Species-specific typing of DNA based on palindrome frequency patterns

DNA Materials Assembled from One DNA Strand

Due to the specific base-pairing recognition, clear nanostructure, programmable sequence and responsiveness of the DNA molecule, DNA materials have attracted extensive attention and been widely used in controlled release, drug delivery and tissue engineering. Generally, the strategies for preparing DNA materials are based on the assembly of multiple DNA strands. The construction of DNA materials using only one DNA strand can not only save time and cost, but also avoid defects in final assemblies generated by the inaccuracy of DNA ratios, which potentially promote the large-scale production and practical application of DNA materials. In order to use one DNA strand to form assemblies, the sequences have to be palindromes with lengths that need to be controlled carefully. In this review, we introduced the development of DNA assembly and mainly summarized current reported materials formed by one DNA strand. We also discussed the principle for the construction of DNA materials using one DNA strand.

Palindromic Vectors, Symmetropy and Symmentropy as Symmetry Descriptors of Binary Data

Today, the palindromic analysis of biological sequences, based exclusively on the study of "mirror" symmetry properties, is almost unavoidable. However, other types of symmetry, such as those present in friezes, could allow us to analyze binary sequences from another point of view. New tools, such as symmetropy and symmentropy, based on new types of palindromes allow us to discriminate binarized 1/f noise sequences better than Lempel-Ziv complexity. These new palindromes with new types of symmetry also allow for better discrimination of binarized DNA sequences. A relative error of 6% of symmetropy is obtained from the HUMHBB and YEAST1 DNA sequences. A factor of 4 between the slopes obtained from the linear fits of the local symmentropies for the two DNA sequences shows the discriminative capacity of the local symmentropy. Moreover, it is highlighted that a certain number of these new palindromes of sizes greater than 30 bits are more discriminating than those of smaller sizes assimilated to those from an independent and identically distributed random variable.

Role of Restriction-Modification Systems in Prokaryotic Evolution and Ecology

Restriction-modification (R-M) systems are able to methylate or cleave DNA depending on methylation status of their recognition site. It allows them to protect bacterial cells from invasion by foreign DNA. Comparative analysis of a large number of available bacterial genomes and methylomes clearly demonstrates that the role of R-M systems in bacteria is wider than only defense. R-M systems maintain heterogeneity of a bacterial population and are involved in adaptation of bacteria to change in their environmental conditions. R-M systems can be essential for host colonization by pathogenic bacteria. Phase variation and intragenomic recombinations are sources of the fast evolution of the specificity of R-M systems. This review focuses on the influence of R-M systems on evolution and ecology of prokaryotes.

A base composition analysis of natural patterns for the preprocessing of metagenome sequences

Background

On the pretext that sequence reads and contigs often exhibit the same kinds of base usage that is also observed in the sequences from which they are derived, we offer a base composition analysis tool. Our tool uses these natural patterns to determine relatedness across sequence data. We introduce spectrum sets (sets of motifs) which are permutations of bacterial restriction sites and the base composition analysis framework to measure their proportional content in sequence data. We suggest that this framework will increase the efficiency during the pre-processing stages of metagenome sequencing and assembly projects.

Results

Our method is able to differentiate organisms and their reads or contigs. The framework shows how to successfully determine the relatedness between these reads or contigs by comparison of base composition. In particular, we show that two types of organismal-sequence data are fundamentally different by analyzing their spectrum set motif proportions (coverage). By the application of one of the four possible spectrum sets, encompassing all known restriction sites, we provide the evidence to claim that each set has a different ability to differentiate sequence data. Furthermore, we show that the spectrum set selection having relevance to one organism, but not to the others of the data set, will greatly improve performance of sequence differentiation even if the fragment size of the read, contig or sequence is not lengthy.

Conclusions

We show the proof of concept of our method by its application to ten trials of two or three freshly selected sequence fragments (reads and contigs) for each experiment across the six organisms of our set. Here we describe a novel and computationally effective pre-processing step for metagenome sequencing and assembly tasks. Furthermore, our base composition method has applications in phylogeny where it can be used to infer evolutionary distances between organisms based on the notion that related organisms often have much conserved code.

Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots

Generating the raw data for a de novo genome assembly project for a target eukaryotic species is relatively easy. This democratization of access to large-scale data has allowed many research teams to plan to assemble the genomes of non-model organisms. These new genome targets are very different from the traditional, inbred, laboratory-reared model organisms. They are often small, and cannot be isolated free of their environment – whether ingested food, the surrounding host organism of parasites, or commensal and symbiotic organisms attached to or within the individuals sampled. Preparation of pure DNA originating from a single species can be technically impossible, but assembly of mixed-organism DNA can be difficult, as most genome assemblers perform poorly when faced with multiple genomes in different stoichiometries. This class of problem is common in metagenomic datasets that deliberately try to capture all the genomes present in an environment, but replicon assembly is not often the goal of such programs. Here we present an approach to extracting, from mixed DNA sequence data, subsets that correspond to single species’ genomes and thus improving genome assembly. We use both numerical (proportion of GC bases and read coverage) and biological (best-matching sequence in annotated databases) indicators to aid partitioning of draft assembly contigs, and the reads that contribute to those contigs, into distinct bins that can then be subjected to rigorous, optimized assembly, through the use of taxon-annotated GC-coverage plots (TAGC plots). We also present Blobsplorer, a tool that aids exploration and selection of subsets from TAGC-annotated data. Partitioning the data in this way can rescue poorly assembled genomes, and reveal unexpected symbionts and commensals in eukaryotic genome projects. The TAGC plot pipeline script is available from https://github.com/blaxterlab/blobology, and the Blobsplorer tool from https://github.com/mojones/Blobsplorer.

Implications of HIV RNA structure for recombination, speciation, and the neutralism-selectionism controversy

The conflict between the needs to encode both a protein (impaired by non-synonymous mutation), and nucleic acid structure (impaired by synonymous or non-synonymous mutation), can sometimes be resolved in favour of the nucleic acid because its structure is critical for a selectively advantageous genome-wide activity--recombination. However, above a sequence difference threshold, recombination is impaired. It may then be advantageous for new species to arise. Building on the work of Grantham and others critical of the neutralist viewpoint, heuristic support for this hypothesis emerged from studies of the base composition and structure of retroviral genomes. The extreme enrichment in the purine A of the RNA of human immunodeficiency virus (HIV-1), parallels the mild purine-loading of the RNAs of most organisms, for which there is an adaptive explanation--immune evasion. However, human T cell leukaemia virus (HTLV-1), with the potential to invade the same host cell, shows extreme enrichment in the pyrimidine C. Assuming the low GC% HIV and the high GC% HTLV-1 to share a common ancestor, it was postulated that differences in GC% had arisen to prevent homologous recombination between these emerging lentiviral species. Sympatrically isolated by this intracellular reproductive barrier, prototypic HIV-1 seized the AU-rich (low GC%) high ground (thus committing to purine A rather than purine G). Prototypic HTLV-1 forwent this advantage and evolved an independent evolutionary strategy--similar to that of the GC%-rich Epstein-Barr virus--profound latency maintained by transcription of one purine-rich mRNA. The evidence supporting these interpretations is reviewed.

The genome of the heartworm, Dirofilaria immitis, reveals drug and vaccine targets

The heartworm Dirofilaria immitis is an important parasite of dogs. Transmitted by mosquitoes in warmer climatic zones, it is spreading across southern Europe and the Americas at an alarming pace. There is no vaccine, and chemotherapy is prone to complications. To learn more about this parasite, we have sequenced the genomes of D. immitis and its endosymbiont Wolbachia. We predict 10,179 protein coding genes in the 84.2 Mb of the nuclear genome, and 823 genes in the 0.9-Mb Wolbachia genome. The D. immitis genome harbors neither DNA transposons nor active retrotransposons, and there is very little genetic variation between two sequenced isolates from Europe and the United States. The differential presence of anabolic pathways such as heme and nucleotide biosynthesis hints at the intricate metabolic interrelationship between the heartworm and Wolbachia. Comparing the proteome of D. immitis with other nematodes and with mammalian hosts, we identify families of potential drug targets, immune modulators, and vaccine candidates. This genome sequence will support the development of new tools against dirofilariasis and aid efforts to combat related human pathogens, the causative agents of lymphatic filariasis and river blindness.—Godel, C., Kumar, S., Koutsovoulos, G., Ludin, P., Nilsson, D., Comandatore, F., Wrobel, N., Thompson, M., Schmid, C. D., Goto, S., Bringaud, F., Wolstenholme, A., Bandi, C., Epe, C., Kaminsky, R., Blaxter, M., Mäser, P. The genome of the heartworm, Dirofilaria immitis, reveals drug and vaccine targets.