Apoptotic gene loss in Cnidaria is associated with transition to parasitism.

The phylum Cnidaria consists of several morphologically diverse classes including Anthozoa, Cubozoa, Hydrozoa, Polypodiozoa, Scyphozoa, Staurozoa, and Myxozoa. Myxozoa comprises two subclasses of obligate parasites-Myxosporea and Malacosporea, which demonstrate various degrees of simplification. Myxosporea were previously reported to lack the majority of core protein domains of apoptotic proteins including caspases, Bcl-2, and APAF-1 homologs. Other sequenced Cnidaria, including the parasite Polypodium hydriforme from Polypodiozoa do not share this genetic feature. Whether this loss of core apoptotic proteins is unique to Myxosporea or also present in its sister subclass Malacosporea was not previously investigated. We show that the presence of core apoptotic proteins gradually diminishes from free-living Cnidaria to Polypodium to Malacosporea to Myxosporea. This observation does not favor the hypothesis of catastrophic simplification of Myxosporea at the genetic level, but rather supports a stepwise adaptation to parasitism that likely started from early parasitic ancestors that gave rise to Myxozoa.

There is still no evidence of SARS-CoV-2 laboratory origin: Response to Segreto and Deigin (10.1002/bies.202100137).

The causative agent of COVID-19 SARS-CoV-2 has led to over 4 million deaths worldwide. Understanding the origin of this coronavirus is important for the prevention of future outbreaks. The dominant point of view that the virus transferred to humans either directly from bats or through an intermediate mammalian host has been challenged by Segreto and Deigin, who claim that the genome of SARS-CoV-2 has certain features suggestive of its artificial creation. Following their response to our commentary, here we continue the discussion of the proposed arguments for this hypothesis. We show that neither the existence of a furin cleavage site in SARS-CoV-2, nor the presence of specific sequences within the nucleotide insertion encoding that site are evidence for intelligent design. We also explain why existing genetic data, viral diversity and past human history suggest that a natural origin of the virus is the most likely scenario. Genetic evidence suggesting otherwise is yet to be presented.

There is no evidence of SARS-CoV-2 laboratory origin: Response to Segreto and Deigin (DOI: 10.1002/bies.202000240).

The origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the subject of many hypotheses. One of them, proposed by Segreto and Deigin, assumes artificial chimeric construction of SARS-CoV-2 from a backbone of RaTG13-like CoV and receptor binding domain (RBD) of a pangolin MP789-like CoV, followed by serial cell or animal passage. Here we show that this hypothesis relies on incorrect or weak assumptions, and does not agree with the results of comparative genomics analysis. The genetic divergence between SARS-CoV-2 and both its proposed ancestors is too high to have accumulated in a lab, given the timeframe of several years. Furthermore, comparative analysis of S-protein gene sequences suggests that the RBD of SARS-CoV-2 probably represents an ancestral non-recombinant variant. These and other arguments significantly weaken the hypothesis of a laboratory origin for SARS-CoV-2, while the hypothesis of a natural origin is consistent with all available genetic and experimental data.

Excessive G-U transversions in novel allele variants in SARS-CoV-2 genomes.

BACKGROUND: SARS-CoV-2 is a novel coronavirus that causes COVID-19 infection, with a closest known relative found in bats. For this virus, hundreds of genomes have been sequenced. This data provides insights into SARS-CoV-2 adaptations, determinants of pathogenicity and mutation patterns. A comparison between patterns of mutations that occurred before and after SARS-CoV-2 jumped to human hosts may reveal important evolutionary consequences of zoonotic transmission. METHODS: We used publically available complete genomes of SARS-CoV-2 to calculate relative frequencies of single nucleotide variations. These frequencies were compared with relative substitutions frequencies between SARS-CoV-2 and related animal coronaviruses. A similar analysis was performed for human coronaviruses SARS-CoV and HKU1. RESULTS: We found a 9-fold excess of G-U transversions among SARS-CoV-2 mutations over relative substitution frequencies between SARS-CoV-2 and a close relative coronavirus from bats (RaTG13). This suggests that mutation patterns of SARS-CoV-2 have changed after transmission to humans. The excess of G-U transversions was much smaller in a similar analysis for SARS-CoV and non-existent for HKU1. Remarkably, we did not find a similar excess of complementary C-A mutations in SARS-CoV-2. We discuss possible explanations for these observations.

Corrigendum to "Comparative Analysis of Context-Dependent Mutagenesis Using Human and Mouse Models".

[This corrects the article DOI: 10.1155/2013/989410.].

Coding palindromes in mitochondrial genes of Nematomorpha.

Inverted repeats are common DNA elements, but they rarely overlap with protein-coding sequences due to the ensuing conflict with the structure and function of the encoded protein. We discovered numerous perfect inverted repeats of considerable length (up to 284 bp) embedded within the protein-coding genes in mitochondrial genomes of four Nematomorpha species. Strikingly, both arms of the inverted repeats encode conserved regions of the amino acid sequence. We confirmed enzymatic activity of the respiratory complex I encoded by inverted repeat-containing genes. The nucleotide composition of inverted repeats suggests strong selection at the amino acid level in these regions. We conclude that the inverted repeat-containing genes are transcribed and translated into functional proteins. The survey of available mitochondrial genomes reveals that several other organisms possess similar albeit shorter embedded repeats. Mitochondrial genomes of Nematomorpha demonstrate an extraordinary evolutionary compromise where protein function and stringent secondary structure elements within the coding regions are preserved simultaneously.

Published GMO studies find no evidence of harm when corrected for multiple comparisons.

A number of widely debated research articles claiming possible technology-related health concerns have influenced the public opinion on genetically modified food safety. We performed a statistical reanalysis and review of experimental data presented in some of these studies and found that quite often in contradiction with the authors' conclusions the data actually provides weak evidence of harm that cannot be differentiated from chance. In our opinion the problem of statistically unaccounted multiple comparisons has led to some of the most cited anti-genetically modified organism health claims in history. We hope this analysis puts the original results of these studies into proper context.

Preservation of methylated CpG dinucleotides in human CpG islands.

BACKGROUND: CpG dinucleotides are extensively underrepresented in mammalian genomes. It is widely accepted that genome-wide CpG depletion is predominantly caused by an elevated CpG > TpG mutation rate due to frequent cytosine methylation in the CpG context. Meanwhile the CpG content in genomic regions called CpG islands (CGIs) is noticeably higher. This observation is usually explained by lower CpG > TpG substitution rates within CGIs due to reduced cytosine methylation levels. RESULTS: By combining genome-wide data on substitutions and methylation levels in several human cell types we have shown that cytosine methylation in human sperm cells was strongly and consistently associated with increased CpG > TpG substitution rates. In contrast, this correlation was not observed for embryonic stem cells or fibroblasts. Surprisingly, the decreased sperm CpG methylation level was insufficient to explain the reduced CpG > TpG substitution rates in CGIs. CONCLUSIONS: While cytosine methylation in human sperm cells is strongly associated with increased CpG > TpG substitution rates, substitution rates are significantly reduced within CGIs even after sperm CpG methylation levels and local GC content are controlled for. Our findings are consistent with strong negative selection preserving methylated CpGs within CGIs including intergenic ones.

Midichlorians--the biomeme hypothesis: is there a microbial component to religious rituals?

BACKGROUND: Cutting edge research of human microbiome diversity has led to the development of the microbiome-gut-brain axis concept, based on the idea that gut microbes may have an impact on the behavior of their human hosts. Many examples of behavior-altering parasites are known to affect members of the animal kingdom. Some prominent examples include Ophiocordyceps unilateralis (fungi), Toxoplasma gondii (protista), Wolbachia (bacteria), Glyptapanteles sp. (arthropoda), Spinochordodes tellinii (nematomorpha) and Dicrocoelium dendriticum (flat worm). These organisms belong to a very diverse set of taxonomic groups suggesting that the phenomena of parasitic host control might be more common in nature than currently established and possibly overlooked in humans. PRESENTATION OF THE HYPOTHESIS: Some microorganisms would gain an evolutionary advantage by encouraging human hosts to perform certain rituals that favor microbial transmission. We hypothesize that certain aspects of religious behavior observed in the human society could be influenced by microbial host control and that the transmission of some religious rituals could be regarded as the simultaneous transmission of both ideas (memes) and parasitic organisms. TESTING THE HYPOTHESIS: We predict that next-generation microbiome sequencing of samples obtained from gut or brain tissues of control subjects and subjects with a history of voluntary active participation in certain religious rituals that promote microbial transmission will lead to the discovery of microbes, whose presence has a consistent and positive association with religious behavior. Our hypothesis also predicts a decline of participation in religious rituals in societies with improved sanitation. IMPLICATIONS OF THE HYPOTHESIS: If proven true, our hypothesis may provide insights on the origin and pervasiveness of certain religious practices and provide an alternative explanation for recently published positive associations between parasite-stress and religiosity. The discovery of novel microorganisms that affect host behavior may improve our understanding of neurobiology and neurochemistry, while the diversity of such organisms may be of interest to evolutionary biologists and religious scholars. REVIEWERS: This article was reviewed by Prof. Dan Graur, Dr. Rob Knight and Dr. Eugene Koonin.

Comparative analysis of context-dependent mutagenesis using human and mouse models.

Substitution rates strongly depend on their nucleotide context. One of the most studied examples is the excess of C > T mutations in the CG context in various groups of organisms, including vertebrates. Studies on the molecular mechanisms underlying this mutation regularity have provided insights into evolution, mutagenesis, and cancer development. Recently several other hypermutable motifs were identified in the human genome. There is an increased frequency of T > C mutations in the second position of the words ATTG and ATAG and an increased frequency of A > C mutations in the first position of the word ACAA. For a better understanding of evolution, it is of interest whether these mutation regularities are human specific or present in other vertebrates, as their presence might affect the validity of currently used substitution models and molecular clocks. A comprehensive analysis of mutagenesis in 4 bp mutation contexts requires a vast amount of mutation data. Such data may be derived from the comparisons of individual genomes or from single nucleotide polymorphism (SNP) databases. Using this approach, we performed a systematical comparison of mutation regularities within 2-4 bp contexts in Mus musculus and Homo sapiens and uncovered that even closely related organisms may have notable differences in context-dependent mutation regularities.

Comparative analysis of context-dependent mutagenesis in humans and fruit flies.

In general, mutation frequencies are context-dependent: specific adjacent nucleotides may influence the probability to observe a specific type of mutation in a genome. Recently, several hypermutable motifs were identified in the human genome. Namely, there is an increased frequency of T>C mutations in the second position of the words ATTG and ATAG and an increased frequency of A>C mutations in the first position of the word ACAA. Previous studies have also shown that there is a remarkable difference between the mutagenesis of humans and drosophila. While C>T mutations are overrepresented in the CG context in humans (and other vertebrates), this mutation regularity is not observed in Drosophila melanogaster. Such differences in the observed regularities of mutagenesis between representatives of different taxa might reflect differences in the mechanisms involved in mutagenesis. We performed a systematical comparison of mutation regularities within 2-4 bp contexts in Homo sapiens and Drosophila melanogaster and found that the aforementioned contexts are not hypermutable in fruit flies. It seems that most mutation contexts affect mutation rates in a similar manner in H. sapiens and D. melanogaster; however, several important exceptions are noted and discussed.

New words in human mutagenesis.

BACKGROUND: The substitution rates within different nucleotide contexts are subject to varying levels of bias. The most well known example of such bias is the excess of C to T (C > T) mutations in CpG (CG) dinucleotides. The molecular mechanisms underlying this bias are important factors in human genome evolution and cancer development. The discovery of other nucleotide contexts that have profound effects on substitution rates can improve our understanding of how mutations are acquired, and why mutation hotspots exist. RESULTS: We compared rates of inherited mutations in 1-4 bp nucleotide contexts using reconstructed ancestral states of human single nucleotide polymorphisms (SNPs) from intergenic regions. Chimp and orangutan genomic sequences were used as outgroups. We uncovered 3.5 and 3.3-fold excesses of T > C mutations in the second position of ATTG and ATAG words, respectively, and a 3.4-fold excess of A > C mutations in the first position of the ACAA word. CONCLUSIONS: Although all the observed biases are less pronounced than the 5.1-fold excess of C > T mutations in CG dinucleotides, the three 4 bp mutation contexts mentioned above (and their complementary contexts) are well distinguished from all other mutation contexts. This provides a challenge to discover the underlying mechanisms responsible for the observed excesses of mutations.

Asymmetric and non-uniform evolution of recently duplicated human genes.

BACKGROUND: Gene duplications are a source of new genes and protein functions. The innovative role of duplication events makes families of paralogous genes an interesting target for studies in evolutionary biology. Here we study global trends in the evolution of human genes that resulted from recent duplications. RESULTS: The pressure of negative selection is weaker during a short time immediately after a duplication event. Roughly one fifth of genes in paralogous gene families are evolving asymmetrically: one of the proteins encoded by two closest paralogs accumulates amino acid substitutions significantly faster than its partner. This asymmetry cannot be explained by differences in gene expression levels. In asymmetric gene pairs the number of deleterious mutations is increased in one copy, while decreased in the other copy as compared to genes constituting non-asymmetrically evolving pairs. The asymmetry in the rate of synonymous substitutions is much weaker and not significant. CONCLUSIONS: The increase of negative selection pressure over time after a duplication event seems to be a major trend in the evolution of human paralogous gene families. The observed asymmetry in the evolution of paralogous genes shows that in many cases one of two gene copies remains practically unchanged, while the other accumulates functional mutations. This supports the hypothesis that slowly evolving gene copies preserve their original functions, while fast evolving copies obtain new specificities or functions.

Exclusive sequences of different genomes.

We studied the distribution of 1-7 bp words in a dataset that includes 139 complete eukaryotic genomes, 33 masked eukaryotic genomes and coding regions from 35 genomes. We tested different statistical models to determine over- and under-represented words. The method described by Karlin et al. has the strongest predictive power compared to other methods. Using this method we identified over- and under-represented words consistent within a large array of taxonomic groups. Some of those words have not yet been described as exclusive. For example, CGCG is over-represented in CG-deficient organisms. We also describe exceptions for widely known exclusive words, such as CG and TA.

Human trash ESTs--sequences from cDNA collection that are not aligned to genome assembly.

Expressed sequence tags (ESTs) represent 500-1000-bp-long sequences corresponding to mRNAs derived from different sources (cell lines, tissues, etc.). The human EST database contains over 8,000,000 sequences, with over 4,000,000,000 total nucleotides. RNA molecules are transcribed from a genomic DNA template; therefore, all ESTs should match corresponding genomes. Nevertheless, we have found in the human EST database approximately 11,000 ESTs not matching sequences in the human genome database. The presence of "trash" ESTs (TESTs) in the EST database could result from DNA or RNA contamination of the laboratory equipment, tissues, or cell lines. TESTs could also represent sequences from unidentified human genes or from species inhabiting the human body. Here, we attempt to identify the sources of human EST database contaminations. In particular, we discuss systematic contamination of the mammalian EST databases with sequences of plants.