Tatajuba ― Exploring the distribution of homopolymer tracts

Length variation of homopolymeric tracts, which induces phase variation, is known to regulate gene expression leading to phenotypic variation in a wide range of bacterial species. There is no specialised bioinformatics software which can, at scale, exhaustively explore and describe these features from sequencing data. Identifying these is non-trivial as sequencing and bioinformatics methods are prone to introducing artefacts when presented with homopolymeric tracts due to the decreased base diversity. We present tatajuba, which can automatically identify potential homopolymeric tracts and their putative phenotypic impact, allowing for rapid investigation. We use it to detect all tracts in two separate datasets, one of Campylobacter jejuni and one of three Bordetella species, and to highlight those tracts that are polymorphic across samples. With this we confirm homopolymer tract variation with phenotypic impact found in previous studies and additionally find many more with potential variability. The software is written in C and is available under the open source license GNU GPL version 3 from https://github.com/quadram-institute-bioscience/tatajuba.

DNA polymorphism of dogs (Canis familiaris) and its application. IV. mtDNA

The structural organization of the mitochondrial genome of dogs is briefly considered, paying more attention to its variable areas, including the control region and its hypervariable parts HV1 and HV2, as well as a block of tandem decameric repeats and a homopolymer tract of cytosines and thymines. It is noted that the detected polymorphism of mitogenomes forming the clades with haplotypes, with few exceptions, are practically unrelated to dog breeds and their geographical place of residence. In general, the polymorphism of the mitochondrial DNA of dogs does not allow unambiguously identifying a specific individual and in criminalistics, in most cases, it is possible with one or another probability, depending on the variable areas taken into analysis, only to exclude suspected dogs that could lead to their owners from further investigation. Moreover, this requires the creation of population databases of canine mitogenomes, which can be used to calculate the probability of coincidence of haplotypes. Examples of individual cases of investigation of crimes in which polymorphism of DNA of dogs were used, including those that ended with a conviction, are given. Attention is drawn to the need for wider introduction into forensic practice of usage of canine DNA, which can obtained from traces left by dogs mainly in the form of saliva or wool (individual hairs).

Genomic and Genetic Analysis of Bordetella Bacteriophages Encoding Reverse Transcriptase-Mediated Tropism-Switching Cassettes

ABSTRACT Liu et al. recently described a group of related temperate bacteriophages that infect Bordetella subspecies and undergo a unique template-dependent, reverse transcriptase-mediated tropism switching phenomenon (Liu et al., Science 295: 2091-2094, 2002). Tropism switching results from the introduction of single nucleotide substitutions at defined locations in the VR1 (variable region 1) segment of the mtd (major tropism determinant) gene, which determines specificity for receptors on host bacteria. In this report, we describe the complete nucleotide sequences of the 42.5- to 42.7-kb double-stranded DNA genomes of three related phage isolates and characterize two additional regions of variability. Forty-nine coding sequences were identified. Of these coding sequences, bbp36 contained VR2 (variable region 2), which is highly dynamic and consists of a variable number of identical 19-bp repeats separated by one of three 5-bp spacers, and bpm encodes a DNA adenine methylase with unusual site specificity and a homopolymer tract that functions as a hotspot for frameshift mutations. Morphological and sequence analysis suggests that these Bordetella phage are genetic hybrids of P22 and T7 family genomes, lending further support to the idea that regions encoding protein domains, single genes, or blocks of genes are readily exchanged between bacterial and phage genomes. Bordetella bacteriophages are capable of transducing genetic markers in vitro, and by using animal models, we demonstrated that lysogenic conversion can take place in the mouse respiratory tract during infection.