scholarly journals Integrative rDNAomics—Importance of the Oldest Repetitive Fraction of the Eukaryote Genome

Genes ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 345 ◽  
Author(s):  
Radka Symonová
Keyword(s):  
Copy Number ◽  
Evolutionary Dynamics ◽  
Cellular Aging ◽  
Multiple Roles ◽  
Rrna Genes ◽  
Integrative Approach ◽  
Evolutionary Context ◽  
Stress Sensing ◽  
And Control ◽  
Repetitive Fraction

Nuclear ribosomal RNA (rRNA) genes represent the oldest repetitive fraction universal to all eukaryotic genomes. Their deeply anchored universality and omnipresence during eukaryotic evolution reflects in multiple roles and functions reaching far beyond ribosomal synthesis. Merely the copy number of non-transcribed rRNA genes is involved in mechanisms governing e.g., maintenance of genome integrity and control of cellular aging. Their copy number can vary in response to environmental cues, in cellular stress sensing, in development of cancer and other diseases. While reaching hundreds of copies in humans, there are records of up to 20,000 copies in fish and frogs and even 400,000 copies in ciliates forming thus a literal subgenome or an rDNAome within the genome. From the compositional and evolutionary dynamics viewpoint, the precursor 45S rDNA represents universally GC-enriched, highly recombining and homogenized regions. Hence, it is not accidental that both rDNA sequence and the corresponding rRNA secondary structure belong to established phylogenetic markers broadly used to infer phylogeny on multiple taxonomical levels including species delimitation. However, these multiple roles of rDNAs have been treated and discussed as being separate and independent from each other. Here, I aim to address nuclear rDNAs in an integrative approach to better assess the complexity of rDNA importance in the evolutionary context.

Effects of the diploidisation process upon the 5S and 35S rDNA sequences in the allopolyploid species of the Dilatata group of Paspalum (Poaceae, Paniceae)

2019 ◽  
Vol 67 (7) ◽  
pp. 521
Author(s):  
Magdalena Vaio ◽  
Cristina Mazzella ◽  
Marcelo Guerra ◽  
Pablo Speranza
Keyword(s):  
Evolutionary Dynamics ◽  
In Situ Hybridisation ◽  
5S Rdna ◽  
Its Region ◽  
Variable Number ◽  
Rrna Genes ◽  
Fluorescence In Situ Hybridisation ◽  
Rdna Sites ◽  
35S Rdna ◽  
Genome Restructuring

The Dilatata group of Paspalum includes species and biotypes native to temperate South America. Among them, five sexual allotetraploids (x = 10) share the same IIJJ genome formula: P. urvillei Steud, P. dasypleurum Kunze ex Desv., P. dilatatum subsp. flavescens Roseng., B.R. Arrill. & Izag., and two biotypes P. dilatatum Vacaria and P. dilatatum Virasoro. Previous studies suggested P. intermedium Munro ex Morong & Britton and P. juergensii Hack. or related species as their putative progenitors and donors of the I and J genome, respectively, and pointed to a narrow genetic base for their maternal origin. It has not yet been established whether the various members of the Dilatata group are the result of a single or of multiple allopolyploid formations. Here, we aimed to study the evolutionary dynamics of rRNA genes after allopolyploidisation in the Dilatata group of Paspalum and shed some light into the genome restructuring of the tetraploid taxa with the same genome formula. We used double target fluorescence in situ hybridisation of 35S and 5S rDNA probes and sequenced the nrDNA internal transcribed spacer (ITS) region. A variable number of loci at the chromosome ends were observed for the 35S rDNA, from 2 to 6, suggesting gain and loss of sites. For the 5S rDNA, only one centromeric pair of signals was observed, indicating a remarkable loss after polyploidisation. All ITS sequences generated were near identical to the one found for P. intermedium. Although sequences showed a directional homogeneisation towards the putative paternal progenitor in all tetraploid species, the observed differences in the number and loss of rDNA sites suggest independent ongoing diploidisation processes in all taxa and genome restructuring following polyploidy.

EVOLUTION WITH ENDOGENOUS MUTATIONS

2005 ◽  
Vol 07 (02) ◽  
pp. 229-240 ◽  
Author(s):  
IVAR KOLSTAD
Keyword(s):  
Evolutionary Dynamics ◽  
Basin Of Attraction ◽  
Equilibrium Selection ◽  
Mutation Rates ◽  
And Control

Bergin and Lipman (1996) prove that equilibrium selection in the evolutionary dynamics of Kandori et al. (1993) and Young (1993), is not robust to variations in mutation rates across states. Specifically, a risk dominant equilibrium can be selected against if mutation rates are higher in its basin of attraction than elsewhere. Van Damme and Weibull (1998) model mutations as a compromise between payoff losses and control costs, which implies lower mutation rates in the risk dominant equilibrium. This paper argues that this result is not driven by control costs, but by players focusing on payoff losses when choosing mutation rates.

scholarly journals An integrative approach to investigate the respective roles of single-nucleotide variants and copy-number variants in Attention-Deficit/Hyperactivity Disorder

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Leandro de Araújo Lima ◽  
Ana Cecília Feio-dos-Santos ◽  
Sintia Iole Belangero ◽  
Ary Gadelha ◽  
Rodrigo Affonseca Bressan ◽  
...  
Keyword(s):  
Attention Deficit Hyperactivity Disorder ◽  
Attention Deficit ◽  
Copy Number ◽  
De Novo ◽  
Copy Number Variants ◽  
Integrative Approach ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Hyperactivity Disorder ◽  
New Genes

Abstract Many studies have attempted to investigate the genetic susceptibility of Attention-Deficit/Hyperactivity Disorder (ADHD), but without much success. The present study aimed to analyze both single-nucleotide and copy-number variants contributing to the genetic architecture of ADHD. We generated exome data from 30 Brazilian trios with sporadic ADHD. We also analyzed a Brazilian sample of 503 children/adolescent controls from a High Risk Cohort Study for the Development of Childhood Psychiatric Disorders, and also previously published results of five CNV studies and one GWAS meta-analysis of ADHD involving children/adolescents. The results from the Brazilian trios showed that cases with de novo SNVs tend not to have de novo CNVs and vice-versa. Although the sample size is small, we could also see that various comorbidities are more frequent in cases with only inherited variants. Moreover, using only genes expressed in brain, we constructed two “in silico” protein-protein interaction networks, one with genes from any analysis, and other with genes with hits in two analyses. Topological and functional analyses of genes in this network uncovered genes related to synapse, cell adhesion, glutamatergic and serotoninergic pathways, both confirming findings of previous studies and capturing new genes and genetic variants in these pathways.

scholarly journals LiquidCNA: tracking subclonal evolution from longitudinal liquid biopsies using somatic copy number alterations

2021 ◽  
Author(s):  
Eszter Lakatos ◽  
Helen Hockings ◽  
Maximilian Mossner ◽  
Michelle Lockley ◽  
Trevor A. Graham
Keyword(s):  
Copy Number ◽  
Evolutionary Dynamics ◽  
Cost Effective ◽  
Copy Number Alterations ◽  
Liquid Biopsies ◽  
Metastatic Lung ◽  
Low Pass ◽  
Somatic Copy Number Alterations

AbstractCell-free DNA (cfDNA) measured via liquid biopsies provides a way for minimally-invasive monitoring of tumour evolutionary dynamics during therapy. Here we present liquidCNA, a method to track subclonal evolution from longitudinally collected cfDNA samples based on somatic copy number alterations (SCNAs). LiquidCNA utilises SCNA profiles derived through cost-effective low-pass whole genome sequencing to automatically and simultaneously genotype and quantify the size of the dominant subclone without requiring prior knowledge of the genetic identity of the emerging clone. We demonstrate the accuracy of liquidCNA in synthetically generated sample sets and in vitro and in silico mixtures of cancer cell lines. Application in vivo in patients with metastatic lung cancer reveals the progressive emergence of a novel tumour sub-population. LiquidCNA is straightforward to use, computationally inexpensive and enables continuous monitoring of subclonal evolution to understand and control therapy-induced resistance.

scholarly journals Comparative Analysis of the Fecal Bacterial Microbiota of Wintering Whooper Swans (Cygnus Cygnus)

2021 ◽  
Vol 8 ◽  
Author(s):  
Wenxia Wang ◽  
Songlin Huang ◽  
Liangliang Yang ◽  
Guogang Zhang
Keyword(s):  
Intestinal Microbiota ◽  
Relative Abundance ◽  
High Throughput Sequencing ◽  
The Body ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Illumina Hiseq ◽  
Linear Discriminant ◽  
Bacterial Microbiota ◽  
And Control

There are many and diverse intestinal microbiota, and they are closely related to various physiological functions of the body. They directly participate in the host's food digestion, nutrient absorption, energy metabolism, immune response, and many other physiological activities and are also related to the occurrence of many diseases. The intestinal microbiota are extremely important for maintaining normal physical health. In order to explore the composition and differences of the intestinal microbiota of whooper swans in different wintering areas, we collected fecal samples of whooper swans in Sanmenxia, Henan, and Rongcheng, Shandong, and we used the Illumina HiSeq platform to perform high-throughput sequencing of bacterial 16S rRNA genes. Comparison between Sanmenxia and Rongcheng showed no significant differences in ACE, Chao 1, Simpson, and Shannon indices (p > 0.05). Beta diversity results showed significant differences in bacterial communities between two groups [analysis of similarity (ANOSIM): R = 0.80, p = 0.011]. Linear discriminant analysis effect size (LEfSe) analysis showed that at the phylum level, the relative abundance of Actinobacteria was significantly higher in Sanmenxia whooper swans than Rongcheng whooper swans. At the genus level, the amount of Psychrobacter and Carnobacterium in Sanmenxia was significantly higher in Rongcheng, while the relative abundance Catellicoccus and Lactobacillus was significantly higher in Rongcheng than in Sanmenxia. This study analyzed the composition, characteristics, and differences of the intestinal microbiota of the whooper swans in different wintering environments and provided theoretical support for further exploring the relationship between the intestinal microbiota of the whooper swans and the external environment. And it played an important role in the overwintering physiology and ecology, population management, and epidemic prevention and control of whooper swans.

scholarly journals Landscapes of fear: from trophic cascades to applied management and population ecology

2017 ◽  
Author(s):  
Sonny S Bleicher
Keyword(s):  
Population Biology ◽  
Evolutionary Dynamics ◽  
Focal Point ◽  
Work Group ◽  
Stress Hormones ◽  
Physical Space ◽  
Community Context ◽  
Continuous Measure ◽  
Evolutionary Context ◽  
Study Population

Predator-Prey dynamics, and their trophic impacts, have functioned as a focal point in both community and population biology for five decades. The work-group focusing on these dynamics has however largely changed the focus of their work from trophic effects to the study of non-consumptive effects of predation-- the “ecology of fear”. An increasing number of studies chose to spatially chart wildlife populations’ risk assessment and of those the majority use optimal patch-use (giving-up densities) as a continuous measure of fear. These charts, “landscapes-of-fear” (LOFs) originated in conservation literature and the reintroduction of wolves to Yellowstone. Today, they are used to study population habitat selection and venture into the evolutionary context with studies examining the mechanisms by which species coexist in the same physical space. This review predicts increase in, and encourages the use of, LOFs: as a conservation tool to assess species land-use; as a bridge between ecology and neurology with stress hormones as indicators fear; and as a tool to compare species’ evolutionary dynamics within a community context.

scholarly journals Copy Number Variation of Multiple Genes in SAPHO Syndrome

2019 ◽  
Vol 47 (9) ◽  
pp. 1323-1329
Author(s):  
Changlong Guo ◽  
Xin Tian ◽  
Feifei Han ◽  
Lihong Liu ◽  
Jianen Gao ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Candidate Genes ◽  
Copy Number ◽  
Nuclear Family ◽  
Sapho Syndrome ◽  
Unknown Etiology ◽  
Comparative Genomic ◽  
Number Variation ◽  
And Control ◽  
Control Samples

Objective.SAPHO (synovitis, acne, pustulosis, hyperostosis, osteitis) syndrome is a type of rare chronic aseptic inflammation of unknown etiology. To date, no research to our knowledge has reported copy number variation (CNV) of genes that could affect predisposition to SAPHO syndrome. We investigated the association between CNV profile and SAPHO syndrome.Methods.We used array comparative genomic hybridization (CGH) to screen for CNV in a nuclear family including 2 patients and a healthy control. We then validated the copy numbers of candidate genes found in the array CGH assay and other candidate genes by TaqMan real-time PCR in 360 case and control samples.Results.Ten regions from 8 chromosomes were found to have abnormal gene copies in the nuclear family, so the CNV of candidate genes (ADAM5, CSF2RA, IL3RA, and 9 other genes) were tested by TaqMan PCR. Significant copy number loss of CSF2RA (p = 0.000) and NOD2 (p = 0.005), and significant copy number gain of MEGF6 (p = 0.002) and ADAM5 (p = 0.000) were seen in patients with SAPHO compared with controls at the a = 0.05 level. There were no differences in the other 8 candidate genes between patient and control samples (p > 0.05).Conclusion.Our study established the first association between CNV in CSF2RA, NOD2, MEGF6, and ADAM5 and SAPHO syndrome. These findings may offer insight into the pathogenesis of SAPHO and provide the basis for improved diagnosis and treatment.

Impact of artificial reefs on sediment bacterial structure and function in Bohai Bay

2019 ◽  
Vol 65 (3) ◽  
pp. 191-200 ◽  
Author(s):  
Yu Wang ◽  
Jinsheng Sun ◽  
Enjun Fang ◽  
Biao Guo ◽  
Yuanyuan Dai ◽  
...  
Keyword(s):  
Artificial Reef ◽  
Control Area ◽  
Structure And Function ◽  
Artificial Reefs ◽  
Rrna Genes ◽  
Bohai Bay ◽  
Reef Area ◽  
The Future ◽  
And Function ◽  
And Control

Artificial reefs have significantly altered ecological and environmental conditions compared with natural reefs, but how these changes affect sediment bacteria structure and function is unknown. Here, we compared the structure and function of the sediment bacterial community in the artificial reef area, the future artificial reef area, and the control area in Bohai Bay by 16S rRNA genes sequencing. Our results indicated that bacteria communities in the sediment were both taxonomically and functionally different between the reef area and control area. In the artificial reef area, the α-diversity was significantly lower, whereas the β-diversity was significantly higher. Functional genes related to chemo-heterotrophy, nitrate reduction, hydrocarbon degradation, and the human pathogens and human gut were more abundant, whereas genes related to the metabolism of sulfur compounds were less abundant in the artificial reef than in the control area. The differences in bacterial communities were primarily determined by depth in the artificial reef area, and by total organic carbon in the future reef area and control area. This study provides the first overview of molecular ecology to assess the impacts of artificial reefs on the bacteria community.

scholarly journals Long Tandem Arrays of Cassandra Retroelements and Their Role in Genome Dynamics in Plants

2020 ◽  
Vol 21 (8) ◽  
pp. 2931 ◽  
Author(s):  
Ruslan Kalendar ◽  
Olga Raskina ◽  
Alexander Belyayev ◽  
Alan H. Schulman
Keyword(s):  
Copy Number ◽  
5S Rdna ◽  
5S Rrna ◽  
Rrna Genes ◽  
Gene Copy ◽  
Rrna Gene ◽  
Long Terminal Repeats ◽  
5S Rrna Genes ◽  
Pol Iii ◽  
Tandem Arrays

Retrotransposable elements are widely distributed and diverse in eukaryotes. Their copy number increases through reverse-transcription-mediated propagation, while they can be lost through recombinational processes, generating genomic rearrangements. We previously identified extensive structurally uniform retrotransposon groups in which no member contains the gag, pol, or env internal domains. Because of the lack of protein-coding capacity, these groups are non-autonomous in replication, even if transcriptionally active. The Cassandra element belongs to the non-autonomous group called terminal-repeat retrotransposons in miniature (TRIM). It carries 5S RNA sequences with conserved RNA polymerase (pol) III promoters and terminators in its long terminal repeats (LTRs). Here, we identified multiple extended tandem arrays of Cassandra retrotransposons within different plant species, including ferns. At least 12 copies of repeated LTRs (as the tandem unit) and internal domain (as a spacer), giving a pattern that resembles the cellular 5S rRNA genes, were identified. A cytogenetic analysis revealed the specific chromosomal pattern of the Cassandra retrotransposon with prominent clustering at and around 5S rDNA loci. The secondary structure of the Cassandra retroelement RNA is predicted to form super-loops, in which the two LTRs are complementary to each other and can initiate local recombination, leading to the tandem arrays of Cassandra elements. The array structures are conserved for Cassandra retroelements of different species. We speculate that recombination events similar to those of 5S rRNA genes may explain the wide variation in Cassandra copy number. Likewise, the organization of 5S rRNA gene sequences is very variable in flowering plants; part of what is taken for 5S gene copy variation may be variation in Cassandra number. The role of the Cassandra 5S sequences remains to be established.

Increased TERC gene copy number and cells in senescence in primary sclerosing cholangitis compared to colitis and control patients

Gene ◽  
2013 ◽  
Vol 529 (2) ◽  
pp. 245-249 ◽  
Author(s):  
Ido Laish ◽  
Hila Katz ◽  
Yael Sulayev ◽  
Meytal Liberman ◽  
Timna Naftali ◽  
...  
Keyword(s):  
Primary Sclerosing Cholangitis ◽  
Copy Number ◽  
Sclerosing Cholangitis ◽  
Gene Copy Number ◽  
Gene Copy ◽  
And Control
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