Asymptotically increasing compliance of genomes with Chargaff's second parity rules through inversions and inverted transpositions

The first complete mitochondrial genome sequences of the crimson rose (Pachliopta hector) (Papilionidae: Troidini) and phylogenetic analysis

BACKGROUND

Pachliopta hector, known as the crimson rose, is a sizable swallowtail butterfly within the genus Pachliopta (roses) and part of the red-bodied swallowtails group. The mitochondrial genome (mitogenome) offers valuable insights for phylogenetic studies and the evolutionary biology of Pachliopta hector.

METHODS AND RESULTS

In this study, we sequenced, characterized, and annotated the mitogenome of P. hector. The complete mitogenome is 15,477 bp long and includes 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and one control region, all arranged within a single scaffold. The mitogenome exhibits a strong A + T bias of 81.84%, along with a negative AT skew (-0.0379) and a negative GC skew (-0.1989). All PCGs initiate with a standard ATN start codon, while TAA or TAG serves as the common stop codons. Codon usage analysis revealed that the most frequently used amino acids in the mitogenome are Phe, Ile, Leu1, Met, and Asn. Most tRNAs displayed the typical cloverleaf secondary structure, except for trnI, trnS1, and trnF. The loop and DHU stem were absent in trnS1, while both trnF and trnI lacked the TΨC loop. A phylogenetic analysis was performed with 17 other species from the tribe Troidini along with 42 species from tribe Leptocircini, Papilionini, and Teinopalpini, within the subfamily Papilioninae was conducted using Bayesian inference (BI) and maximum likelihood (ML) based on the nucleotide sequences of the 13 mitochondrial PCGs. All the four tribes under Papilioninae were well separated.

CONCLUSIONS

The findings suggest that P. hector is a member of the Troidini under subfamily Papilioninae shares sister clade with Pachliopta aristolochiae and Losaria neptunus. The BI and ML tree supported well-defined monophyletic groups at the tribe level and illustrated the relationship between the groups ((Teinopalpini and Papilionini) + Leptocircini) + Troidini)). This research may provide valuable insights into the evolution of P. hector and phylogenetic relationship of tribes Troidini under subfamily Papilioninae.

Chargaff's second parity rule lies at the origin of additive genetic interactions in quantitative traits to make omnigenic selection possible

Background

Francis Crick's central dogma provides a residue-by-residue mechanistic explanation of the flow of genetic information in living systems. However, this principle may not be sufficient for explaining how random mutations cause continuous variation of quantitative highly polygenic complex traits. Chargaff's second parity rule (CSPR), also referred to as intrastrand DNA symmetry, defined as near-exact equalities G ≈ C and A ≈ T within a single DNA strand, is a statistical property of cellular genomes. The phenomenon of intrastrand DNA symmetry was discovered more than 50 years ago; at present, it remains unclear what its biological role is, what the mechanisms are that force cellular genomes to comply strictly with CSPR, and why genomes of certain noncellular organisms have broken intrastrand DNA symmetry. The present work is aimed at studying a possible link between intrastrand DNA symmetry and the origin of genetic interactions in quantitative traits.

Methods

Computational analysis of single-nucleotide polymorphisms in human and mouse populations and of nucleotide composition biases at different codon positions in bacterial and human proteomes.

Results

The analysis of mutation spectra inferred from single-nucleotide polymorphisms observed in murine and human populations revealed near-exact equalities of numbers of reverse complementary mutations, indicating that random genetic variations obey CSPR. Furthermore, nucleotide compositions of coding sequences proved to be statistically interwoven via CSPR because pyrimidine bias at the 3rd codon position compensates purine bias at the 1st and 2nd positions.

Conclusions

According to Fisher's infinitesimal model, we propose that accumulation of reverse complementary mutations results in a continuous phenotypic variation due to small additive effects of statistically interwoven genetic variations. Therefore, additive genetic interactions can be inferred as a statistical entanglement of nucleotide compositions of separate genetic loci. CSPR challenges the neutral theory of molecular evolution-because all random mutations participate in variation of a trait-and provides an alternative solution to Haldane's dilemma by making a gene function diffuse. We propose that CSPR is symmetry of Fisher's infinitesimal model and that genetic information can be transferred in an implicit contactless manner.

Generalised interrelations among mutation rates drive the genomic compliance of Chargaff's second parity rule

Chargaff's second parity rule (PR-2), where the complementary base and k-mer contents are matching within the same strand of a double stranded DNA (dsDNA), is a phenomenon that invited many explanations. The strict compliance of nearly all nuclear dsDNA to PR-2 implies that the explanation should also be similarly adamant. In this work, we revisited the possibility of mutation rates driving PR-2 compliance. Starting from the assumption-free approach, we constructed kinetic equations for unconstrained simulations. The results were analysed for their PR-2 compliance by employing symbolic regression and machine learning techniques. We arrived to a generalised set of mutation rate interrelations in place in most species that allow for their full PR-2 compliance. Importantly, our constraints explain PR-2 in genomes out of the scope of the prior explanations based on the equilibration under mutation rates with simpler no-strand-bias constraints. We thus reinstate the role of mutation rates in PR-2 through its molecular core, now shown, under our formulation, to be tolerant to previously noted strand biases and incomplete compositional equilibration. We further investigate the time for any genome to reach PR-2, showing that it is generally earlier than the compositional equilibrium, and well within the age of life on Earth.

Strand asymmetries across genomic processes

Across biological systems, a number of genomic processes, including transcription, replication, DNA repair, and transcription factor binding, display intrinsic directionalities. These directionalities are reflected in the asymmetric distribution of nucleotides, motifs, genes, transposon integration sites, and other functional elements across the two complementary strands. Strand asymmetries, including GC skews and mutational biases, have shaped the nucleotide composition of diverse organisms. The investigation of strand asymmetries often serves as a method to understand underlying biological mechanisms, including protein binding preferences, transcription factor interactions, retrotransposition, DNA damage and repair preferences, transcription-replication collisions, and mutagenesis mechanisms. Research into this subject also enables the identification of functional genomic sites, such as replication origins and transcription start sites. Improvements in our ability to detect and quantify DNA strand asymmetries will provide insights into diverse functionalities of the genome, the contribution of different mutational mechanisms in germline and somatic mutagenesis, and our knowledge of genome instability and evolution, which all have significant clinical implications in human disease, including cancer. In this review, we describe key developments that have been made across the field of genomic strand asymmetries, as well as the discovery of associated mechanisms.

An Explanation of Exceptions from Chargaff's Second Parity Rule/Strand Symmetry of DNA Molecules

In this article, we show that mono/oligonucleotide quadruplets, as basic structures of DNA, along with our classification of trinucleotides, disclose an organization of genomes based on purine-pyrimidine symmetry. Moreover, the structure and stability of DNA are influenced by the Watson-Crick pairing and the natural law of DNA creation and conservation, according to which the same mono- or oligonucleotide insertion must be inserted simultaneously into both strands of DNA. Taken together, they lead to quadruplets with central mirror symmetry and bidirectional DNA strand orientation and are incorporated into Chargaff's second parity rule (CSPR). Performing our quadruplet frequency analysis of all human chromosomes and of Neuroblastoma BreakPoint Family (NBPF) genes, which code Olduvai protein domains in the human genome, we show that the coding part of DNA violates CSPR. This may shed new light and give rise to a novel hypothesis on DNA creation and its evolution. In this framework, the logarithmic relationship between oligonucleotide order and minimal DNA sequence length, to establish the validity of CSPR, automatically follows from the quadruplet structure of the genomic sequence. The problem of the violation of CSPR in rare symbionts is discussed.

Binary oppositions, algebraic holography and stochastic rules in genetic informatics

The article is devoted to the author's results of the algebraic analysis of molecular genetic systems, including a set of structured DNA alphabets and long nucleotide sequences in single-stranded DNA of eukaryotic and prokaryotic genomes. A connection of the system of DNA n-plets alphabets with principles of algebraic holography is shown, which concerns a popular theme of holography principles in genetically inherited physiology. In addition, a relation between DNA n-plets alphabets and the Poincaré disk model of Lobachevski hyperbolic geometry is revealed. This relation can explain known facts of the relationship of physiological phenomena with hyperbolic geometry. Considering long DNA sequences as a bunch of many parallel texts written in different n-plets alphabets led to the discovery of some universal rules of the stochastic organization of genomic DNAs. These rules are discussed concerning the general problem of the biological dualism "probability-vs-determinism". In general, the presented results give pieces of evidence in favor of the efficiency of a model approach to living organisms as quantum-informational algebraic-harmonic essences.

Noether's Theorem as a Metaphor for Chargaff's 2nd Parity Rule in Genomics

In the present note, the genomic compositional rule largely known as 'Chargaff's 2nd parity rule' (asserting equimolarity between Adenine-Thymine and Guanine-Cytosine in any of the two DNA strands) is regarded in association with Noether's theorem linking symmetries with conservation laws in physics. In the case of the genome, the strict physical and mathematical prerequisites of Noether's theorem do not hold. However, we conclude that a metaphor can be established with Noether's theorem, as inter-strand symmetry concerning DNA functionality engenders specific features in genome composition. Inversely, when inter-strand symmetry does not hold, the corresponding quantitative relations fail to appear. This association is also considered from the point of view of the existence of emergent laws and properties in evolutionary genomics.

Affinity and Correlation in DNA

A statistical analysis of important DNA sequences and related proteins has been performed to study the relationships between monomers, and some general considerations about these macromolecules can be provided from the results. First, the most important relationship between sites in all the DNA sequences examined is that between two consecutive base pairs. This is an indication of an energetic stabilization due to the stacking interaction of these couples of base pairs. Secondly, the difference between human chromosome sequences and their coding parts is relevant both in the relationships between sites and in some specific compositional rules, such as the second Chargaff rule. Third, the evidence of the relationship in two successive triplets of DNA coding sequences generates a relationship between two successive amino acids in the proteins. This is obviously impossible if all the relationships between the sites are statistical evidence and do not involve causes; therefore, in this article, due to stacking interactions and this relationship in coding sequences, we will divide the concept of the relationship between sites into two concepts: affinity and correlation, the first with physical causes and the second without. Finally, from the statistical analyses carried out, it will emerge that the human genome is uniform, with the only significant exception being the Y chromosome.

Algebraic harmony and probabilities in genomes. Long-range coherence in quantum code biology

According to the founders of quantum mechanics and quantum biology P. Jordan and E. Schrödinger, the main difference between living and inanimate objects is the dictatorial influence of genetic molecules on the whole living organism. Code biology can make a valuable contribution to understanding this dictatorial influence of genetic molecules whose ensemble is endowed with many interconnected alphabets and codes. The paper is devoted to probability rules of nucleotide sequences of single-stranded DNA in eukaryotic and prokaryotic genomes. These rules are connected with n-plets alphabets of DNA whose nucleotide sequences are considered as bunches of many parallel texts written in interconnected n-plets alphabets. The rules draw attention to genomic phenomena of special tetragroupings of n-plets and new genomic symmetries. A generalization of the second Chargaff's rule is described. They show the existence of long-range coherence in genomic DNA sequences and reveal new connections of structural features of genomic sequences with formalisms of quantum mechanics and quantum informatics. The author supposes that the received results are related to the known vibration-resonance theory of G. Frohlich about long-range coherence in biological systems, that is, about collective quantum effects there. The possible influence of the described genetiс probability phenomena on the genetically inherited physiological structures is noted and discussed.

Neutralism versus selectionism: Chargaff's second parity rule, revisited

Of Chargaff's four "rules" on DNA base frequencies, the functional interpretation of his second parity rule (PR2) is the most contentious. Thermophile base compositions (GC%) were taken by Galtier and Lobry (1997) as favoring Sueoka's neutral PR2 hypothesis over Forsdyke's selective PR2 hypothesis, namely that mutations improving local within-species recombination efficiency had generated a genome-wide potential for the strands of duplex DNA to separate and initiate recombination through the "kissing" of the tips of stem-loops. However, following Chargaff's GC rule, base composition mainly reflects a species-specific, genome-wide, evolutionary pressure. GC% could not have consistently followed the dictates of temperature, since it plays fundamental roles in both sustaining species integrity and, through primarily neutral genome-wide mutation, fostering speciation. Evidence for a local within-species recombination-initiating role of base order was obtained with a novel technology that masked the contribution of base composition to nucleic acid folding energy. Forsdyke's results were consistent with his PR2 hypothesis, appeared to resolve some root problems in biology and provided a theoretical underpinning for alignment-free taxonomic analyses using relative oligonucleotide frequencies (k-mer analysis). Moreover, consistent with Chargaff's cluster rule, discovery of the thermoadaptive role of the "purine-loading" of open reading frames made less tenable the Galtier-Lobry anti-selectionist arguments.

DNA sequence symmetries from randomness: the origin of the Chargaff's second parity rule

Most living organisms rely on double-stranded DNA (dsDNA) to store their genetic information and perpetuate themselves. This biological information has been considered as the main target of evolution. However, here we show that symmetries and patterns in the dsDNA sequence can emerge from the physical peculiarities of the dsDNA molecule itself and the maximum entropy principle alone, rather than from biological or environmental evolutionary pressure. The randomness justifies the human codon biases and context-dependent mutation patterns in human populations. Thus, the DNA 'exceptional symmetries,' emerged from the randomness, have to be taken into account when looking for the DNA encoded information. Our results suggest that the double helix energy constraints and, more generally, the physical properties of the dsDNA are the hard drivers of the overall DNA sequence architecture, whereas the selective biological processes act as soft drivers, which only under extraordinary circumstances overtake the overall entropy content of the genome.

Revisiting the Relationships Between Genomic G + C Content, RNA Secondary Structures, and Optimal Growth Temperature

Over twenty years ago Galtier and Lobry published a manuscript entitled "Relationships between Genomic G + C Content, RNA Secondary Structure, and Optimal Growth Temperature" in the Journal of Molecular Evolution that showcased the lack of a relationship between genomic G + C content and optimal growth temperature (OGT) in a set of about 200 prokaryotes. Galtier and Lobry also assessed the relationship between RNA secondary structures (rRNA stems, tRNAs) and OGT, and in this case a clear relationship emerged. Increasing structured RNA G + C content (particularly in regions that are double-stranded) correlates with increased OGT. Both of these fundamental relationships have withstood test of many additional sequences and spawned a variety of different applications that include prediction of OGT from rRNA sequence and computational ncRNA identification approaches. In this work, I present the motivation behind Galtier and Lobry's original paper and the larger questions addressed by the work, how these questions have evolved over the last two decades, and the impact of Galtier and Lobry's manuscript in fields beyond these questions.

Hyperbolic rules of the cooperative organization of eukaryotic and prokaryotic genomes

The author's method of oligomer sums for analysis of oligomer compositions of eukaryotic and prokaryotic genomes is described. The use of this method revealed the existence of general rules for the cooperative oligomeric organization of a wide list of genomes. These rules are called hyperbolic because they are associated with hyperbolic sequences including the harmonic progression 1, 1/2, 1/3, .., 1/n. These rules are demonstrated by examples of quantitative analysis of many genomes from the human genome to the genomes of archaea and bacteria. The hyperbolic (harmonic) rules, speaking about the existence of algebraic invariants in full genomic sequences, are considered as candidates for the role of universal rules for the cooperative organization of genomes. The results concerns additionally the problem of the origin of life. The described phenomenological results were obtained as consequences of the previously published author's quantum-information model of long DNA sequences. The oligomer sums method was also applied to the analysis of long genes and viruses including the COVID-19 virus; this revealed, in characteristics of many of them, the phenomenon of such rhythmically repeating deviations from model hyperbolic sequences, which are associated with DNA triplets. In addition, an application of the oligomer sums method is shown to the analysis of amino acid sequences in long proteins like the protein Titin. The topics of the algebraic harmony in living bodies and of the quantum-information approach in biology are discussed.

On the origin of degeneracy in the genetic code

The degeneracy of amino acid coding is one of the most crucial and enigmatic aspects of the genetic code. Different theories about the origin of the genetic code have been developed. However, to date, there is no comprehensive hypothesis on the mechanism that might have generated the degeneracy as we observe it. Here, we provide a new theory that explains the origin of the degeneracy based only on symmetry principles. The approach allows one to describe exactly the degeneracy of the early code (progenitor of the genetic code of LUCA, the last universal common ancestor) which is hypothesized to have the same degeneracy as the present vertebrate mitochondrial genetic code. The theory is based upon the tessera code, that fits as the progenitor of the early code. Moreover, we describe in detail the possible evolutionary transitions implied by our theory. The approach is supported by a unified mathematical framework that accounts for the degeneracy properties of both nuclear and mitochondrial genetic codes. Our work provides a new perspective to the understanding of the origin of the genetic code and the roles of symmetry principles in the organization of genetic information.

Novel look at DNA and life-Symmetry as evolutionary forcing

After explanation of the Chargaff´s first parity rule in terms of the Watson-Crick base-pairing between the two DNA strands, the Chargaff´s second parity rule for each strand of DNA (also named strand symmetry), which cannot be explained by Watson-Crick base-pairing only, is still a challenging issue already fifty years. We show that during evolution DNA preserves its identity in the form of quadruplet A+T and C+G rich matrices based on purine-pyrimidine mirror symmetries of trinucleotides. Identical symmetries are present in our classification of trinucleotides and the genetic code table. All eukaryotes and almost all prokaryotes (bacteria and archaea) have quadruplet mirror symmetries in structural form and frequencies following the principle of Chargaff's second parity rule and Natural symmetry law of DNA creation and conservation. Some rare symbionts have mirror symmetry only in their structural form within each DNA strand. Based on our matrix analysis of closely related species, humans and Neanderthals, we find that the circular cycle of inverse proportionality between trinucleotides preserves identical relative frequencies of trinucleotides in each quadruplet and in the whole genome. According to our calculations, a change in frequencies in quadruplet matrices could lead to the creation of new species. Violation of quadruplet symmetries is practically inconsistent with life. DNA symmetries provide a key for understanding the restriction of disorder (entropy) due to mutations in the evolution of DNA.

Decoding the Inversion Symmetry Underlying Transcription Factor DNA-Binding Specificity and Functionality in the Genome

Understanding why a transcription factor (TF) binds to a specific DNA element in the genome and whether that binding event affects transcriptional output remains a great challenge. In this study, we demonstrate that TF binding in the genome follows inversion symmetry (IS). In addition, the specific DNA elements where TFs bind in the genome are determined by internal IS within the DNA element. These DNA-binding rules quantitatively define how TFs select the appropriate regulatory targets from a large number of similar DNA elements in the genome to elicit specific transcriptional and cellular responses. Importantly, we also demonstrate that these DNA-binding rules extend to DNA elements that do not support transcriptional activity. That is, the DNA-binding rules are obeyed, but the retention time of the TF at these non-functional DNA elements is not long enough to initiate and/or maintain transcription. We further demonstrate that IS is universal within the genome. Thus, IS is the DNA code that TFs use to interact with the genome and dictates (in conjunction with known DNA sequence constraints) which of those interactions are functionally active.

Evaluation of the Persistence of Higher-Order Strand Symmetry in Genomic Sequences by Novel Word Symmetry Distance Analysis

For the ubiquitous phenomenon of strand symmetry, it has been shown that it may persist for higher-order oligonucleotides. However, there is no consensus about to what extent (order of oligonucleotides or length of words) strand symmetry still persists. To determine the extent of strand symmetry in genomic sequences is critically important for the further understanding of the phenomenon. Based on previous studies, we have developed an algorithm for the novel word symmetry distance analysis. We applied it to evaluate the higher-order strand symmetry for 206 archaeal genomes and 2,659 bacterial genomes. Our results show that the new approach could provide a clear-cut criterion to determine the extent of strand symmetry for a group of genomes or individual genomes. According to the new measure, strand symmetry would tend to persist for up to 8-mers in archaeal genomes, and up to 9-mers in bacterial genomes. And the persistence may vary from 6- to 9-mers in individual genomes. Moreover, higher-order strand symmetry would tend to positively correlate with GC content and mononucleotide symmetry levels of genomic sequences. The variations of higher-order strand symmetry among genomes would indicate that strand symmetry itself may not be strictly relevant to biological functions, which would provide some insights into the origin and evolution of the phenomenon.

Evolution of Genomic Base Composition: From Single Cell Microbes to Multicellular Animals

Whole genome sequencing (WGS) of thousands of microbial genomes has provided considerable insight into evolutionary mechanisms in the microbial world. While substantially fewer eukaryotic genomes are available for analyses the number is rapidly increasing. This mini-review summarizes broadly evolutionary dynamics of base composition in the different domains of life from the perspective of prokaryotes. Common and different evolutionary mechanisms influencing genomic base composition in eukaryotes and prokaryotes are discussed. The conclusion from the data currently available suggests that while there are similarities there are also striking differences in how genomic base composition has evolved within prokaryotes and eukaryotes. For instance, homologous recombination appears to increase GC content locally in eukaryotes due to a non-selective process termed GC-biased gene conversion (gBGC). For prokaryotes on the other hand, increase in genomic GC content seems to be driven by the environment and selection. We find that similar phenomena observed for some organisms in each respective domain may be caused by very different mechanisms: while gBGC and recombination rates appear to explain the negative correlation between GC3 (GC content based on the third codon nucleotides) and genome size in some eukaryotes uptake of AT rich DNA sequences is the main reason for a similar negative correlation observed in prokaryotes. We provide further examples that indicate that base composition in prokaryotes and eukaryotes have evolved under very different constraints.

The first complete mitochondrial genome of marigold pest thrips, Neohydatothrips samayunkur (Sericothripinae) and comparative analysis

Complete mitogenomes from the order Thysanoptera are limited to representatives of the subfamily Thripinae. Therefore, in the present study, we sequenced the mitochondrial genome of Neohydatothrips samayunkur (15,295 bp), a member of subfamily Sericothripinae. The genome possesses the canonical 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs) as well as two putative control regions (CRs). The majority strand was 77.42% A + T content, and 22.58% G + C with weakly positive AT skew (0.04) and negative GC skew (-0.03). The majority of PCGs start with ATN codons as observed in other insect mitochondrial genomes. The GCG codon (Alanine) was not used in N. samayunkur. Most tRNAs have the typical cloverleaf secondary structure, however the DHU stem and loop were absent in trnV and trnS1, while the TΨC loop was absent in trnR and trnT. The two putative control regions (CR1 and CR2) show 99% sequence similarity indicated a possible duplication, and shared 57 bp repeats were identified. N. samayunkur showed extensive gene rearrangements, with 11 PCGs, 22 tRNAs, and two rRNAs translocated when compared to the ancestral insect. The gene trnL2 was separated from the 'trnL2-cox2' gene block, which is a conserved, ancestral gene order found in all previously sequenced thrips mitogenomes. Both maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees resulted in similar topologies. The phylogenetic position of N. samayunkur indicates that subfamily Sericothripinae is sister to subfamily Thripinae. More molecular data from different taxonomic groups is needed to understand thrips phylogeny and evolution.

The complete mitochondrial genome of Melon thrips, Thrips palmi (Thripinae): Comparative analysis

The melon thrips, Thrips palmi is a serious pest and vector for plant viruses on a wide range of economically important crops. DNA barcoding evidenced the presence of cryptic diversity in T. palmi and that warrants exhaustive molecular studies. Our present study is on decoding the first complete mitochondrial genome of T. palmi (15,333 bp) through next-generation sequencing (NGS). The T. palmi mt genome contains 37 genes, including 13 Protein coding genes (PCGs), two ribosomal RNA (rRNAs), 22 transfer RNA (tRNAs), and two control regions (CRs). The majority strand of T. palmi revealed 78.29% A+T content, and 21.72% G+C content with positive AT skew (0.09) and negative GC skew (-0.06). The ATN initiation codons were observed in 12 PCGs except for cox1 which have unique start codon (TTG). The relative synonymous codon usage (RSCU) analysis revealed Phe, Leu, Ile, Tyr, Asn, Lys and Met were the most frequently used amino acids in all PCGs. The codon (CGG) which is assigned to Arginine in most insects but absent in T. palmi. The Ka/Ks ratio ranges from 0.078 in cox1 to 0.913 in atp8. We observed the typical cloverleaf secondary structure in most of the tRNA genes with a few exceptions; absence of DHU stem and loop in trnV and trnS, absence of DHU loop in trnE, lack of T-arm and loop in trnN. The T. palmi gene order (GO) was compared with ancestral GO and observed an extensive gene arrangement in PCGs, tRNAs and rRNAs. The cox2 gene was separated from the gene block 'cox2-trnL2' in T. palmi as compared with the other thrips mt genomes, including ancestor GO. Further, the nad1, trnQ, trnC, trnL1, trnV, trnF, rrnS, and rrnL were inversely transpositioned in T. palmi GO. The gene blocks 'trnQ-trnS2-trnD' and 'trnN-trnE-trnS1-trnL1' seems to be genus specific. The T. palmi mt genome contained 24 intergenic spacer regions and 12 overlapping regions. The 62 bp of CR2 shows the similarity with CR1 indicating a possible duplication. The occurrence of multiple CRs in thrips mt genomes seems to be a derived trait which needs further investigation. Although, the study depicted extensive gene rearrangements in T. palmi mt genome, but the negative GC skew reflects only strand asymmetry. Both the ML and BI phylogenetic trees revealed the close relationships of Thrips with Scirtothrips as compared to Frankliniella. Thus, more mt genomes of the diverse thrips species are required to understand the in-depth phylogenetic and evolutionary relationships.

The common origin of symmetry and structure in genetic sequences

Biologists have long sought a way to explain how statistical properties of genetic sequences emerged and are maintained through evolution. On the one hand, non-random structures at different scales indicate a complex genome organisation. On the other hand, single-strand symmetry has been scrutinised using neutral models in which correlations are not considered or irrelevant, contrary to empirical evidence. Different studies investigated these two statistical features separately, reaching minimal consensus despite sustained efforts. Here we unravel previously unknown symmetries in genetic sequences, which are organized hierarchically through scales in which non-random structures are known to be present. These observations are confirmed through the statistical analysis of the human genome and explained through a simple domain model. These results suggest that domain models which account for the cumulative action of mobile elements can explain simultaneously non-random structures and symmetries in genetic sequences.

Comparing Reverse Complementary Genomic Words Based on Their Distance Distributions and Frequencies

In this work, we study reverse complementary genomic word pairs in the human DNA, by comparing both the distance distribution and the frequency of a word to those of its reverse complement. Several measures of dissimilarity between distance distributions are considered, and it is found that the peak dissimilarity works best in this setting. We report the existence of reverse complementary word pairs with very dissimilar distance distributions, as well as word pairs with very similar distance distributions even when both distributions are irregular and contain strong peaks. The association between distribution dissimilarity and frequency discrepancy is also explored, and it is speculated that symmetric pairs combining low and high values of each measure may uncover features of interest. Taken together, our results suggest that some asymmetries in the human genome go far beyond Chargaff's rules. This study uses both the complete human genome and its repeat-masked version.

Exceptional Symmetry by Genomic Word : A Statistical Analysis

Single-strand DNA symmetry is pointed as a universal law observed in the genomes from all living organisms. It is a somewhat broadly defined concept, which has been refined into some more specific measurable effects. Here we discuss the exceptional symmetry effect. Exceptional symmetry is the symmetry effect beyond that expected in independence contexts, and it can be measured for each word, for each equivalent composition group, or globally, combining the effects of all possible words of a given length. Global exceptional symmetry was found in several species, but there are genomic words with no exceptional symmetry effect, whereas others show a very high exceptional symmetry effect. In this work, we discuss a measure to evaluate the exceptional symmetry effect by symmetric word pair, and compare it with others. We present a detailed study of the exceptional symmetry by symmetric pairs and take the CG content into account. We also introduce and discuss the exceptional symmetry profile for the DNA of each organism, and we perform a multiple comparison for 31 genomes: 7 viruses; 5 archaea; 5 bacteria; 14 eukaryotes.

Inversion symmetry of DNA k-mer counts: validity and deviations

Background

The generalization of the second Chargaff rule states that counts of any string of nucleotides of length k on a single chromosomal strand equal the counts of its inverse (reverse-complement) k-mer. This Inversion Symmetry (IS) holds for many species, both eukaryotes and prokaryotes, for ranges of k which may vary from 7 to 10 as chromosomal lengths vary from 2Mbp to 200 Mbp. The existence of IS has been demonstrated in the literature, and other pair-wise candidate symmetries (e.g. reverse or complement) have been ruled out.

Results

Studying IS in the human genome, we find that IS holds up to k = 10. It holds for complete chromosomes, also after applying the low complexity mask. We introduce a numerical IS criterion, and define the k-limit, KL, as the highest k for which this criterion is valid. We demonstrate that chromosomes of different species, as well as different human chromosomal sections, follow a universal logarithmic dependence of KL ~ 0.7 ln(L), where L is the length of the chromosome.

We introduce a statistical IS-Poisson model that allows us to apply confidence measures to our numerical findings. We find good agreement for large k, where the variance of the Poisson distribution determines the outcome of the analysis. This model predicts the observed logarithmic increase of KL with length. The model allows us to conclude that for low k, e.g. k = 1 where IS becomes the 2^nd Chargaff rule, IS violation, although extremely small, is significant. Studying this violation we come up with an unexpected observation for human chromosomes, finding a meaningful correlation with the excess of genes on particular strands.

Conclusions

Our IS-Poisson model agrees well with genomic data, and accounts for the universal behavior of k-limits. For low k we point out minute, yet significant, deviations from the model, including excess of counts of nucleotides T vs A and G vs C on positive strands of human chromosomes. Interestingly, this correlates with a significant (but small) excess of genes on the same positive strands.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3012-8) contains supplementary material, which is available to authorized users.

A stationary distribution associated to a set of laws whose initial states are grouped into classes. An application in genomics

Let I be a finite set and S be a nonempty strict subset of I which is partitioned into classes, and let C(s) be the class containing s ∈ S. Let (Ps: s ∈ S) be a family of distributions on IN, where each Ps applies to sequences starting with the symbol s. To this family, we associate a class of distributions P(π) on IN which depends on a probability vector π. Our main results assume that, for each s ∈ S, Ps regenerates with distribution Ps' when it encounters s' ∈ S ∖ C(s). From semiregenerative theory, we determine a simple condition on π for P(π) to be time stationary. We give a similar result for the following more complex model. Once a symbol s' ∈ S ∖ C(s) has been encountered, there is a decision to be made: either a new region of type C(s') governed by Ps' starts or the region continues to be a C(s) region. This decision is modeled as a random event and its probability depends on s and s'. The aim in studying these kinds of models is to attain a deeper statistical understanding of bacterial DNA sequences. Here I is the set of codons and the classes (C(s): s ∈ S) identify codons that initiate similar genomic regions. In particular, there are two classes corresponding to the start and stop codons which delimit coding and noncoding regions in bacterial DNA sequences. In addition, the random decision to continue the current region or begin a new region of a different class reflects the well-known fact that not every appearance of a start codon marks the beginning of a new coding region.

Trinucleotide's quadruplet symmetries and natural symmetry law of DNA creation ensuing Chargaff's second parity rule

For almost 50 years the conclusive explanation of Chargaff's second parity rule (CSPR), the equality of frequencies of nucleotides A=T and C=G or the equality of direct and reverse complement trinucleotides in the same DNA strand, has not been determined yet. Here, we relate CSPR to the interstrand mirror symmetry in 20 symbolic quadruplets of trinucleotides (direct, reverse complement, complement, and reverse) mapped to double-stranded genome. The symmetries of Q-box corresponding to quadruplets can be obtained as a consequence of Watson-Crick base pairing and CSPR together. Alternatively, assuming Natural symmetry law for DNA creation that each trinucleotide in one strand of DNA must simultaneously appear also in the opposite strand automatically leads to Q-box direct-reverse mirror symmetry which in conjunction with Watson-Crick base pairing generates CSPR. We demonstrate quadruplet's symmetries in chromosomes of wide range of organisms, from Escherichia coli to Neanderthal and human genomes, introducing novel quadruplet-frequency histograms and 3D-diagrams with combined interstrand frequencies. These "landscapes" are mutually similar in all mammals, including extinct Neanderthals, and somewhat different in most of older species. In human chromosomes 1-12, and X, Y the "landscapes" are almost identical and slightly different in the remaining smaller and telocentric chromosomes. Quadruplet frequencies could provide a new robust tool for characterization and classification of genomes and their evolutionary trajectories.

Systematic exchanges between nucleotides: Genomic swinger repeats and swinger transcription in human mitochondria

Chargaff׳s second parity rule, quasi-equal single strand frequencies for complementary nucleotides, presumably results from insertion of repeats and inverted repeats during sequence genesis. Vertebrate mitogenomes escape this rule because repeats are counterselected: their hybridization produces loop bulges whose deletion is deleterious. Some DNA/RNA sequences match mitogenomes only after assuming one among 23 systematic nucleotide exchanges (swinger DNA/RNA: nine symmetric, e.g. A ↔ C; and 14 asymmetric, e.g. A → C → G → A). Swinger-transformed repeats do not hybridize, escaping selection against deletions due to bulge formation. Blast analyses of the human mitogenome detect swinger repeats for all 23 swinger types, more than in randomized sequences with identical length and nucleotide contents. Mean genomic swinger repeat lengths increase with observed human swinger RNA frequencies: swinger repeat and swinger RNA productions appear linked, perhaps by swinger RNA retrotranscription. Mean swinger repeat lengths are proportional to reading frame retrievability, post-swinger transformation, by the natural circular code. Genomic swinger repeats confirm at genomic level, independently of swinger RNA detection, occurrence of swinger polymerizations. They suggest that repeats, and swinger repeats in particular, contribute to genome genesis.

Swinger RNAs with sharp switches between regular transcription and transcription systematically exchanging ribonucleotides: Case studies

During RNA transcription, DNA nucleotides A,C,G, T are usually matched by ribonucleotides A, C, G and U. However occasionally, this rule does not apply: transcript-DNA homologies are detectable only assuming systematic exchanges between ribonucleotides. Nine symmetric (X ↔ Y, e.g. A ↔ C) and fourteen asymmetric (X ↔ Y ↔ Z, e.g. A ↔ C ↔ G) exchanges exist, called swinger transcriptions. Putatively, polymerases occasionally stabilize in unspecified swinger conformations, possibly similar to transient conformations causing punctual misinsertions. This predicts chimeric transcripts, part regular, part swinger-transformed, reflecting polymerases switching to swinger polymerization conformation(s). Four chimeric Genbank transcripts (three from human mitochondrion and one murine cytosolic) are described here: (a) the 5' and 3' extremities reflect regular polymerization, the intervening sequence exchanges systematically between ribonucleotides (swinger rule G ↔ U, transcript (1), with sharp switches between regular and swinger sequences; (b) the 5' half is 'normal', the 3' half systematically exchanges ribonucleotides (swinger rule C ↔ G, transcript (2), with an intercalated sequence lacking homology; (c) the 3' extremity fits A ↔ G exchanges (10% of transcript length), the 5' half follows regular transcription; the intervening region seems a mix of regular and A ↔ G transcriptions (transcript 3); (d) murine cytosolic transcript 4 switches to A ↔ U + C ↔ G, and is fused with A ↔ U + C ↔ G swinger transformed precursor rRNA. In (c), each concomitant transcript 5' and 3' extremities match opposite genome strands. Transcripts 3 and 4 combine transcript fusions with partial swinger transcriptions. Occasional (usually sharp) switches between regular and swinger transcriptions reveal greater coding potential than detected until now, suggest stable polymerase swinger conformations.

Sharp switches between regular and swinger mitochondrial replication: 16S rDNA systematically exchanging nucleotides A<->T+C<->G in the mitogenome of Kamimuria wangi

Swinger DNAs are sequences whose homology with known sequences is detected only by assuming systematic exchanges between nucleotides. Nine symmetric (X<->Y, i.e. A<->C) and fourteen asymmetric (X->Y->Z, i.e. A->C->G) exchanges exist. All swinger DNA previously detected in GenBank follow the A<->T+C<->G exchange, while mitochondrial swinger RNAs distribute among different swinger types. Here different alignment criteria detect 87 additional swinger mitochondrial DNAs (86 from insects), including the first swinger gene embedded within a complete genome, corresponding to the mitochondrial 16S rDNA of the stonefly Kamimuria wangi. Other Kamimuria mt genome regions are "regular", stressing unanswered questions on (a) swinger polymerization regulation; (b) swinger 16S rDNA functions; and (c) specificity to rDNA, in particular 16S rDNA. Sharp switches between regular and swinger replication, together with previous observations on swinger transcription, suggest that swinger replication might be due to a switch in polymerization mode of regular polymerases and the possibility of swinger-encoded information, predicted in primordial genes such as rDNA.

Persistence and breakdown of strand symmetry in the human genome

Afreixo, V., Bastos, C.A.C., Garcia, S.P., Rodrigues, J.M.O.S., Pinho, A.J., Ferreira, P.J.S.G., 2013. The breakdown of the word symmetry in the human genome. J. Theor. Biol. 335, 153-159 analyzed the word symmetry (strand symmetry or the second parity rule) in the human genome. They concluded that strand symmetry holds for oligonucleotides up to 6 nt and is no longer statistically significant for oligonucleotides of higher orders. However, although they provided some new results for the issue, their interpretation would not be fully justified. Also, their conclusion needs to be further evaluated. Further analysis of their results, especially those of equivalence tests and word symmetry distance, shows that strand symmetry would persist for higher-order oligonucleotides up to 9 nt in the human genome, at least for its overall frequency framework (oligonucleotide frequency pattern).

High order intra-strand partial symmetry increases with organismal complexity in animal evolution

For sufficiently long genomic sequence, the frequency of any short nucleotide fragment on one strand is approximately equal to the frequency of its reverse complement on the same strand. Despite being studied over two decades, the precise mechanism involved has not yet been made clear. In this study, we calculated the high order intra-strand partial symmetry (IPS) for 14 animal species by using a fixed sliding window method to scan each genome sequence. The study showed that the IPS was positive associated with organismal complexity measured by the number of distinct cell types. The results indicated that the IPS might be resulted from the increasing of functional non-coding DNAs, and plays an important role in the evolution process of complex body plans.

Species radiation by DNA replication that systematically exchanges nucleotides?

RNA and DNA syntheses share many properties. Therefore, the existence of 'swinger' RNAs, presumed 'orphan' transcripts matching genomic sequences only if transcription systematically exchanged nucleotides, suggests replication producing swinger DNA. Transcripts occur in many short-lived copies, the few cellular DNA molecules are long-lived. Hence pressures for functional swinger DNAs are greater than for swinger RNAs. Protein coding properties of swinger sequences differ from original sequences, suggesting rarity of corresponding swinger DNA. For genes producing structural RNAs, such as tRNAs and rRNAs, three exchanges (A<->T, C<->G and A<->T+C<->G) conserve self-hybridization properties. All nuclear eukaryote swinger DNA sequences detected in GenBank are for rRNA genes assuming A<->T+C<->G exchanges. In brachyuran crabs, 25 species had A<->T+C<->G swinger 18S rDNA, all matching the reverse-exchanged version of regular 18S rDNA of a related species. In this taxon, swinger replication of 18S rDNA apparently associated with, or even resulted in species radiation. A<->T+C<->G transformation doesn't invert sequence direction, differing from inverted repeats. Swinger repeats (detectable only assuming swinger transformations, A<->T+C<->G swinger repeats most frequent) within regular human rRNAs, independently confirm swinger polymerizations for most swinger types. Swinger replication might be an unsuspected molecular mechanism for ultrafast speciation.

DNA viewed as an out-of-equilibrium structure

The complexity of the primary structure of human DNA is explored using methods from nonequilibrium statistical mechanics, dynamical systems theory, and information theory. A collection of statistical analyses is performed on the DNA data and the results are compared with sequences derived from different stochastic processes. The use of χ^{2} tests shows that DNA can not be described as a low order Markov chain of order up to r=6. Although detailed balance seems to hold at the level of a binary alphabet, it fails when all four base pairs are considered, suggesting spatial asymmetry and irreversibility. Furthermore, the block entropy does not increase linearly with the block size, reflecting the long-range nature of the correlations in the human genomic sequences. To probe locally the spatial structure of the chain, we study the exit distances from a specific symbol, the distribution of recurrence distances, and the Hurst exponent, all of which show power law tails and long-range characteristics. These results suggest that human DNA can be viewed as a nonequilibrium structure maintained in its state through interactions with a constantly changing environment. Based solely on the exit distance distribution accounting for the nonequilibrium statistics and using the Monte Carlo rejection sampling method, we construct a model DNA sequence. This method allows us to keep both long- and short-range statistical characteristics of the native DNA data. The model sequence presents the same characteristic exponents as the natural DNA but fails to capture spatial correlations and point-to-point details.

System analysis of synonymous codon usage biases in archaeal virus genomes

Recent studies of geothermally heated aquatic ecosystems have found widely divergent viruses with unusual morphotypes. Archaeal viruses isolated from these hot habitats usually have double-stranded DNA genomes, linear or circular, and can infect members of the Archaea domain. In this study, the synonymous codon usage bias (SCUB) and dinucleotide composition in the available complete archaeal virus genome sequences have been investigated. It was found that there is a significant variation in SCUB among different Archaeal virus species, which is mainly determined by the base composition. The outcome of correspondence analysis (COA) and Spearman׳s rank correlation analysis shows that codon usage of selected archaeal virus genes depends mainly on GC richness of genome, and the gene׳s function, albeit with smaller effects, also contributes to codon usage in this virus. Furthermore, this investigation reveals that aromaticity of each protein is also critical in affecting SCUB of these viral genes although it was less important than that of the mutational bias. Especially, mutational pressure may influence SCUB in SIRV1, SIRV2, ARV1, AFV1, and PhiCh1 viruses, whereas translational selection could play a leading role in HRPV1׳s SCUB. These conclusions not only can offer an insight into the codon usage biases of archaeal virus and subsequently the possible relationship between archaeal viruses and their host, but also may help in understanding the evolution of archaeal viruses and their gene classification, and more helpful to explore the origin of life and the evolution of biology.

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The SCUB of archaeal virus genes depends mainly on GC richness of genome.

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The mutational pressure is the main factor that influences SCUB.

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The aromaticity of each protein is also critical in affecting SCUB.

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The translational selection could play a leading role in HRPV1׳s SCUB.

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The mode is helpful to explore the origin of life and the evolution of biology.

DNA conformational transitions induced by supercoiling control transcription in chromatin

Regulation of transcription in eukaryotes is considered in the light of recent findings demonstrating the presence of negative and positive superhelical tension in chromatin. This tension induces conformational transitions in DNA duplex. Particularly, the transition into A-form renders DNA accessible and waylaying for initiation of transcription producing RNA molecules long known to belong to the A-conformation. Competition between conformational transitions in various DNA sequences for the energy of elastic spring opens a possibility for understanding of fine tuning of transcription at a distance.

Characterization of Toxoplasma gondii subtelomeric-like regions: identification of a long-range compositional bias that is also associated with gene-poor regions

BACKGROUND

Chromosome ends are composed of telomeric repeats and subtelomeric regions, which are patchworks of genes interspersed with repeated elements. Although chromosome ends display similar arrangements in different species, their sequences are highly divergent. In addition, these regions display a particular nucleosomal composition and bind specific factors, therefore producing a special kind of heterochromatin. Using data from currently available draft genomes we have characterized these putative Telomeric Associated Sequences in Toxoplasma gondii.

RESULTS

An all-vs-all pairwise comparison of T. gondii assembled chromosomes revealed the presence of conserved regions of ∼ 30 Kb located near the ends of 9 of the 14 chromosomes of the genome of the ME49 strain. Sequence similarity among these regions is ∼ 70%, and they are also highly conserved in the GT1 and VEG strains. However, they are unique to Toxoplasma with no detectable similarity in other Apicomplexan parasites. The internal structure of these sequences consists of 3 repetitive regions separated by high-complexity sequences without annotated genes, except for a gene from the Toxoplasma Specific Family. ChIP-qPCR experiments showed that nucleosomes associated to these sequences are enriched in histone H4 monomethylated at K20 (H4K20me1), and the histone variant H2A.X, suggesting that they are silenced sequences (heterochromatin). A detailed characterization of the base composition of these sequences, led us to identify a strong long-range compositional bias, which was similar to that observed in other genomic silenced fragments such as those containing centromeric sequences, and was negatively correlated to gene density.

CONCLUSIONS

We identified and characterized a region present in most Toxoplasma assembled chromosomes. Based on their location, sequence features, and nucleosomal markers we propose that these might be part of subtelomeric regions of T. gondii. The identified regions display a unique trinucleotide compositional bias, which is shared (despite the lack of any detectable sequence similarity) with other silenced sequences, such as those making up the chromosome centromeres. We also identified other genomic regions with this compositional bias (but no detectable sequence similarity) that might be functionally similar.

Fundamental role of start/stop regulators in whole DNA and new trinucleotide classification

The origin and logic of genetic code are two of greatest mysteries of life sciences. Analyzing DNA sequences we showed that the start/stop trinucleotides have broader importance than just marking start and stop of exons in coding DNA. On this basis, here we introduced new classification of trinucleotides and showed that all A+T rich trinucleotides consisting of three different nucleotides arise from start-ATG, stop-TGA and stop-TAG using their complement, reverse complement and reverse transformations. Due to the same transformations during generations of crossing-over they can switch from one form to the other. By direct process the start-ATG and stop-TAG can irreversibly transform into stop-TAA. By transformation into A+T rich trinucleotides and 16/32 C+G rich they can lose the start/stop function and take the role of a sense codon in reversible way. The remaining 16 C+G trinucleotides cannot directly transform into start/stop trinucleotides and thus remain a firm skeleton for structuring the C+G rich DNA. We showed that start/stops strongly enrich the A+T rich noncoding DNA through frequently extended forms. From the evolutionary viewpoint the start/stops are chief creators of prevailing A+T rich noncoding DNA, and of more stable coding DNA. We propose that start/stops have basic role as "seeds" in trinucleotide evolution of noncoding and coding sequences and lead to asymmetry between A+T and C+G rich DNA. By dynamical transformations during evolution they enabled pronounced phylogenetic broadness, keeping the regulator function.

Conservation vs. variation of dinucleotide frequencies across bacterial and archaeal genomes: evolutionary implications

During the long history of biological evolution, genome structures have undergone enormous changes. Nevertheless, some traits or vestiges of the primordial genome (defined as the most primitive nucleic acid genome for life on earth in this paper) may remain in modern genetic systems. It is of great importance to find these traits or vestiges for the study of the origin and evolution of genomes. As the shorter is a sequence, the less probable it would be modified during genome evolution. And if mutated, it would be easier to reappear at the same site or another site. Consequently, the genomic frequencies of very short nucleotide sequences, such as dinucleotides, would have considerable chances to be conserved during billions of years of evolution. Prokaryotic genomes are very diverse and with a wide range of GC content. Therefore, in order to find traits or vestiges of the primordial genome remained in modern genetic systems, we have studied the characteristics of dinucleotide frequencies across bacterial and archaeal genomes. We analyzed the dinucleotide frequency patterns of the whole-genome sequences from more than 1300 prokaryotic species (bacterial and archaeal genomes available as of December 2012). The results show that the frequencies of the dinucleotides AC, AG, CA, CT, GA, GT, TC, and TG are well-conserved across various genomes, while the frequencies of other dinucleotides vary considerably among species. The dinucleotide frequency conservation/variation pattern seems to correlate with the distributions of dinucleotides throughout a genome and across genomes. Further analysis indicates that the phenomenon would be determined by strand symmetry of genomic sequences (the second parity rule) and GC content variations among genomes. We discussed some possible origins of strand symmetry. And we propose that the phenomenon of frequency conservation of some dinucleotides may provide insights into the genomic composition of the primordial genetic system.

Patterns of nucleotide asymmetries in plant and animal genomes

Symmetry in biology provides many intriguing puzzles to the scientist's mind. Chargaff's second parity rule states a symmetric distribution of oligonucleotides within a single strand of double-stranded DNA. While this rule has been verified in a wide range of microbial genomes, it still awaits explanation. In our study, we inquired into patterns of mono- and trinucleotide intra-strand parity in complex plant genomic sequences that became available during the last few years, and compared these to equally complex animal genomes. The degree and patterns of deviation from Chargaff's second rule were different between plant and animal species. We observed a universal inter-chromosomal homogeneity of mononucleotide skews in coding sequences of plant chromosomes, while the base composition of animal coding sequences differed between chromosomes even within a single species. We also found differences in the base composition of dicot introns in comparison to those of monocots. These genome-wide patterns were limited to genic regions and were not encountered in inter-genic sequences. We discuss the implications of our findings in relation to hypotheses about functional correlations of intra-strand parity which have hitherto been put forward. Furthermore, we propose more recent polyploidization and subsequent homogenization of homoeologues as a possible reason for more homogeneous skew patterns in plants.

Two common profiles exist for genomic oligonucleotide frequencies

Background

It was reported that there is a majority profile for trinucleotide frequencies among genomes. And further study has revealed that two common profiles, rather than one majority profile, exist for genomic trinucleotide frequencies. However, the origins of the common/majority profile remain elusive. Moreover, it is not clear whether the features of common profile may be extended to oligonucleotides other than trinucleotides.

Findings

We analyzed 571 prokaryotic genomes (chromosomes) and some selected eukaryotic nuclear genomes as well as other genetic systems to study their compositional features. We found that there are also two common profiles for genomic oligonucleotide frequencies: one is from low-GC content genomes, and the other is from high-GC content genomes. Furthermore, each common profile is highly correlated to the average profile of random sequences with corresponding GC content and generated according to first-order symmetry.

Conclusions

The causes for the existence of two common profiles would mainly be GC content variations and strand symmetry of genomic sequences. Therefore, both GC content and strand symmetry would play important roles in genome evolution.

Influence of certain forces on evolution of synonymous codon usage bias in certain species of three basal orders of aquatic insects

Forces that influence the evolution of synonymous codon usage bias are analyzed in six species of three basal orders of aquatic insects. The rationale behind choosing six species of aquatic insects (three from Ephemeroptera, one from Plecoptera, and two from Odonata) for the present analysis is based on phylogenetic position at the basal clades of the Order Insecta facilitating the understanding of the evolution of codon bias and of factors shaping codon usage patterns in primitive clades of insect lineages and their subtle differences in some of their ecological and environmental requirements in terms of habitat-microhabitat requirements, altitudinal preferences, temperature tolerance ranges, and consequent responses to climate change impacts. The present analysis focuses on open reading frames of the 13 protein-coding genes in the mitochondrial genome of six carefully chosen insect species to get a comprehensive picture of the evolutionary intricacies of codon bias. In all the six species, A and T contents are observed to be significantly higher than G and C, and are used roughly equally. Since transcription hypothesis on codon usage demands A richness and T poorness, it is quite likely that mutation pressure may be the key factor associated with synonymous codon usage (SCU) variations in these species because the mutation hypothesis predicts AT richness and GC poorness in the mitochondrial DNA. Thus, AT-biased mutation pressure seems to be an important factor in framing the SCU variation in all the selected species of aquatic insects, which in turn explains the predominance of A and T ending codons in these species. This study does not find any association between microhabitats and codon usage variations in the mitochondria of selected aquatic insects. However, this study has identified major forces, such as compositional constraints and mutation pressure, which shape patterns of codon usage in mitochondrial genes in the primitive clades of insect lineages.

Fractal genome sequences

The existence of fractal sets of DNA sequences have long been suspected on the basis of statistical analyses of genome data. In this article we identify for the first time explicitly the GA-sequences as a class of fractal genomic sequences that are easy to recognize and to extract, and are scattered densely throughout the chromosomes of a large number of genomes from different species and kingdoms including the human genome. Their existence and their fractality may have significant consequences for our understanding of the origin and evolution of genomes. Furthermore, as universal and natural markers they may be used to chart and explore the non-coding regions.

A model capturing novel strand symmetries in bacterial DNA

Chargaff's second parity rule for short oligonucleotides states that the frequency of any short nucleotide sequence on a strand is approximately equal to the frequency of its reverse complement on the same strand. Recent studies have shown that, with the exception of organellar DNA, this parity rule generally holds for double-stranded DNA genomes and fails to hold for single-stranded genomes. While Chargaff's first parity rule is fully explained by the Watson-Crick pairing in the DNA double helix, a definitive explanation for the second parity rule has not yet been determined. In this work, we propose a model based on a hidden Markov process for approximating the distributional structure of primitive DNA sequences. Then, we use the model to provide another possible theoretical explanation for Chargaff's second parity rule, and to predict novel distributional aspects of bacterial DNA sequences.

Nucleosome positioning pattern derived from oligonucleotide compositions of genomic sequences

Availability of nucleosome positioning pattern(s) is crucial for chromatin studies. The matrix form of the pattern has been recently derived (I. Gabdank, D. Barash, E. N. Trifonov. J Biomol Struct Dyn 26, 403-412 (2009), and E. N. Trifonov. J Biomol Struct Dyn 27, 741-746 (2010)). In its simplified linear form it is described by the motif CGRAAATTTYCG. Oligonucleotide components of the motif (say, triplets GRA, RAA, AAA, etc.) would be expected to appear in eukaryotic sequences more frequently. In this work we attempted the reconstruction of the bendability patterns for 13 genomes by a novel approach-extension of highest frequency trinucleotides. The consensus of the patterns reconstructed on the basis of trinucleotide frequencies in 13 eukaryotic genomes is derived: CRAAAATTTTYG. It conforms to the earlier established sequence motif. The reconstruction, thus, attests to the universality of the nucleosome DNA bendability pattern.

Genome analysis with distance to the nearest dissimilar nucleotide

DNA may be represented by sequences of four symbols, but it is often useful to convert those symbols into real or complex numbers for further analysis. Several mapping schemes have been used in the past, but most of them seem to be unrelated to any intrinsic characteristic of DNA. The objective of this work was to study a mapping scheme that is directly related to DNA characteristics, and that could be useful in discriminating between different species. Recently, we have proposed a methodology based on the inter-nucleotide distance, which proved to contribute to the discrimination among species. In this paper, we introduce a new distance, the distance to the nearest dissimilar nucleotide, which is the distance of a nucleotide to first occurrence of a different nucleotide. This distance is related to the repetition structure of single nucleotides. Using the information resulting from the concatenation of the distance to the nearest dissimilar and the inter-nucleotide distance, we found that this new distance brings additional discriminative capabilities. This suggests that the distance to the nearest dissimilar nucleotide might contribute with useful information about the evolution of the species.