scholarly journals Human-like telomeres in Zostera marina reveal a mode of transition from the plant to the human telomeric sequences

2020 ◽  
Author(s):  
Vratislav Peska ◽  
Martin Mátl ◽  
Terezie Mandákova ◽  
Daniel Vitales ◽  
Petr Fajkus ◽  
...  
Keyword(s):  
Zostera Marina ◽  
Mechanistic Model ◽  
Genome Structure ◽  
Telomeric Sequence ◽  
Evolutionary Pathway ◽  
Telomeric Sequences ◽  
Plant Genomes ◽  
Genomic Signatures ◽  
Experimental Approaches ◽  
Template Region

AbstractA previous study describing the genome of Zostera marina, the most widespread seagrass in the Northern hemisphere, revealed some genomic signatures of adaptation to the aquatic environment. Important features related to the ‘back-to-the-sea’ reverse evolutionary pathway were found, such as the loss of stomatal genes, while other functions like an algal-like cell wall composition were acquired. Beyond these, the genome structure and organization were comparable to the majority of plant genomes sequenced, except for one striking feature that went unnoticed at that time: the presence of human-like instead of the expected plant-type telomeric sequences. By using different experimental approaches including FISH, NGS and Ba131 analysis, we have confirmed its telomeric location in the chromosomes of Z. marina. We have also identified its telomerase RNA subunit (TR), confirming the presence of the human-type telomeric sequence in the template region. Remarkably, this region was found to be very variable even in clades with a highly conserved telomeric sequence across their species. Based on this observation, we propose that alternative annealing preferences in the template borders can explain the transition between the plant and human telomeric sequences. The further identification of paralogues of TR in several plant genomes brought us to the hypothesis that plants may keep an increased ability to change their telomeric sequence. We discuss the implications of this occurrence in the evolution of telomeres while introducing a mechanistic model for the transition from the plant to the human telomeric sequences.

scholarly journals Human-like telomeres in Zostera marina reveal a mode of transition from the plant to the human telomeric sequences

2020 ◽  
Vol 71 (19) ◽  
pp. 5786-5793
Author(s):  
Vratislav Peska ◽  
Martin Mátl ◽  
Terezie Mandáková ◽  
Daniel Vitales ◽  
Petr Fajkus ◽  
...  
Keyword(s):  
Zostera Marina ◽  
Mechanistic Model ◽  
Genome Structure ◽  
Telomeric Sequence ◽  
Fish Genome ◽  
Telomeric Sequences ◽  
Plant Genomes ◽  
Genomic Signatures ◽  
Experimental Approaches ◽  
Next Generation Sequencing Ngs

Abstract A previous study describing the genome of Zostera marina, the most widespread seagrass in the Northern hemisphere, revealed some genomic signatures of adaptation to the aquatic environment such as the loss of stomatal genes, while other functions such as an algal-like cell wall composition were acquired. Beyond these, the genome structure and organization were comparable with those of the majority of plant genomes sequenced, except for one striking feature that went unnoticed at that time: the presence of human-like instead of the expected plant-type telomeric sequences. By using different experimental approaches including fluorescence in situ hybridization (FISH), genome skimming by next-generation sequencing (NGS), and analysis of non-coding transcriptome, we have confirmed its telomeric location in the chromosomes of Z. marina. We have also identified its telomerase RNA (TR) subunit, confirming the presence of the human-type telomeric sequence in the template region. Remarkably, this region was found to be very variable even in clades with a highly conserved telomeric sequence across their species. Based on this observation, we propose that alternative annealing preferences in the template borders can explain the transition between the plant and human telomeric sequences. The further identification of paralogues of TR in several plant genomes led us to the hypothesis that plants may retain an increased ability to change their telomeric sequence. We discuss the implications of this occurrence in the evolution of telomeres while introducing a mechanistic model for the transition from the plant to the human telomeric sequences.

scholarly journals Telomeric DNA sequences in beetle taxa vary with species richness

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Daniela Prušáková ◽  
Vratislav Peska ◽  
Stano Pekár ◽  
Michal Bubeník ◽  
Lukáš Čížek ◽  
...  
Keyword(s):  
Species Richness ◽  
Dna Sequences ◽  
Genome Instability ◽  
Telomeric Sequence ◽  
Dna Repeats ◽  
Telomeric Dna ◽  
Common Pattern ◽  
Telomeric Sequences ◽  
Genomic Changes ◽  
Protective Structures

AbstractTelomeres are protective structures at the ends of eukaryotic chromosomes, and disruption of their nucleoprotein composition usually results in genome instability and cell death. Telomeric DNA sequences have generally been found to be exceptionally conserved in evolution, and the most common pattern of telomeric sequences across eukaryotes is (TxAyGz)n maintained by telomerase. However, telomerase-added DNA repeats in some insect taxa frequently vary, show unusual features, and can even be absent. It has been speculated about factors that might allow frequent changes in telomere composition in Insecta. Coleoptera (beetles) is the largest of all insect orders and based on previously available data, it seemed that the telomeric sequence of beetles varies to a great extent. We performed an extensive mapping of the (TTAGG)n sequence, the ancestral telomeric sequence in Insects, across the main branches of Coleoptera. Our study indicates that the (TTAGG)n sequence has been repeatedly or completely lost in more than half of the tested beetle superfamilies. Although the exact telomeric motif in most of the (TTAGG)n-negative beetles is unknown, we found that the (TTAGG)n sequence has been replaced by two alternative telomeric motifs, the (TCAGG)n and (TTAGGG)n, in at least three superfamilies of Coleoptera. The diversity of the telomeric motifs was positively related to the species richness of taxa, regardless of the age of the taxa. The presence/absence of the (TTAGG)n sequence highly varied within the Curculionoidea, Chrysomeloidea, and Staphylinoidea, which are the three most diverse superfamilies within Metazoa. Our data supports the hypothesis that telomere dysfunctions can initiate rapid genomic changes that lead to reproductive isolation and speciation.

Characterization of two telomeric DNA processing reactions in Saccharomyces cerevisiae

1988 ◽  
Vol 8 (11) ◽  
pp. 4642-4650
Author(s):  
A W Murray ◽  
T E Claus ◽  
J W Szostak
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cell Division ◽  
Dna Polymerase ◽  
Dna Sequences ◽  
Inverted Repeat ◽  
Telomeric Sequence ◽  
Telomeric Dna ◽  
Telomeric Sequences ◽  
Telomere Elongation

We have investigated two reactions that occur on telomeric sequences introduced into Saccharomyces cerevisiae cells by transformation. The elongation reaction added repeats of the yeast telomeric sequence C1-3A to telomeric sequences at the end of linear DNA molecules. The reaction worked on the Tetrahymena telomeric sequence C4A2 and also on the simple repeat CA. The reaction was orientation specific: it occurred only when the GT-rich strand ran 5' to 3' towards the end of the molecule. Telomere elongation occurred by non-template-directed DNA synthesis rather than any type of recombination with chromosomal telomeres, because C1-3A repeats could be added to unrelated DNA sequences between the CA-rich repeats and the terminus of the transforming DNA. The elongation reaction was very efficient, and we believe that it was responsible for maintaining an average telomere length despite incomplete replication by template-directed DNA polymerase. The resolution reaction processed a head-to-head inverted repeat of telomeric sequences into two new telomeres at a frequency of 10(-2) per cell division.

scholarly journals Characterization of two telomeric DNA processing reactions in Saccharomyces cerevisiae.

1988 ◽  
Vol 8 (11) ◽  
pp. 4642-4650 ◽  
Author(s):  
A W Murray ◽  
T E Claus ◽  
J W Szostak
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cell Division ◽  
Dna Polymerase ◽  
Dna Sequences ◽  
Inverted Repeat ◽  
Telomeric Sequence ◽  
Telomeric Dna ◽  
Telomeric Sequences ◽  
Telomere Elongation

We have investigated two reactions that occur on telomeric sequences introduced into Saccharomyces cerevisiae cells by transformation. The elongation reaction added repeats of the yeast telomeric sequence C1-3A to telomeric sequences at the end of linear DNA molecules. The reaction worked on the Tetrahymena telomeric sequence C4A2 and also on the simple repeat CA. The reaction was orientation specific: it occurred only when the GT-rich strand ran 5' to 3' towards the end of the molecule. Telomere elongation occurred by non-template-directed DNA synthesis rather than any type of recombination with chromosomal telomeres, because C1-3A repeats could be added to unrelated DNA sequences between the CA-rich repeats and the terminus of the transforming DNA. The elongation reaction was very efficient, and we believe that it was responsible for maintaining an average telomere length despite incomplete replication by template-directed DNA polymerase. The resolution reaction processed a head-to-head inverted repeat of telomeric sequences into two new telomeres at a frequency of 10(-2) per cell division.

scholarly journals Organization of subtelomeric repeats in Plasmodium berghei.

1990 ◽  
Vol 10 (5) ◽  
pp. 2423-2427 ◽  
Author(s):  
E Dore ◽  
T Pace ◽  
M Ponzi ◽  
L Picci ◽  
C Frontali
Keyword(s):  
Plasmodium Berghei ◽  
Tandem Repeats ◽  
Telomeric Sequence ◽  
Chromosome Size ◽  
Base Pairs ◽  
Telomeric Sequences ◽  
Subtelomeric Repeats

Several (but not all) Plasmodium berghei chromosomes bear in the subtelomeric position a cluster of 2.3-kilobase (kb) tandem repeats. The 2.3-kb unit contains 160 base pairs of telomeric sequence. The resulting subtelomeric structure is one in which stretches of telomeric sequences are periodically spaced by a 2.1-kb reiterated sequence. This periodic organization of internal telomeric sequences might be related to chromosome-size polymorphisms involving the loss or addition of subtelomeric 2.3-kb units.

scholarly journals A mechanistic model of linkage analysis in allohexaploids

2015 ◽  
Author(s):  
Huan Li ◽  
Xuli Zhu ◽  
Ke Mao ◽  
Rongling Wu ◽  
Qin Yan
Keyword(s):  
Linkage Analysis ◽  
Mechanistic Model ◽  
Genome Structure ◽  
Real Data ◽  
Biological Research ◽  
Preferential Pairing ◽  
Modeling Framework ◽  
Ploidy Levels ◽  
The Em Algorithm ◽  
And Function

Despite their pivotal role in agriculture and biological research, polyploids, a group of organisms with more than two sets of chromosomes, are very difficult to study. Increasing studies have used high-density genetic linkage maps to investigate the genome structure and function of polyploids and to identify genes underlying polyploid traits. However, although models for linkage analysis have been well established for diploids, with some essential modifications for tetraploids, no models have been available thus far for polyploids at higher ploidy levels. The linkage analysis of polyploids typically requires knowledge about their meiotic mechanisms, depending on the origin of polyplody. Here we describe a computational modeling framework for linkage analysis in allohexaploids by integrating their preferential chromosomal-pairing meiotic feature into a mixture model setting. The framework, implemented with the EM algorithm, allows the simultaneous estimates of preferential pairing factors and the recombination fraction. We investigated statistical properties of the framework through extensive computer simulation and validated its usefulness and utility by analyzing a real data from a full-sib family of allohexaploid persimmon. Our attempt in linkage analysis of allohexaploids by incorporating their meiotic mechanism lays a foundation for allohexaploid genetic mapping and also provides a new horizon to explore allohexaploid parental kinship.

scholarly journals What can patterns of differentiation across plant genomes tell us about adaptation and speciation?

2012 ◽  
Vol 367 (1587) ◽  
pp. 364-373 ◽  
Author(s):  
Jared L. Strasburg ◽  
Natasha A. Sherman ◽  
Kevin M. Wright ◽  
Leonie C. Moyle ◽  
John H. Willis ◽  
...  
Keyword(s):  
Genome Scan ◽  
Adaptive Divergence ◽  
Reproductive Barriers ◽  
Quantitative Trait Loci Mapping ◽  
Sampling Strategies ◽  
Genome Scans ◽  
Plant Genomes ◽  
Genomic Signatures ◽  
Genomic Location ◽  
Genomic Regions

Genome scans have become a common approach to identify genomic signatures of natural selection and reproductive isolation, as well as the genomic bases of ecologically relevant phenotypes, based on patterns of polymorphism and differentiation among populations or species. Here, we review the results of studies taking genome scan approaches in plants, consider the patterns of genomic differentiation documented and their possible causes, discuss the results in light of recent models of genomic differentiation during divergent adaptation and speciation, and consider assumptions and caveats in their interpretation. We find that genomic regions of high divergence generally appear quite small in comparisons of both closely and more distantly related populations, and for the most part, these differentiated regions are spread throughout the genome rather than strongly clustered. Thus, the genome scan approach appears well-suited for identifying genomic regions or even candidate genes that underlie adaptive divergence and/or reproductive barriers. We consider other methodologies that may be used in conjunction with genome scan approaches, and suggest further developments that would be valuable. These include broader use of sequence-based markers of known genomic location, greater attention to sampling strategies to make use of parallel environmental or phenotypic transitions, more integration with approaches such as quantitative trait loci mapping and measures of gene flow across the genome, and additional theoretical and simulation work on processes related to divergent adaptation and speciation.

scholarly journals Inflammation as a Cancer Co-Initiator: New Mechanistic Model Predicts Low/Negligible Risk at Noninflammatory Carcinogen Doses

Dose-Response ◽  
2019 ◽  
Vol 17 (2) ◽  
pp. 155932581984783 ◽  
Author(s):  
Kenneth T. Bogen
Keyword(s):  
Stem Cells ◽  
Dna Adducts ◽  
Tissue Repair ◽  
Malignant Tumors ◽  
Mechanistic Model ◽  
Alternative Theory ◽  
Environmental Carcinogen ◽  
Inflammatory Agent ◽  
Experimental Approaches ◽  
Aflatoxin B

Linear-no-threshold (LNT) risk extrapolation has long been applied to estimate risks posed by low-level environmental carcinogen exposures, based on the 60-year-old multistage somatic mutation/clonal expansion (MSM) cancer theory. Recent evidence supports an alternative theory: Malignant tumors arise most efficiently from a stem cell that incurs requisite mutations and also is activated by inflammation to an epigenetically mediated and maintained state of adaptive hyperplasia (AH). This new inflammation-MSM (ISM) theory posits that inflammation-activated stem cells normally restricted to sites of injury-induced inflammation and tissue repair become uniquely susceptible to efficient carcinogenesis if normal post-inflammation AH termination is blocked by mutation. This theory posits that inflammation generally thus co-initiates cancer and transiently amplifies activated stem cells, implying that MSM theory (eg, the 2-stage stochastic “Moolgavkar, Venzon, Knudson [MVK]” model) is incomplete. Because inflammation dose–response typically is not LNT, the ISM theory predicts this is also true for most (perhaps all) carcinogens. The ISM (but not the MVK) model is shown to be consistent with recent data showing ∼100% carcinoma incidence (but not DNA adducts) in livers of rats exposed to aflatoxin B1 and was eliminated when that dose was co-administered with a highly potent anti-inflammatory agent. Experimental approaches to test ISM theory more robustly are discussed.

scholarly journals Optimization study of the catalytic activity of DNAzymes based on telomeric G-quadruplexes

2012 ◽  
Vol 10 (2) ◽  
pp. 368-372 ◽  
Author(s):  
Joanna Kosman ◽  
Bernard Juskowiak
Keyword(s):  
Catalytic Activity ◽  
Thermal Treatment ◽  
Metal Cation ◽  
Telomeric Sequence ◽  
Telomeric Sequences ◽  
Optimization Study ◽  
Brij 58 ◽  
Activity Measurements ◽  
G Quadruplex ◽  
Colorimetric Indicator

AbstractOptimization studies of the procedure for peroxidase activity measurements with DNAzymes based on telomeric sequences and colorimetric indicator reactions are reported. Effect of metal cation, nature and concentration of surfactant, as well as thermal treatment of G-quadruplex sample are investigated. Nature of metal cation exhibited modest influence on the system performance. Great improvement of enzymatic activity of the telomeric quadruplexes in the presence of Brij 58 surfactant was observed. Further improvement of catalytic activity of the system based on human telomeric sequence was attained by applying a thermal treatment (heating/rapid cooling) procedure to prepare G-quadruplex/hemin complexes.

scholarly journals Genomic signatures and insights into host niche adaptation of the entomopathogenic fungus Metarhizium humberi

2021 ◽  
Author(s):  
Natasha Sant′Anna Iwanicki ◽  
Ana Beatriz Riguetti Zanardo Botelho ◽  
Ingeborg Klingen ◽  
Italo Delalibera Júnior ◽  
Simeon Rossmann ◽  
...  
Keyword(s):  
Biological Control ◽  
Insect Pests ◽  
Repetitive Sequences ◽  
Genome Structure ◽  
Point Mutations ◽  
Broad Host Range ◽  
Agricultural Pests ◽  
Genomic Signatures ◽  
Host Interaction ◽  
Niche Adaptation

Abstract The genus Metarhizium is composed of species used in biological control programes of agricultural pests worldwide. This genus includes common fungal pathogen of many insects and mites and endophytes that can increase plant growth. Metarhizium humberi was recently described as a new species. This species is highly virulent against some insect pests and promotes growth in sugarcane, strawberry, and soybean crops. In the present study, we sequenced the genome of M. humberi, isolate ESALQ1638, and performed a functional analysis to determine its genomic signatures and highlight the genes and biological processes associated with its lifestyle. The genome annotation predicted 10633 genes in M. humberi, of which 92.0% are assigned putative functions, and ∼17% of the genome was annotated as repetitive sequences. We found that 18.5% of the M. humberi genome is similar to experimentally validated proteins associated with pathogen-host interaction. Compared to the genomes of eight Metarhizium species, the M. humberi ESALQ1638 genome revealed some unique traits that stood out, e.g.,, more genes functionally annotated as polyketide synthases (PKs), overrepresended GO-terms associated to transport of ions, organic and amino acid, a higher percentage of repetitive elements, and higher levels of RIP-induced point mutations. The M. humberi genome will serve as a resource for promoting studies on genome structure and evolution that can contribute to research on biological control and plant biostimulation. Thus, the genomic data supported the broad host range of this species within the generalist PARB clade and suggested that M. humberi ESALQ1638 might be particularly good at producing secondary metabolites and might be more efficient in transporting amino acids an organics compounds.

Sign in / Sign up

Export Citation Format

Share Document