Genetic Structures Of Sand Fly (Diptera: Psychodidae) Populations In A Leishmaniasis Endemic Region Of Turkey

The object of this study was to determine the genetic structures of three vector species, Phlebotomus tobbi, Phlebotomus papatasi, and Phlebotomus sergenti, in the Cukurova Region of Turkey, an endemic focus of cutaneous leishmaniasis. The genetic diversity indices, neutrality tests and hierarchical analysis of molecular variance (AMOVA) were performed using partial sequences of ITS2 and cytochrome b gene regions. In all species, within population genetic variation was higher than between population variation for ITS2 gene region. Fst values were low and non-significant for P. sergenti, and were higher for P. papatasi and P. tobbi indicating a weak structuring between populations. AMOVA tests suggest any substantial isolation between populations within species. AMOVA analysis of cyt b gene region revealed significant genetic structuring between populations for P. papatasi and P. sergenti. Fst values were relatively high and significant for these species indicating a certain degree of isolation between populations. However, in P. tobbi, any significant population genetic structuring was detected. Tajima's D and Fu's Fs values were negative and significant in all three species might be indicating a demographic expansion.Wo

The Rate And Spectrum Of Spontaneous Mutations In Mycobacterium Smegmatis, A Bacterium Naturally Devoid Of The Postreplicative Mismatch Repair Pathway

Mycobacterium smegmatis is a bacterium that is naturally devoid of known postreplicative DNA mismatch repair (MMR) homologs, mutS and mutL, providing an opportunity to investigate how the mutation rate and spectrum has evolved in the absence of a highly conserved primary repair pathway. Mutation accumulation experiments of M. smegmatis yielded a base-substitution mutation rate of 5.27 × 10−10 per site per generation, or 0.0036 per genome per generation, which is surprisingly similar to the mutation rate in MMR-functional unicellular organisms. Transitions were found more frequently than transversions, with the A:T→G:C transition rate significantly higher than the G:C→A:T transition rate, opposite to what is observed in most studied bacteria. We also found that the transition-mutation rate of M. smegmatis is significantly lower than that of other naturally MMR-devoid or MMR-knockout organisms. Two possible candidates that could be responsible for maintaining high DNA fidelity in this MMR-deficient organism are the ancestral-like DNA polymerase DnaE1, which contains a highly efficient DNA proofreading histidinol phosphatase (PHP) domain, and/or the existence of a uracil-DNA glycosylase B (UdgB) homolog that might protect the GC-rich M. smegmatis genome against DNA damage arising from oxidation or deamination. Our results suggest that M. smegmatis has a noncanonical Dam (DNA adenine methylase) methylation system, with target motifs differing from those previously reported. The mutation features of M. smegmatis provide further evidence that genomes harbor alternative routes for improving replication fidelity, even in the absence of major repair pathways.PubMedWoSScopu

Low Base-Substitution Mutation Rate but High Rate of Slippage Mutations in the Sequence Repeat-Rich Genome of Dictyostelium discoideum

We describe the rate and spectrum of spontaneous mutations for the social amoeba Dictyostelium discoideum, a key model organism in molecular, cellular, evolutionary and developmental biology. Whole-genome sequencing of 37 mutation accumulation lines of D. discoideum after an average of 1,500 cell divisions yields a base-substitution mutation rate of 2.47 × 10−11 per site per generation, substantially lower than that of most eukaryotic and prokaryotic organisms, and of the same order of magnitude as in the ciliates Paramecium tetraurelia and Tetrahymena thermophila. Known for its high genomic AT content and abundance of simple sequence repeats, we observe that base-substitution mutations in D. discoideum are highly A/T biased. This bias likely contributes both to the high genomic AT content and to the formation of simple sequence repeats in the AT-rich genome of Dictyostelium discoideum. In contrast to the situation in other surveyed unicellular eukaryotes, indel rates far exceed the base-substitution mutation rate in this organism with a high proportion of 3n indels, particularly in regions without simple sequence repeats. Like ciliates, D. discoideum has a large effective population size, reducing the power of random genetic drift, magnifying the effect of selection on replication fidelity, in principle allowing D. discoideum to evolve an extremely low base-substitution mutation rate

Background Mutational Features of the Radiation-Resistant Bacterium Deinococcus Radiodurans

Deinococcus bacteria are extremely resistant to radiation, oxidation, and desiccation. Resilience to these factors has been suggested to be due to enhanced damage prevention and repair mechanisms, as well as highly efficient antioxidant protection systems. Here, using mutation-accumulation experiments, we find that the GC-rich Deinococcus radiodurans has an overall background genomicmutation rate similar to that of E. coli, but differs inmutation spectrum, with the A/T to G/C mutation rate (based on a total count of 88 A: T -> G: C transitions and 82 A: T -> C: G transversions) per site per generation higher than that in the other direction (based on a total count of 157 G: C -> A: T transitions and 33 G: C -> T: A transversions). We propose that this unique spectrumis shaped mainly by the abundant uracil DNA glycosylases reducing G: C -> A: T transitions, adenine methylation elevating A: T -> C: G transversions, and absence of cytosine methylation decreasing G: C -> A: T transitions. As opposed to the greater than 100x elevation of the mutation rate in MMR- (DNA Mismatch Repair deficient) strains of most other organisms, MMR- D. radiodurans only exhibits a 4-fold elevation, raising the possibility that other DNA repair mechanisms compensate for a relatively low-efficiency DNA MMR pathway. As D. radiodurans has plentiful insertion sequence (IS) elements in the genome and the activities of IS elements are rarely directly explored, we also estimated the insertion (transposition) rate of the IS elements to be 2.50 x 10(-3) per genome per generation in the wild-type strain; knocking out MMR did not elevate the IS element insertion rate in this organism.WoSScopu

Visualizing codon usage within and across genomes : concepts and tools

Cost and time of genome sequencing have plummeted over the last decade. This leads to explosive growth of genetic databases and development of novel sequencing-based approaches to study various biological phenomena. The database growth was particularly beneficial for investigation of protein-coding sequences at the codon level, requiring the access to large sets of related genomes. Such studies are expected to illuminate biological forces that shape primary structure of coding sequences and predict their evolutionary trajectories more precisely. In addition to fundamental interest, codon usage studies are of ample practical value, for example, in drug discovery and genomic medicine areas. Nevertheless, the depth of our understanding of codon-related issues is currently shallower as compared to what we know about nucleotide and amino acid sequences. Besides the lack of adequate datasets in the early days of molecular biology, codon usage studies, in our opinion, suffer from underdevelopment of easy-to-use tools to analyze and visualize how codon sequence changes along the gene and across the homologous genes in course of evolution. In this review, we aim to describe main areas of codon usage studies with an emphasis on the tools that allow visual interpretation of the data. We discuss underlying principles of different approaches, what kind of statistics lends confidence in their results and what has to be done to further boost the field of codon usage research