The correlation between rDNA copy number and genome size in eukaryotes

Prokopowich, Cheryl D.; Gregory, T. Ryan; Crease, Teresa J.

doi:10.1139/g02-103

Cited by 382 publications

(315 citation statements)

References 15 publications

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“…This might be the most plausible reason that in the same species, for example, Euglena gracilis, the reported copy number of rRNA genes differs in different documents (Table 3). Prokopowich et al (2003) provided the first convincing evidence of a strong positive relationship between genome size and rDNA copy number by surveying 94 species of animals and 68 species of plants. In contrast to this finding, the copy number of rRNA genes in S. japonica seems not very appropriate for its genome size of about 545 Mb (Ye et al 2015), although the copy number still stands within the range of the available data from algae (Table 3).…”

Section: Discussionmentioning

confidence: 99%

Characterization and physical mapping of nuclear ribosomal RNA (rRNA) genes in the haploid gametophytes of Saccharina japonica (Phaeophyta)

et al. 2017

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Nuclear tandemly repeated ribosomal RNA genes (18S-5.8S-25S rDNA and 5S rDNA) have been proven to be excellent cytogenetic markers for karyotype analysis of various higher plants by using the fluorescence in situ hybridization (FISH) technique. To illustrate physical mapping of these rDNAs in brown seaweed, Saccharina japonica, chromosomes, an approximately 5400-bp transcription unit of 18S-5.8S-25S rDNA was assembled by cloning the 25S rDNA after paired-end sequencing of two screened clones from a bacterial artificial chromosome library of kelp gametophytes. In contrast to the conserved 18S-5.8S-25S rDNA and ITS1 in S. japonica, the 245-bp ITS2 was variable in sequence. The cloned 5S rDNA revealed that the 120-bp conserved coding region was separated by a diverse intergenic spacer sequence that were 250, 445, 905, or 1335 bp in length. On average, the 18S-5.8S-25S rDNA of kelp female and male gametophytes had 45 and 41 copies per haploid genome, respectively, as detected by quantitative real-time PCR, whereas the 5S rDNA had 2590 and 2648 copies, respectively. Southern hybridization with labeled probes of 18S rDNA or 5S rDNA demonstrated that kelp gametophytes possessed only one locus each of the 18S-5.8S-25S or 5S rDNAs. This was further confirmed by FISH analysis using the same labeled probes, thus illustrating that 18S-5.8S-25S rDNA is located at the intercalary region of chromosome 23, whereas 5S rDNA at the sub-telomeric region of chromosomes 27. The localization of these rDNAs using the FISH technique has facilitated the identification of individual chromosomes and karyotype analysis of this kelp.

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Section: Discussionmentioning

confidence: 99%

Characterization and physical mapping of nuclear ribosomal RNA (rRNA) genes in the haploid gametophytes of Saccharina japonica (Phaeophyta)

et al. 2017

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“…Previous studies indicate that MAST-4 has about 30 copies of the rDNA operon . This is considered a relatively low number, and could be associated to a comparatively small (o50 Mb) genome (Prokopowich et al, 2003). So far, there is no evidence for a large number of rDNA copies in MASTs that could have biased our analyses.…”

Section: Activity Levels In Mastsmentioning

confidence: 93%

Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing

et al. 2012

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Flagellated heterotrophic microeukaryotes have key roles for the functioning of marine ecosystems as they channel large amounts of organic carbon to the upper trophic levels and control the population sizes of bacteria and archaea. Still, we know very little on the diversity patterns of most groups constituting this evolutionary heterogeneous assemblage. Here, we investigate 11 groups of uncultured flagellates known as MArine STramenopiles (MASTs). MASTs are ecologically very important and branch at the base of stramenopiles. We explored the diversity patterns of MASTs using pyrosequencing (18S rDNA) in coastal European waters. We found that MAST groups range from highly to lowly diversified. Pyrosequencing (hereafter '454') allowed us to approach to the limits of taxonomic diversity for all MAST groups, which varied in one order of magnitude (tens to hundreds) in terms of operational taxonomic units (98% similarity). We did not evidence large differences in activity, as indicated by ratios of DNA:RNA-reads. Most groups were strictly planktonic, although we found some groups that were active in sediments and even in anoxic waters. The proportion of reads per size fraction indicated that most groups were composed of very small cells (B2-5 lm). In addition, phylogenetically different assemblages appeared to be present in different size fractions, depths and geographic zones. Thus, MAST diversity seems to be highly partitioned in spatial scales. Altogether, our results shed light on these ecologically very important but poorly known groups of uncultured marine flagellates.

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“…Combined with other suggested relationships with genome size (e.g. rDNA copy number [30]; centromere size [65]), a pattern is emerging in which most or all components of eukaryotic genomes scale up in content as genomes become larger. Testing this and other hypotheses about genome structure, composition and size will require the use of additional data, especially from species with much larger genomes than have typically been studied to date.…”

Section: (F ) Concluding Remarksmentioning

confidence: 99%

What's in a genome? The C-value enigma and the evolution of eukaryotic genome content

Elliott

Gregory

2015

Phil. Trans. R. Soc. B

227

209

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One contribution of 17 to a theme issue 'Eukaryotic origins: progress and challenges'. What's in a genome? The C-value enigma and the evolution of eukaryotic genome content Tyler A. Elliott and T. Ryan Gregory Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1 Some notable exceptions aside, eukaryotic genomes are distinguished from those of Bacteria and Archaea in a number of ways, including chromosome structure and number, repetitive DNA content, and the presence of introns in protein-coding regions. One of the most notable differences between eukaryotic and prokaryotic genomes is in size. Unlike their prokaryotic counterparts, eukaryotes exhibit enormous (more than 60 000-fold) variability in genome size which is not explained by differences in gene number. Genome size is known to correlate with cell size and division rate, and by extension with numerous organism-level traits such as metabolism, developmental rate or body size. Less well described are the relationships between genome size and other properties of the genome, such as gene content, transposable element content, base pair composition and related features. The rapid expansion of 'complete' genome sequencing projects has, for the first time, made it possible to examine these relationships across a wide range of eukaryotes in order to shed new light on the causes and correlates of genome size diversity. This study presents the results of phylogenetically informed comparisons of genome data for more than 500 species of eukaryotes. Several relationships are described between genome size and other genomic parameters, and some recommendations are presented for how these insights can be extended even more broadly in the future.

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The correlation between rDNA copy number and genome size in eukaryotes

Cited by 382 publications

References 15 publications

Characterization and physical mapping of nuclear ribosomal RNA (rRNA) genes in the haploid gametophytes of Saccharina japonica (Phaeophyta)

Characterization and physical mapping of nuclear ribosomal RNA (rRNA) genes in the haploid gametophytes of Saccharina japonica (Phaeophyta)

Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing

What's in a genome? The C-value enigma and the evolution of eukaryotic genome content

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