Showing papers on "Ribosomal DNA published in 2019"
TL;DR: The 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.
Abstract: 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.
127 citations
TL;DR: The observations identified an evolutionarily conserved marker of aging that is easily ascertained, grounded on nucleolar biology, and could serve as a universal marker to gauge individual age and response to interventions in humans as well as laboratory and wild organisms across a wide diversity of species.
Abstract: The ribosomal DNA (rDNA) is the most evolutionarily conserved segment of the genome and gives origin to the nucleolus, an energy intensive nuclear organelle and major hub influencing myriad molecular processes from cellular metabolism to epigenetic states of the genome. The rDNA/nucleolus has been directly and mechanistically implicated in aging and longevity in organisms as diverse as yeasts, Drosophila, and humans. The rDNA is also a significant target of DNA methylation that silences supernumerary rDNA units and regulates nucleolar activity. Here, we introduce an age clock built exclusively with CpG methylation within the rDNA. The ribosomal clock is sufficient to accurately estimate individual age within species, is responsive to genetic and environmental interventions that modulate life-span, and operates across species as distant as humans, mice, and dogs. Further analyses revealed a significant excess of age-associated hypermethylation in the rDNA relative to other segments of the genome, and which forms the basis of the rDNA clock. Our observations identified an evolutionarily conserved marker of aging that is easily ascertained, grounded on nucleolar biology, and could serve as a universal marker to gauge individual age and response to interventions in humans as well as laboratory and wild organisms across a wide diversity of species.
86 citations
TL;DR: The data indicate that rDNA break localization at the nucleolar periphery is not a direct consequence of transcriptional repression but rather is an active process that shares features with the mobilization of persistent DSB in active genes and heterochromatin.
Abstract: The ribosomal DNA (rDNA) represents a particularly unstable locus undergoing frequent breakage. DNA double-strand breaks (DSBs) within rDNA induce both rDNA transcriptional repression and nucleolar segregation, but the link between the two events remains unclear. Here we found that DSBs induced on rDNA trigger transcriptional repression in a cohesin-and HUSH (human silencing hub) complex-dependent manner throughout the cell cycle. In S/G2 cells, transcriptional repression is further followed by extended resection within the interior of the nucleolus, DSB mobilization at the nucleolar periphery within nucleolar caps, and repair by homologous recombination. We showed that nuclear envelope invaginations frequently connect the nucleolus and that rDNA DSB mobilization, but not transcriptional repression, involves the nuclear envelope-associated LINC complex and the actin pathway. Altogether , our data indicate that rDNA break localization at the nucleolar periphery is not a direct consequence of transcriptional repression but rather is an active process that shares features with the mobilization of persistent DSB in active genes and heterochromatin.
60 citations
TL;DR: How cells govern rDNA stability and how rDNA break repair influences expansion and contraction of repeat length are reviewed, a process likely associated with human disease.
Abstract: More than half of the human genome consists of repetitive sequences, with the ribosomal DNA (rDNA) representing two of the largest repeats. Repetitive rDNA sequences may form a threat to genomic integrity and cellular homeostasis due to the challenging aspects of their transcription, replication, and repair. Predisposition to cancer, premature aging, and neurological impairment in ataxia-telangiectasia and Bloom syndrome, for instance, coincide with increased cellular rDNA repeat instability. However, the mechanisms by which rDNA instability contributes to these hereditary syndromes and tumorigenesis remain unknown. Here, we review how cells govern rDNA stability and how rDNA break repair influences expansion and contraction of repeat length, a process likely associated with human disease. Recent advancements in CRISPR-based genome engineering may help to explain how cells keep their rDNA intact in the near future.
53 citations
TL;DR: This review is focused on the rDNA and associated proteins in the context of genome organization and discusses the perspective that rDNA may also be organized in topological domains constrained by structural maintenance of chromosome protein complexes such as cohesin and condensin.
Abstract: The nucleolus constitutes a prominent nuclear compartment, a membraneless organelle that was first documented in the 1830s. The fact that specific chromosomal regions were present in the nucleolus was recognized by Barbara McClintock in the 1930s, and these regions were termed nucleolar organizing regions, or NORs. The primary function of ribosomal DNA (rDNA) is to produce RNA components of ribosomes. Yet, ribosomal DNA also plays a pivotal role in nuclear organization by assembling the nucleolus. This review is focused on the rDNA and associated proteins in the context of genome organization. Recent advances in understanding chromatin organization suggest that chromosomes are organized into topological domains by a DNA loop extrusion process. We discuss the perspective that rDNA may also be organized in topological domains constrained by structural maintenance of chromosome protein complexes such as cohesin and condensin. Moreover, biophysical studies indicate that the nucleolar compartment may be formed by active processes as well as phase separation, a perspective that lends further insight into nucleolar organization. The application of the latest perspectives and technologies to this organelle help further elucidate its role in nuclear structure and function.
53 citations
TL;DR: Evidence uncovering mechanisms of regulation of instability and copy number variation at the rDNA and their role in adaptation to the environment is reviewed, which could serve to understand the basic principles governing the behavior of other tandem repeats and their roles in shaping the genome.
Abstract: Ribosomes are large, multi-subunit ribonucleoprotein complexes, essential for protein synthesis. To meet the high cellular demand for ribosomes, all eukaryotes have numerous copies of ribosomal DNA (rDNA) genes that encode ribosomal RNA (rRNA), usually far in excess of the requirement for ribosome biogenesis. In all eukaryotes studied, rDNA genes are arranged in one or more clusters of tandem repeats localized to nucleoli. The tandem arrangement of repeats, combined with the high rates of transcription at the rDNA loci, and the difficulty of replicating repetitive sequences make the rDNA inherently unstable and particularly susceptible to large variations in repeat copy number. Despite mounting evidence suggesting extra-ribosomal functions of the rDNA, its repetitive nature has excluded it from traditional sequencing-based studies. However, more recently, several studies have revealed the unique potential of the rDNA to act as a "canary in the coalmine," being particularly sensitive to genomic stresses and acting as a source of adaptive response. Here, we review evidence uncovering mechanisms of regulation of instability and copy number variation at the rDNA and their role in adaptation to the environment, which could serve to understand the basic principles governing the behavior of other tandem repeats and their role in shaping the genome.
50 citations
TL;DR: This work compared eleven species, representative for the five duckweed genera, to search for potential correlations between genome size, cell and nuclei volume, simplified body architecture, chromosome numbers and rDNA loci and found genome size is positively correlated with guard cell and nucleus volume and with the neoteny level and inversely with the frond size.
Abstract: Duckweeds are small, free-floating, largely asexual and highly neotenous organisms. They display the most rapid growth among flowering plants and are of growing interest in aquaculture and genome biology. Genomic and chromosomal data are still rare. Applying flow-cytometric genome size measurement, microscopic determination of frond, cell and nucleus morphology, as well as fluorescence in situ hybridization (FISH) for localization of ribosomal DNA (rDNA), we compared eleven species, representative for the five duckweed genera to search for potential correlations between genome size, cell and nuclei volume, simplified body architecture (neoteny), chromosome numbers and rDNA loci. We found a ~14-fold genome size variation (from 160 to 2203 Mbp), considerable differences in frond size and shape, highly variable guard cell and nucleus size, chromosome number (from 2n = 36 to 82) and number of 5S and 45S rDNA loci. In general, genome size is positively correlated with guard cell and nucleus volume (p < 0.001) and with the neoteny level and inversely with the frond size. In individual cases these correlations could be blurred for instance by particular body and cell structures which seem to be linked to specific floating styles. Chromosome number and rDNA loci variation between the tested species was independent of the genome size. We could not confirm previously reported intraspecific variation of chromosome numbers between individual clones of the genera Spirodela and Landoltia.
40 citations
TL;DR: It is suggested that complete plastome and ribosomal DNA sequences can substantially increase species discriminatory power in plants, but they are not powerful enough to fully resolve phylogenetic relationships and discriminate all species, particularly in evolutionarily young and complex plant groups.
Abstract: Complete plastid genome (plastome) sequences and nuclear ribosomal DNA (nrDNA) regions have been proposed as candidates for the next generation of DNA barcodes for plant species discrimination. However, the efficacy of this approach still lacks comprehensive evaluation. We carried out a case study in the economically important but phylogenetically and taxonomically difficult genus Panax (Araliaceae). We generated a large data set of plastomes and nrDNA sequences from multiple accessions per species. Our data improved the phylogenetic resolution and levels of species discrimination in Panax, compared to any previous studies using standard DNA barcodes. This provides new insights into the speciation, lineage diversification and biogeography of the genus. However, both plastome and nrDNA failed to completely resolve the phylogenetic relationships in the Panax bipinnatifidus species complex, and only half of the species within it were recovered as monophyletic units. The results suggest that complete plastome and ribosomal DNA sequences can substantially increase species discriminatory power in plants, but they are not powerful enough to fully resolve phylogenetic relationships and discriminate all species, particularly in evolutionarily young and complex plant groups. To gain further resolving power for closely related species, the addition of substantial numbers of nuclear markers is likely to be required.
39 citations
TL;DR: Superresolution microscopy is used to describe linkages between ribosomal DNA on heterologous human chromosomes whose formation depends on the transcription factor UBF and topoisomerase II.
Abstract: The spatial organization of the genome is enigmatic. Direct evidence of physical contacts between chromosomes and their visualization at nanoscale resolution has been limited. We used superresolution microscopy to demonstrate that ribosomal DNA (rDNA) can form linkages between chromosomes. We observed rDNA linkages in many different human cell types and demonstrated their resolution in anaphase. rDNA linkages are coated by the transcription factor UBF and their formation depends on UBF, indicating that they regularly occur between transcriptionally active loci. Overexpression of c-Myc increases rDNA transcription and the frequency of rDNA linkages, further suggesting that their formation depends on active transcription. Linkages persist in the absence of cohesion, but inhibition of topoisomerase II prevents their resolution in anaphase. We propose that linkages are topological intertwines occurring between transcriptionally active rDNA loci spatially colocated in the same nucleolar compartment. Our findings suggest that active DNA loci engage in physical interchromosomal connections that are an integral and pervasive feature of genome organization.
37 citations
TL;DR: This review summarizes the most important findings related to the nucleolar stress response (NSR), whereby a series of cell insults have a special impact on the nucleolus, leading ultimately to cell cycle arrest, apoptosis, senescence or differentiation.
Abstract: Once thought a mere ribosome factory, the nucleolus has been viewed in recent years as an extremely sensitive gauge of diverse cellular stresses. Emerging concepts in nucleolar biology include the nucleolar stress response (NSR), whereby a series of cell insults have a special impact on the nucleolus. These insults include, among others, ultra-violet radiation (UV), nutrient deprivation, hypoxia and thermal stress. While these stresses might influence nucleolar biology directly or indirectly, other perturbances whose origin resides in the nucleolar biology also trigger nucleolar and systemic stress responses. Among the latter, we find mutations in nucleolar and ribosomal proteins, ribosomal RNA (rRNA) processing inhibitors and ribosomal DNA (rDNA) transcription inhibition. The p53 protein also mediates NSR, leading ultimately to cell cycle arrest, apoptosis, senescence or differentiation. Hence, NSR is gaining importance in cancer biology. The nucleolar size and ribosome biogenesis, and how they connect with the Target of Rapamycin (TOR) signalling pathway, are also becoming important in the biology of aging and cancer. Simple model organisms like the budding yeast Saccharomyces cerevisiae, easy to manipulate genetically, are useful in order to study nucleolar and rDNA structure and their relationship with stress. In this review, we summarize the most important findings related to this topic.
34 citations
TL;DR: From nucleolus-associated domains (NADs) to the regulation of imprinted loci and X chromosome inactivation, as well as rDNA contact maps that anchor and position the rDNA relative to the rest of the genome are discussed.
28 Jan 2019
TL;DR: It is demonstrated that during malignant progression the rDNA chromatin converts to the open state, which is required for tumor cell survival, and that a specific transcription factor regulates this transition by altering r DNA chromatin, resulting in the reorganization of contacts between rDNA and the genome.
Abstract: The three-dimensional organization of the genome contributes to its maintenance and regulation. While chromosomal regions associate with nucleolar ribosomal RNA genes (rDNA), the biological significance of rDNA-genome interactions and whether they are dynamically regulated during disease remain unclear. rDNA chromatin exists in multiple inactive and active states and their transition is regulated by the RNA polymerase I transcription factor UBTF. Here, using a MYC-driven lymphoma model, we demonstrate that during malignant progression the rDNA chromatin converts to the open state, which is required for tumor cell survival. Moreover, this rDNA transition co-occurs with a reorganization of rDNA-genome contacts which correlate with gene expression changes at associated loci, impacting gene ontologies including B-cell differentiation, cell growth and metabolism. We propose that UBTF-mediated conversion to open rDNA chromatin during malignant transformation contributes to the regulation of specific gene pathways that regulate growth and differentiation through reformed long-range physical interactions with the rDNA.
TL;DR: The results support the notion that there is significant intra-specific variability in Protoceratium reticulatum and the biogeography of the different ribotypes is consistent with specific ecological preferences.
TL;DR: 72 new sequences are characterized, including 40 mitochondrial cytochrome oxidase c subunit I (COI) sequences, 29 mitochondrial small sub unit ribosomal DNA sequences and three small subunit ribosome DNA sequences from 47 isolates of 44 morphospecies are characterized and mitochondrial genes support the monophyly of the order Philasterida.
08 Jul 2019
TL;DR: It is reported that addition of NaCl to culture media expands the growth range of H. werneckii to 37 °C, which explains its colonisation of human skin, with its increased salinity.
Abstract: The polymorphic black yeast Hortaea werneckii (Capnodiales, Ascomycota) is extremely halotolerant (growth from 0 to 30% [w/v] NaCl) and has been extensively studied as a model for halotolerance in Eukaryotes for over two decades. Its most frequent sources are hypersaline environments and adjacent sea-water habitats in temperate, subtropical and tropical climates. Although typically saprobic, H. werneckii can also act as a commensal coloniser on human skin, causing tinea nigra on hands and soles. Here, we report that addition of NaCl to culture media expands the growth range of H. werneckii to 37 °C, which explains its colonisation of human skin, with its increased salinity. The morphological and physiological plasticity/ versatility of H. werneckii indicate that a species complex might be involved. This was investigated in this polyphasic taxonomic analysis based on the global diversity of H. werneckii strains collected from hypersaline environments, and from humans and animals. Analysis of D1/D2domains of 28S and internal transcribed spacer rDNA revealed 10 and 17 genotypes, respectively, that were not always compliant. The genotypes have global distributions. Human and environmental strains with the same genotypes are intermingled. Due to the limited number of phylogenetically informative characters in the ribosomal DNA dataset, the partial genes encoding for β-tubulin (BTB) and mini-chromosome maintenance protein (MCM7) were also sequenced. The use of these genes was hampered by ambiguous sequences obtained by Sanger sequencing, as a consequence of the diploid and highly heterozygous genome of many H. werneckii strains. Analysis of the BTB and MCM7 genes showed that in some cases two copies of the gene from the same genome are positioned in distant phylogenetic clusters of the intraspecific gene tree. Analysis of whole-genome sequences of selected H. werneckii strains generally confirmed the phylogenetic distances estimated on the basis of ribosomal genes, but also showed substantial reticulation within the phylogenetic history of the strains. This is in line with the hypothesis that the diploid genomes of H. werneckii were formed by hybridizations, which have sometimes occurred between relatively divergent strains.
TL;DR: It is shown that "DJ-like" sequences and abutting rDNA arrays are inverted as a unit in comparison to humans, and this findings lead us to revaluate the molecular definition of NORs, identify novel genomic structural variation, and provide a rationale for the distinctive chromosomal organization ofNORs.
Abstract: Human nucleolar organizer regions (NORs), containing ribosomal gene (rDNA) arrays, are located on the p-arms of acrocentric chromosomes (HSA13-15, 21, and 22). Absence of these p-arms from genome references has hampered research on nucleolar formation. Previously, we assembled a distal junction (DJ) DNA sequence contig that abuts rDNA arrays on their telomeric side, revealing that it is shared among the acrocentrics and impacts nucleolar organization. To facilitate inclusion into genome references, we describe sequencing the DJ from all acrocentrics, including three versions of HSA21, ∼3 Mb of novel sequence. This was achieved by exploiting monochromosomal somatic cell hybrids containing single human acrocentric chromosomes with NORs that retain functional potential. Analyses revealed remarkable DJ sequence and functional conservation among human acrocentrics. Exploring chimpanzee acrocentrics, we show that "DJ-like" sequences and abutting rDNA arrays are inverted as a unit in comparison to humans. Thus, rDNA arrays and linked DJs represent a conserved functional locus. We provide direct evidence for exchanges between heterologous human acrocentric p-arms, and uncover extensive structural variation between chromosomes and among individuals. These findings lead us to revaluate the molecular definition of NORs, identify novel genomic structural variation, and provide a rationale for the distinctive chromosomal organization of NORs.
TL;DR: Surprisingly, three marine isolates belong to Chlorella vulgaris according to the phylogenetic analyses, but showed a high phenotypic plasticity, and showed the typical morphology of C. vulgaris under freshwater conditions, they increased the cell shape and formed cell packages under marine conditions.
Abstract: Green algal species of spherical cell shape are generally considered to belong to the genus Chlorella, which are mostly freshwater or terrestrial organisms. Phylogenetic studies have shown that this genus is polyphyletic and belongs to different classes. However, until now, only freshwater or terrestrial strains have been studied. Here we investigated 11 strains of 'marine' Chlorella deposited in public culture collections, which we studied using an integrative approach. These strains were largely isolated from marine rock pools and brackish estuaries. SSU and ITS regions of the nuclear encoded ribosomal DNA were sequenced, ribosomal secondary structures were analysed and cell morphology, salinity tolerance and reproduction were examined. Our results showed that the marine strains are also of polyphyletic origin. Surprisingly, three marine isolates belong to Chlorella vulgaris according to the phylogenetic analyses, but showed a high phenotypic plasticity. Whereas these strains showed the typical morphology of C. vulgaris under freshwater conditions, they increased the cell shape and formed cell packages under marine conditions. In contrast, the other investigated strains showed no changes after changing the media. Two of the investigated strains belong to the genus Chloroidium, and those remaining represent a new genus, Droopiella.
TL;DR: The data suggest that the common ancestor of Lampyridae possessed adult bioluminescence, with a higher loss rate than gain rate of biolumeinescence during its lineage evolution, and inferred the evolutionary pattern of adult b Bioluminescent in Lampyrids based on the phylogenies of 166 and 144 species.
TL;DR: It is suggested that template choice may be especially important for estimating biodiversity, such as richness and relative abundances, especially in Helotiales and Agaricales, but not for inferring community composition.
Abstract: Describing dynamics of belowground organisms, such as fungi, can be challenging. Results of studies based on environmental DNA (eDNA) may be biased as the template does not discriminate between metabolically active cells and dead biomass. We analyzed ribosomal DNA (rDNA) and ribosomal RNA (rRNA) coextracted from 48 soil samples collected from a manipulated snow depth experiment in two distinct vegetation types in Svalbard, in the High Arctic. Our main goal was to compare if the rDNA and rRNA metabarcoding templates produced congruent results that would lead to consistent ecological interpretation. Data derived from both rDNA and rRNA clustered according to vegetation types. Different sets of environmental variables explained the community composition based on the metabarcoding template. rDNA and rRNA-derived community composition of symbiotrophs and saprotrophs, unlike pathotrophs, clustered together in a similar way as when the community composition was analyzed using all OTUs in the study. Mean OTU richness was higher for rRNA, especially in symbiotrophs. The metabarcoding template was more important than vegetation type in explaining differences in richness. The proportion of symbiotrophic, saprotrophic and functionally unassigned reads differed between rDNA and rRNA, but showed similar trends. There was no evidence for increased snow depth influence on fungal community composition or richness. Our findings suggest that template choice may be especially important for estimating biodiversity, such as richness and relative abundances, especially in Helotiales and Agaricales, but not for inferring community composition. Differences in study results originating from rDNA or rRNA may directly impact the ecological conclusions of one's study, which could potentially lead to false conclusions on the dynamics of microbial communities in a rapidly changing Arctic.
TL;DR: The Dictyostelid social amoebas are a popular model system for cell- and developmental biology and for evolution of sociality as discussed by the authors, which is a more robust phylogeny than the small subunit (SSU) ribosomal DNA-based phylogenies.
TL;DR: Results regarding both bacterial assemblage and functional traits indicated that the habitat filtering and niche differentiation (treatment units) exerted selection on microbial communities based on functional traits, particular for key ecological functions related to nitrogen cycling.
TL;DR: Phylogeny based on cox1 sequences placed S. miescheriana and S. suihominis as sister species within a clade comprising mainly Sarcocystis spp.
Abstract: A sample of the diaphragm was collected from each of 100 wild boars legally hunted in the Val Grande National Park in north-western Italy and examined for the presence of Sarcocystis infection by histological and molecular methods. In histological sections, thick-walled sarcocysts consistent with those of Sarcocystis miescheriana were detected in 32 wild boars. Genomic DNA extracted from diaphragm samples was initially subjected to PCR amplification of the internal transcribed spacer 1 (ITS1) region, and 97 wild boars were found to harbour a Sarcocystis infection at this screening. Selected DNA samples were then subjected to PCR amplification and sequencing of the ITS1 region and the 18S and 28S ribosomal RNA (rRNA) genes of the nuclear ribosomal DNA unit, while all positive samples were subjected to PCR amplification of the mitochondrial cytochrome c oxidase subunit I (cox1) gene. S. miescheriana was identified in 97 wild boars (97%), while the zoonotic Sarcocystis suihominis was identified in one wild boar (1%), which also harboured S. miescheriana. Intra-specific sequence variation was found in all four DNA regions of S. miescheriana examined and in the 18S rRNA gene and ITS1 region of S. suihominis. The partial cox1 gene was amplified and sequenced from 72 isolates of S. miescheriana, yielding 43 haplotypes with pairwise sequence identities of 97.6–99.9%. These haplotypes were 79.1–79.8% identical with the cox1 sequence of S. suihominis. Phylogeny based on cox1 sequences placed S. miescheriana and S. suihominis as sister species within a clade comprising mainly Sarcocystis spp. of ruminants with felids as known or presumed definitive hosts. The same was true for the phylogeny based on 18S rRNA gene sequences.
TL;DR: It is proposed that the pericentromere and nucleolus, in part due to their enrichment of SMC proteins and others, contain similar domains that drive important cellular activities such as segregation, stability, and repair.
Abstract: Both the pericentromere and the nucleolus have unique characteristics that distinguish them amongst the rest of genome. Looping of pericentromeric DNA, due to structural maintenance of chromosome (SMC) proteins condensin and cohesin, drives its ability to maintain tension during metaphase. Similar loops are formed via condensin and cohesin in nucleolar ribosomal DNA (rDNA). Condensin and cohesin are also concentrated in transfer RNA (tRNA) genes, genes which may be located within the pericentromere as well as tethered to the nucleolus. Replication fork stalling, as well as downstream consequences such as genomic recombination, are characteristic of both the pericentromere and rDNA. Furthermore, emerging evidence suggests that the pericentromere may function as a liquid-liquid phase separated domain, similar to the nucleolus. We therefore propose that the pericentromere and nucleolus, in part due to their enrichment of SMC proteins and others, contain similar domains that drive important cellular activities such as segregation, stability, and repair.
29 Jul 2019
TL;DR: Phylogenetic analyses based on a combined dataset comprising the internal transcribed spacer regions (ITS), the largest subunit (LSU) of the ribosomal DNA, partial regions of the elongation factor 1-α (TEF) and the largest and second largest subunits for the RNA polymerase genes (RPB1, RPB2) strongly support the placement of these seven new species in Ophiocordyceps.
Abstract: Seven new species occurring on termites are added to Ophiocordyceps - O. asiatica, O. brunneirubra, O. khokpasiensis, O. mosingtoensis, O. pseudocommunis, O. pseudorhizoidea and O. termiticola, based on morphological and molecular phylogenetic evidence. O. brunneirubra possesses orange to reddish-brown immersed perithecia on cylindrical to clavate stromata. O. khokpasiensis, O. mosingtoensis and O. termiticola have pseudo-immersed perithecia while O. asiatica, O. pseudocommunis and O. pseudorhizoidea all possess superficial perithecia, reminiscent of O. communis and O. rhizoidea. Phylogenetic analyses based on a combined dataset comprising the internal transcribed spacer regions (ITS) and the largest subunit (LSU) of the ribosomal DNA, partial regions of the elongation factor 1-α (TEF) and the largest and second largest subunits for the RNA polymerase genes (RPB1, RPB2) strongly support the placement of these seven new species in Ophiocordyceps.
TL;DR: The authors found that resolution of human rDNA occurs in anaphase after the bulk of the genome, dependent on tankyrase 1, condensin II, and topoisomerase II.
Abstract: Formation of individualized sister chromatids is essential for their accurate segregation. In budding yeast, while most of the genome segregates at the metaphase to anaphase transition, resolution of the ribosomal DNA (rDNA) repeats is delayed. The timing and mechanism in human cells is unknown. Here we show that resolution of human rDNA occurs in anaphase after the bulk of the genome, dependent on tankyrase 1, condensin II, and topoisomerase IIα. Defective resolution leads to rDNA bridges, rDNA damage, and aneuploidy of an rDNA-containing acrocentric chromosome. Thus, temporal regulation of rDNA segregation is conserved between yeast and man and is essential for genome integrity.
TL;DR: Analytical methods are applied to map repair events in rDNA using data generated by the newly developed XR-seq procedure, which measures excision repair genome-wide with single-nucleotide resolution and finds that rDNA is not subject to TCR of damage caused by UV or by cisplatin.
TL;DR: Lichinodium constitutes a formerly unrecognized lineage within the Leotiomycetes, thus being the first lichenized lineage recognized in the superclass Sordariomyceta, and the results show that Lichinodium is sister to Leotiaceae.
Abstract: Here, we show that Lichinodium (Lichinaceae, Lichinomycetes, Ascomycota) constitutes a formerly unrecognized lineage within the Leotiomycetes, thus being the first lichenized lineage recognized in the superclass Sordariomyceta (Leotiomycetes, Laboulbeniomycetes and Sordariomycetes). To infer the position of Lichinodium, we constructed two multilocus phylogenies based on six and five gene regions (nuLSU rDNA, nuSSU rDNA, mtSSU rDNA, RPB1, RPB2 and MCM7) including main Pezizomycotina groups in the first analysis and focusing secondly on a comprehensive selection of Sordariomyceta. The results show that Lichinodium is sister to Leotiaceae. We discuss the morphological and ecological similarities between Lichinodium and other Leotiomycetes, and describe the new order Lichinodiales and family Lichinodiaceae. The sister relationship between Sordariomycetes and Laboulbeniomycetes is here supported as it is the relationship between this clade and the Leotiomycetes. The results also support the polyphyly of Helotiales, the recognition of the Leotiales in a strict sense or the inclusion of the Triblidiales in Leotiomycetes. The photobionts of Lichinodium were sequenced for two genetic markers (rbcLX and 16S rDNA) and identified as Rhizonema, a recently described genus of filamentous cyanobacteria belonging to Nostocaceae. TEM studies revealed that the mycobiont-cyanobiont interface in Lichinodium does not produce haustoria, thus differing from a typical Lichinomycete (e.g. Ephebe).
TL;DR: The phylogenetic tree resulting from Bayesian inference analyses based on concatenated nucleotide sequences of all 36 genes of Plagiorchis maculosus and other xiphidiates mitochondrial genomes indicated that P. maculosUS (and the PlagIORchiidae) is phylogenetically closest to the Brachycladiidae and Paragonimidae.
TL;DR: Live cell imaging is used to quantitate the three-dimensional conformation of yeast Saccharomyces cerevisiae ribosomal DNA and it is determined that spatial reorganisation of these subdomains and establishment of rDNA mitotic organisation is under the control of the cohesin complex.
TL;DR: Three fungal isolates discovered during a survey of fungal diversity of the order Mortierellales from freshwater and pine tree rhizosphere soil samples in Korea were identified as Mortierella elongata, M. horticola, and M. humilis, belonging to an undiscovered taxon.
Abstract: Three fungal isolates designated as CNUFC-YR329-1, CNUFC-PTS103-1, and CNUFC-PTS2-1 were discovered during a survey of fungal diversity of the order Mortierellales from freshwater and pine tree rhizosphere soil samples in Korea. The strains were analyzed morphologically and phylogenetically based on the internal transcribed spacer (ITS) and large subunit (LSU) of ribosomal DNA gene sequences. Based on their morphology and phylogeny, the three isolates were identified as Mortierella elongata, M. horticola, and M. humilis, respectively. To the best of our knowledge, M. elongata, M. horticola, and M. humilis, belonging to an undiscovered taxon, have not been previously described in Korea.