Search results for "Genome Size"
showing 10 items of 92 documents
Comparative Cytogenetic Analysis of Three Stylommatophoran Slugs (Mollusca, Pulmonata)
2009
system is still controversial because phylogeny and systematic relationships at the family level are poorly understood. Besides morphological studies, ribosomal RNA genes and the H3/H4 histone gene cluster (Ambruster et al., 2005; Wade et al., 2006) have also been used to resolve the relationships within this order. Recently, by comparison of primary sequence of mitochondrial and nuclear genes, Grande et al. (2004) resolved the Stylommatophora as the early split monophyletic sister group of all the other gastropod taxa. Available data on the cytogenetics of Stylommatophora are extremely poor (reviewed by Patterson, 1969, and Thiriot-Quievreux, 2003) and mostly concern the haploid (n) and/ o…
Viral Mutation Rates
2010
Accurate estimates of virus mutation rates are important to understand the evolution of the viruses and to combat them. However, methods of estimation are varied and often complex. Here, we critically review over 40 original studies and establish criteria to facilitate comparative analyses. The mutation rates of 23 viruses are presented as substitutions per nucleotide per cell infection (s/n/c) and corrected for selection bias where necessary, using a new statistical method. The resulting rates range from 108 to106 s/n/c for DNA viruses and from 106 to 104 s/n/c for RNA viruses. Similar to what has been shown previously for DNA viruses, there appears to be a negative correlation between mut…
Correlation between mutation rate and genome size in riboviruses: mutation rate of bacteriophage Qβ.
2013
Abstract Genome sizes and mutation rates covary across all domains of life. In unicellular organisms and DNA viruses, they show an inverse relationship known as Drake’s rule. However, it is still unclear whether a similar relationship exists between genome sizes and mutation rates in RNA genomes. Coronaviruses, the RNA viruses with the largest genomes (∼30 kb), encode a proofreading 3′ exonuclease that allows them to increase replication fidelity. However, it is unknown whether, conversely, the RNA viruses with the smallest genomes tend to show particularly high mutation rates. To test this, we measured the mutation rate of bacteriophage Qβ, a 4.2-kb levivirus. Amber reversion-based Luria–D…
Variability in the mutation rates of RNA viruses
2014
ABSTRACT: It is well established that RNA viruses show extremely high mutation rates, but less attention has been paid to the fact that their mutation rates also vary strongly, from 10-6 to 10-4 substitutions per nucleotide per cell infection. The causes explaining this variability are still poorly understood, but candidate factors are the viral genome size and polarity, host-specific gene expression patterns, or the intracellular environment. Differences between animal and plant viruses, or between arthropod-borne and directly transmitted viruses have also been postulated. Finally, RNA viruses may be able to regulate the rate at which new mutations spread in the population by modifying f…
Assembly methods for nanopore-based metagenomic sequencing: a comparative study
2019
ABSTRACTBackgroundMetagenomic sequencing has lead to the recovery of previously unexplored microbial genomes. In this sense, short-reads sequencing platforms often result in highly fragmented metagenomes, thus complicating downstream analyses. Third generation sequencing technologies, such as MinION, could lead to more contiguous assemblies due to their ability to generate long reads. Nevertheless, there is a lack of studies evaluating the suitability of the available assembly tools for this new type of data.FindingsWe benchmarked the ability of different short-reads and long-reads tools to assembly two different commercially available mock communities, and observed remarkable differences i…
NOR regions of polychaete worms of the genus Ophryotrocha studied by chromosome banding techniques and FISH.
2000
This article reports the results of cytogenetic analyses carried out on 10 species of polychaete worms belonging to the genus Ophryotrocha (Dorvilleidae). Nucleolar organizer regions (NORs) were characterized by Ag staining, C-banding, CMA3 staining, and ribosomal fluorescent in situ hybridization (rDNA FISH). Extensive intraspecific variation in NOR number and distribution were observed in O. costlowi, O. sp. macrovifera, O. notoglandulata, O.l. labronica, O. l. pacifica (2n = 6), O. p. puerilis, O. diadema (2n = 8), O. hartmanni, O. gracilis (2n = 10). In O. sp. robusta (2n = 10), Ag-NORs were always located on a single chromosome pair. CMA3 staining suggests a possible trend toward a GC-…
Nuclear DNA content variation inHalimiumandXolantha(Cistaceae)
2008
Abstract Chromosome numbers and nuclear DNA contents were determined in several taxa of two genera of Cistaceae, Halimium and Xolantha. The diploid chromosome number 2n = 18 is stable within the genus Halimium. In Xolantha, the diploid chromosome number 2n = 14 was confirmed in X. tuberaria, and hexaploid (2n = 36) and octoploid (2n = 48) cytotypes were found in X. guttata. DNA amounts, first reported here for these genera, were determined by flow cytometry of propidium iodide-stained nuclei. Within Halimium there is a more than twofold difference in genome size between H. calycinum (7.61 pg DNA) and H. atriplicifolium (3.66 pg DNA). Within the genus Xolantha, absolute genome sizes of 7.3 a…
Impact of barley (Hordeum vulgare L.) transgenic line H228.2A on substrate and rhizosphere microorganisms and the possibility of horizontal gene tran…
2013
Numerous investigations have been carried out to determine the impact of genetically modified plants, such as potato, maize, alfalfa and tobacco, on soil microorganisms and the results are contradictory. We applied classical microbiology methods to study quantitative changes of bacterial and fungal abundance in substrate and rhizosphere from barley (Hordeum vulgare L.) transgenic line H228.2A containing Rpg1 and bar genes, and its parent nontransgenic variety ‘Golden Promise’. In addition, molecular biology methods were used to determine, if horizontal gene transfer from barley transgenic line to soil bacteria has occurred under experimental conditions by screening bacterial genomes for the…
Mining virulence genes using metagenomics.
2011
When a bacterial genome is compared to the metagenome of an environment it inhabits, most genes recruit at high sequence identity. In free-living bacteria (for instance marine bacteria compared against the ocean metagenome) certain genomic regions are totally absent in recruitment plots, representing therefore genes unique to individual bacterial isolates. We show that these Metagenomic Islands (MIs) are also visible in bacteria living in human hosts when their genomes are compared to sequences from the human microbiome, despite the compartmentalized structure of human-related environments such as the gut. From an applied point of view, MIs of human pathogens (e.g. those identified in enter…
Whole genome sequencing of the black grouse (Tetrao tetrix): reference guided assembly suggests faster-Z and MHC evolution
2014
Background The different regions of a genome do not evolve at the same rate. For example, comparative genomic studies have suggested that the sex chromosomes and the regions harbouring the immune defence genes in the Major Histocompatability Complex (MHC) may evolve faster than other genomic regions. The advent of the next generation sequencing technologies has made it possible to study which genomic regions are evolutionary liable to change and which are static, as well as enabling an increasing number of genome studies of non-model species. However, de novo sequencing of the whole genome of an organism remains non-trivial. In this study, we present the draft genome of the black grouse, wh…