGS rDNA in wind-pollinated trees (Fagus L.) encapsulates 55 million years of reticulate evolution and hybrid origins of modern species.The Plant journal : for cell and molecular biology · 2022Article
- Morphological and Genome-Wide Evidence of Homoploid Hybridisation inPlants (Basel, Switzerland) · 2022Article
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6 authors.
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Abstract
introductionRibosomal 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
conclusionWe 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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