Simple sequence repeats (SSRs) in DNA sequences are composed of tandem iterations of short oligonucleotides and may have functional and/or structural properties that distinguish them from general DNA sequences. They are variable in length because of slip-strand mutations and may also affect local structure of the DNA molecule or the encoded proteins. Long SSRs (LSSRs) are common in eukaryotes but rare in most prokaryotes. In pathogens, SSRs can enhance antigenic variance of the pathogen population in a strategy that counteracts the host immune response. We analyze representations of SSRs in >300 prokaryotic genomes and report significant differences among different prokaryotes as well as among different types of SSRs. LSSRs composed of short oligonucleotides (1–4 bp length, designated LSSR ^1–4 ) are often found in host-adapted pathogens with reduced genomes that are not known to readily survive in a natural environment outside the host. In contrast, LSSRs composed of longer oligonucleotides (5–11 bp length, designated LSSR ^5–11 ) are found mostly in nonpathogens and opportunistic pathogens with large genomes. Comparisons among SSRs of different lengths suggest that LSSR ^1–4 are likely maintained by selection. This is consistent with the established role of some LSSR ^1–4 in enhancing antigenic variance. By contrast, abundance of LSSR ^5–11 in some genomes may reflect the SSRs' general tendency to expand rather than their specific role in the organisms' physiology. Differences among genomes in terms of SSR representations and their possible interpretations are discussed.

Tn-seq is a high throughput technique for analysis of transposon mutant libraries. Tn-seq Explorer was developed as a convenient and easy-to-use package of tools for exploration of the Tn-seq data. In a typical application, the user will have obtained a collection of sequence reads adjacent to transposon insertions in a reference genome. The reads are first aligned to the reference genome using one of the tools available for this task. Tn-seq Explorer reads the alignment and the gene annotation, and provides the user with a set of tools to investigate the data and identify possibly essential or advantageous genes as those that contain significantly low counts of transposon insertions. Emphasis is placed on providing flexibility in selecting parameters and methodology most appropriate for each particular dataset. Tn-seq Explorer is written in Java as a menu-driven, stand-alone application. It was tested on Windows, Mac OS, and Linux operating systems. The source code is distributed under the terms of GNU General Public License. The program and the source code are available for download at http://www.cmbl.uga.edu/downloads/programs/Tn_seq_Explorer/ and https://github.com/sina-cb/Tn-seqExplorer.

Summary: We present a new tool for finding local sequence patterns in long DNA sequences. The program, Pattern Locator, uses an intuitive syntax for pattern description, and provides more flexibility than existing programs by allowing combinations of specific nucleotide sequences, direct and inverted repeats, variable length tandem repeats of subpatterns, and a specified number of errors in any part of the pattern. Availability: The program is available for download and as a web service accessible through a CGI interface at . The source code is written in C and distributed under the GNU General Public License. Contact:mrazek@uga.edu

Simple sequence repeats (SSRs) composed of extensive tandem iterations of a single nucleotide or a short oligonucleotide are rare in most bacterial genomes, but they are common among Mycoplasma. Some of these repeats act as contingency loci in association with families of surface antigens. By contraction or expansion during replication, these SSRs increase genetic variance of the population and facilitate avoidance of the immune response of the host. Occurrence and distribution of SSRs are analyzed in complete genomes of 11 Mycoplasma and 3 related Mollicutes in order to gain insights into functional and evolutionary diversity of the SSRs in Mycoplasma. The results revealed an unexpected variety of SSRs with respect to their distribution and composition and suggest that it is unlikely that all SSRs function as contingency loci or recombination hot spots. Various types of SSRs are most abundant in Mycoplasma hyopneumoniae, whereas Mycoplasma penetrans, Mycoplasma mobile, and Mycoplasma synoviae do not contain unusually long SSRs. Mycoplasma hyopneumoniae and Mycoplasma pulmonis feature abundant short adenine and thymine runs periodically spaced at 11 and 12 bp, respectively, which likely affect the supercoiling propensities of the DNA molecule. Physiological roles of long adenine and thymine runs in M. hyopneumoniae appear independent of location upstream or downstream of genes, unlike contingency loci that are typically located in protein-coding regions or upstream regulatory regions. Comparisons among 3 M. hyopneumoniae strains suggest that the adenine and thymine runs are rarely involved in genome rearrangements. The results indicate that the SSRs in the Mycoplasma genomes play diverse roles, including modulating gene expression as contingency loci, facilitating genome rearrangements via recombination, affecting protein structure and possibly protein–protein interactions, and contributing to the organization of the DNA molecule in the cell.

The concept of genome signature allows sequence comparisons without alignment. It relies on the premise that oligonucleotide compositions of DNA segments from the same or closely related genomes tend to be more similar than those from distantly related genomes. This concept has been used in detection of lateral gene transfer, phylogenetic classification of metagenome sequences (binning), and in studies of evolution of viruses and plasmids. The goal of this work is to explore limitations of genome signature in phylogenetic classification of DNA sequences and to identify formal representations of genome signature that expose best the phylogenetic relationships among prokaryotes. We found that genome signatures that best represent phylogenetic relationships are those normalized to factor out differences in G + C content and utilizing the standard A-C-G-T alphabet or the degenerate R-Y (purine–pyrimidine) alphabet. The main limitation of all genome signature representations tested is lack of divergence among some distantly related species. “Crowding” of the genome signature space and absence of molecular clock likely contribute to this phenomenon. We introduce “periodicity signatures”—formal representations of periodic sequence patterns related to DNA curvature—which can discriminate between bacterial and archaeal DNA sequences. Interestingly, archaea of the order Halobacteriaceae have periodic signatures similar to bacteria, possibly due to their early divergence from other archaea, extensive lateral gene transfer, or due to their adaptation to high salt environments. Our results have practical implications for development and application of genome signature–based methods for analysis and classification of DNA sequences.