scholarly journals Genome Reduction in a Hemiclonal Frog Rana esculenta From Radioactively Contaminated Areas

Genetics ◽  
1999 ◽  
Vol 151 (3) ◽  
pp. 1123-1125
Author(s):  
Alexander E Vinogradov ◽  
Alexander T Chubinishvili
Keyword(s):  
Genome Size ◽  
Dna Sequences ◽  
Biological Significance ◽  
Background Level ◽  
Rana Esculenta ◽  
Genome Reduction ◽  
Dna Flow Cytometry ◽  
Genetic Damage ◽  
Chernobyl Fallout ◽  
Radiation Level

Abstract A decrease in genome size was found in the hemiclonal hybridogenetic frog Rana esculenta (R. ridibunda × R. lessonae) from areas of radioactive contamination that resulted from the Chernobyl fallout. This genome reduction was of up to 4% and correlated with the background level of gamma-radiation (linear regression corresponded on average to -0.4% per doubling of radiation level). No change in genome size was observed in the coexisting parental species R. lessonae. There was no correlation between genome size and body mass in R. esculenta froglets, which have metamorphosed in the year of the study. The hemiclonal forms may become a suitable object for study on biological significance of individual DNA sequences (and of genome size as a whole) because mutant animals with deletions in a specified genome can arise after a low radiation dose. The proneness to genetic damage makes such forms also a prospective bioindicator of radioactive (and possibly other mutagenic) pollution with the effects of genetic damage conveniently and rapidly monitored by DNA flow cytometry.

scholarly journals Descending Dysploidy and Bidirectional Changes in Genome Size Accompanied Crepis (Asteraceae) Evolution

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1436
Author(s):  
Magdalena Senderowicz ◽  
Teresa Nowak ◽  
Magdalena Rojek-Jelonek ◽  
Maciej Bisaga ◽  
Laszlo Papp ◽  
...  
Keyword(s):  
Genome Size ◽  
Dna Sequences ◽  
Chromosome Numbers ◽  
Karyotype Evolution ◽  
Base Number ◽  
Ancestral State ◽  
Ancestral Genome ◽  
Independent Events ◽  
Karyotype Asymmetry ◽  
Major Direction

The evolution of the karyotype and genome size was examined in species of Crepis sensu lato. The phylogenetic relationships, inferred from the plastid and nrITS DNA sequences, were used as a framework to infer the patterns of karyotype evolution. Five different base chromosome numbers (x = 3, 4, 5, 6, and 11) were observed. A phylogenetic analysis of the evolution of the chromosome numbers allowed the inference of x = 6 as the ancestral state and the descending dysploidy as the major direction of the chromosome base number evolution. The derived base chromosome numbers (x = 5, 4, and 3) were found to have originated independently and recurrently in the different lineages of the genus. A few independent events of increases in karyotype asymmetry were inferred to have accompanied the karyotype evolution in Crepis. The genome sizes of 33 Crepis species differed seven-fold and the ancestral genome size was reconstructed to be 1 C = 3.44 pg. Both decreases and increases in the genome size were inferred to have occurred within and between the lineages. The data suggest that, in addition to dysploidy, the amplification/elimination of various repetitive DNAs was likely involved in the genome and taxa differentiation in the genus.

scholarly journals Structures and stability of simple DNA repeats from bacteria

2020 ◽  
Vol 477 (2) ◽  
pp. 325-339 ◽  
Author(s):  
Vaclav Brazda ◽  
Miroslav Fojta ◽  
Richard P. Bowater
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Genetic Instability ◽  
Repetitive Sequences ◽  
Biological Significance ◽  
Human Diseases ◽  
Repetitive Dna Sequences ◽  
Dna Repeats ◽  
Diverse Range ◽  
Dna Structures

DNA is a fundamentally important molecule for all cellular organisms due to its biological role as the store of hereditary, genetic information. On the one hand, genomic DNA is very stable, both in chemical and biological contexts, and this assists its genetic functions. On the other hand, it is also a dynamic molecule, and constant changes in its structure and sequence drive many biological processes, including adaptation and evolution of organisms. DNA genomes contain significant amounts of repetitive sequences, which have divergent functions in the complex processes that involve DNA, including replication, recombination, repair, and transcription. Through their involvement in these processes, repetitive DNA sequences influence the genetic instability and evolution of DNA molecules and they are located non-randomly in all genomes. Mechanisms that influence such genetic instability have been studied in many organisms, including within human genomes where they are linked to various human diseases. Here, we review our understanding of short, simple DNA repeats across a diverse range of bacteria, comparing the prevalence of repetitive DNA sequences in different genomes. We describe the range of DNA structures that have been observed in such repeats, focusing on their propensity to form local, non-B-DNA structures. Finally, we discuss the biological significance of such unusual DNA structures and relate this to studies where the impacts of DNA metabolism on genetic stability are linked to human diseases. Overall, we show that simple DNA repeats in bacteria serve as excellent and tractable experimental models for biochemical studies of their cellular functions and influences.

Genome elimination in diploid and triploid Rana esculenta males: cytological evidence from DNA flow cytometry

Genome ◽  
1990 ◽  
Vol 33 (5) ◽  
pp. 619-627 ◽  
Author(s):  
A. E. Vinogradov ◽  
L. J. Borkin ◽  
R. Günther ◽  
J. M. Rosanov
Keyword(s):  
Flow Cytometry ◽  
Genetic Material ◽  
Rana Esculenta ◽  
Mendelian Inheritance ◽  
Study Data ◽  
Dna Flow Cytometry ◽  
Cytological Evidence ◽  
Water Frog ◽  
A Genome ◽  
Rana Lessonae

Cytological aspects of hemiclonal (meroclonal) inheritance in diploid and triploid males of the hybridogenetic frog Rana esculenta (Rana ridibunda × Rana lessonae) have been studied by DNA flow cytometry. The fact that the R. ridibunda genome contains 16% more DNA than the R. lessonae genome provides the ability to discern cells containing genomes of any species from the water-frog complex under study. Data are presented showing that elimination of the R. ridibunda genome occurs in hybridogenetic males from certain populations. In triploid males, the cytogenetic mechanism of hemiclonal inheritance is simpler than in diploids: after the elimination of a genome (always the genome in the minority in the triploid set; "homogenizing elimination"), no compensatory duplication of the remaining genetic material is necessary, as it is in diploids. The process of elimination can be visualized in triploid males by using DNA flow cytometry to identify cells in the special phase of the spermatogonial cell cycle that we termed the E phase.Key words: Rana esculenta, genome elimination, non-Mendelian inheritance, spermatogenesis, DNA flow cytometry.

scholarly journals Whole-Genome Sequence of a Pantoea sp. Strain Isolated from an Olive (Olea europaea L.) Knot

2019 ◽  
Vol 8 (42) ◽  
Author(s):  
Gabriela Vuletin Selak ◽  
Marina Raboteg ◽  
Audrey Dubost ◽  
Danis Abrouk ◽  
Katja Žanić ◽  
...  
Keyword(s):  
Genome Size ◽  
Genome Sequence ◽  
Dna Sequences ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Trna Genes ◽  
Whole Genome ◽  
Ribosomal Operon ◽  
Adriatic Coast ◽  
Olive Trees

Here, we present the total genome sequence of Pantoea sp. strain paga, a plant-associated bacterium isolated from knots present on olive trees grown on the Adriatic Coast. The genome size of Pantoea sp. paga is 5.08 Mb, with a G+C content of 54%. The genome contains 4,776 predicted coding DNA sequences (CDSs), including 70 tRNA genes and 1 ribosomal operon. Obtained genome sequence data will provide insight on the physiology, ecology, and evolution of Pantoea spp.

scholarly journals Draft Genome Sequence of the Extremely Desiccation-Tolerant Cyanobacterium Gloeocapsopsis sp. Strain AAB1

2018 ◽  
Vol 6 (17) ◽  
Author(s):  
Fernando Puente-Sánchez ◽  
Carlos González-Silva ◽  
Victor Parro ◽  
Javier Tamames ◽  
Armando Azua-Bustos
Keyword(s):  
Genome Size ◽  
Genome Sequence ◽  
Dna Sequences ◽  
Draft Genome ◽  
Atacama Desert ◽  
Draft Genome Sequence ◽  
Rrna Genes ◽  
Trna Genes ◽  
Content Type

ABSTRACT Gloeocapsopsis sp. strain AAB1 is an extremely desiccation-tolerant cyanobacterium isolated from translucent quartz stones from the Atacama Desert (Chile). Here, we report its draft genome sequence, which consists of 137 contigs with an ∼5.4-Mb genome size. The annotation revealed 5,641 coding DNA sequences, 38 tRNA genes, and 5 rRNA genes.

scholarly journals Evolutionary Changes of the flhDC Flagellar Master Operon in Shigella Strains

2005 ◽  
Vol 187 (12) ◽  
pp. 4295-4302 ◽  
Author(s):  
Akira Tominaga ◽  
Ruiting Lan ◽  
Peter R. Reeves
Keyword(s):  
Dna Sequences ◽  
Gene Clusters ◽  
Housekeeping Gene ◽  
Genetic Damage ◽  
Flagellar Motility ◽  
Genetic Changes ◽  
Mutational Change ◽  
E Coli ◽  
Evolutionary Changes ◽  
Cluster 2

ABSTRACT Shigella strains are nonmotile. The master operon of flagellar synthesis, flhDC, was analyzed for genetic damage in 46 Shigella strains representing all known serotypes. In 11 strains (B1, B3, B6, B8, B10, B18, D5, F1B, D10, F3A, and F3C) the flhDC operon was completely deleted. PCR and sequence analysis of the flhDC region of the remaining 35 strains revealed many insertions or deletions associated with insertion sequences, and the majority of the strains were found to be defective in their flhDC genes. As these genes also play a role in regulation of nonflagellar genes, the loss may have other consequences or be driven by selection pressures other than those against flagellar motility. It has been suggested that Shigella strains fall mostly into three clusters within Escherichia coli, with five outlier strains, four of which are also within E. coli (G. M. Pupo, R. Lan, and P. R. Reeves, Proc. Natl. Acad. Sci. USA 97:10567-10572, 2000). The distribution of genetic changes in the flhDC region correlated very well with the three clusters and outlier strains found using housekeeping gene DNA sequences, enabling us to follow the sequence of mutational change in the flhDC locus. Two cluster 2 strains were found to have unique flhDC sequences, which are most probably due to recombination during the exchange of the adjacent O-antigen gene clusters.

scholarly journals On the concept of biological function, junk DNA and the gospels of ENCODE and Grauret al.

2013 ◽  
Author(s):  
Claudiu I Bandea
Keyword(s):  
Human Genome ◽  
Genome Size ◽  
Dna Sequences ◽  
Insertional Mutagenesis ◽  
Defense Mechanism ◽  
Biological Function ◽  
Insertion Mutagenesis ◽  
Protective Mechanism ◽  
Junk Dna ◽  
Selective Forces

In a recent article entitled“On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE”, Grauret al.dismantle ENCODE’s evidence and conclusion that 80% of the human genome is functional. However, the article by Grauret al.contains assumptions and statements that are questionable. Primarily, the authors limit their evaluation of DNA’s biological functions to informational roles, sidestepping putative non-informational functions. Here, I bring forward an old hypothesis on the evolution of genome size and on the role of so called ‘junk DNA’ (jDNA), which might explain C-value enigma. According to this hypothesis, the jDNA functions as a defense mechanism against insertion mutagenesis by endogenous and exogenous inserting elements such as retroviruses, thereby protecting informational DNA sequences from inactivation or alteration of their expression. Notably, this model couples the mechanisms and the selective forces responsible for the origin of jDNA with its putative protective biological function, which represents a classic case of‘fighting fire with fire.’One of the key tenets of this theory is that in humans and many other species, jDNAs serves as a protective mechanism against insertional oncogenic transformation. As an adaptive defense mechanism, the amount of protective DNA varies from one species to another based on the rate of its origin, insertional mutagenesis activity, and evolutionary constraints on genome size.

scholarly journals Genome Sequence of Pseudomonas sp. Strain ST1, Isolated from Olive (Olea europaea L.) Knot Galls in Croatia

2019 ◽  
Vol 8 (46) ◽  
Author(s):  
Gabriela Vuletin Selak ◽  
Marina Raboteg ◽  
Pascale Fournier ◽  
Audrey Dubost ◽  
Danis Abrouk ◽  
...  
Keyword(s):  
Genome Size ◽  
Genome Sequence ◽  
Dna Sequences ◽  
Olea Europaea ◽  
Rrna Genes ◽  
Pseudomonas Sp ◽  
Olea Europaea L ◽  
Olea Europaéa

We report the genome sequence of a Pseudomonas sp. strain isolated from olive knot galls. The genome size is 6.101 Mbp with a G+C content of 58%. A total of 6,137 coding DNA sequences (CDS) were predicted, including 52 tRNA and 4 rRNA genes.

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