ArticleBMC genomics2012
Next generation sequencing analysis reveals a relationship between rDNA unit diversity and locus number in Nicotiana diploids.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 59 citations in OpenAlex.
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- Origin of the Rare Hybrid Genus ×Plants (Basel, Switzerland) · 2022Article
- Hybridization and diversity of aquatic macrophyte Sparganium L. (Typhaceae) as revealed by high-throughput nrDNA sequencing.Scientific reports · 2022Article
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- Widespread genetic heterogeneity of human ribosomal RNA genes.RNA (New York, N.Y.) · 2022Article
- A phylogenetic analysis ofPeerJ · 2022Article
- Variation in Ribosomal DNA in the GenusPlants (Basel, Switzerland) · 2021Article
- Empirical evidence for concerted evolution in the 18S rDNA region of the planktonic diatom genus Chaetoceros.Scientific reports · 2021Article
- The Genomics of Plant Satellite DNA.Progress in molecular and subcellular biology · 2021Review
- The Utility of Graph Clustering of 5S Ribosomal DNA Homoeologs in Plant Allopolyploids, Homoploid Hybrids, and Cryptic Introgressants.Frontiers in plant science · 2020Article
- Remarkable variation of ribosomal DNA organization and copy number in gnetophytes, a distinct lineage of gymnosperms.Annals of botany · 2019Article
- Origin and parental genome characterization of the allotetraploid Stylosanthes scabra Vogel (Papilionoideae, Leguminosae), an important legume pasture crop.Annals of botany · 2018Article
- Birth-and-Death Evolution and Reticulation of ITS Segments ofFrontiers in microbiology · 2018Article
- Evolution of blue-flowered species of genus Linum based on high-throughput sequencing of ribosomal RNA genes.BMC evolutionary biology · 2017Article
- Higher-order organisation of extremely amplified, potentially functional and massively methylated 5S rDNA in European pikes (Esox sp.).BMC genomics · 2017Article
- Gene conversion events and variable degree of homogenization of rDNA loci in cultivars of Brassica napus.Annals of botany · 2017Article
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Authors and funding
8 authors at 4 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTandemly arranged nuclear ribosomal DNA (rDNA), encoding 18S, 5.8S and 26S ribosomal RNA (rRNA), exhibit concerted evolution, a pattern thought to result from the homogenisation of rDNA arrays. However rDNA homogeneity at the single nucleotide polymorphism (SNP) level has not been detailed in organisms with more than a few hundred copies of the rDNA unit. Here we study rDNA complexity in species with arrays consisting of thousands of units.
methodsWe examined homogeneity of genic (18S) and non-coding internally transcribed spacer (ITS1) regions of rDNA using Roche 454 and/or Illumina platforms in four angiosperm species, Nicotiana sylvestris, N. tomentosiformis, N. otophora and N. kawakamii. We compared the data with Southern blot hybridisation revealing the structure of intergenic spacer (IGS) sequences and with the number and distribution of rDNA loci. RESULTS AND
conclusionsIn all four species the intragenomic homogeneity of the 18S gene was high; a single ribotype makes up over 90% of the genes. However greater variation was observed in the ITS1 region, particularly in species with two or more rDNA loci, where >55% of rDNA units were a single ribotype, with the second most abundant variant accounted for >18% of units. IGS heterogeneity was high in all species. The increased number of ribotypes in ITS1 compared with 18S sequences may reflect rounds of incomplete homogenisation with strong selection for functional genic regions and relaxed selection on ITS1 variants. The relationship between the number of ITS1 ribotypes and the number of rDNA loci leads us to propose that rDNA evolution and complexity is influenced by locus number and/or amplification of orphaned rDNA units at new chromosomal locations.
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