KaKs_Calculator 3.0: calculating selective pressure on coding and non-coding sequences

KaKs_Calculator 3.0 is an updated toolkit that is capable for calculating selective pressure on both coding and non-coding sequences. Similar to the nonsynonymous/synonymous substitution rate ratio for coding sequences, selection on non-coding sequences can be quantified as non-coding nucleotide substitution rate normalized by synonymous substitution rate of adjacent coding sequences. As testified on empirical data, it shows effectiveness to detect the strength and mode of selection operated on molecular sequences, accordingly demonstrating its great potential to achieve genome-wide scan of natural selection on diverse sequences and identification of potentially functional elements at whole genome scale. The package of KaKs_Calculator 3.0 is freely available for academic use only at https://ngdc.cncb.ac.cn/biocode/tools/BT000001.

Whole-Genome Analysis of Coxsackievirus B3 Reflects Its Genetic Diversity in China and Worldwide

Background Coxsackievirus B3 (CVB3) has emerged as an active pathogen in myocarditis, aseptic meningitis, hand, foot, and mouth disease (HFMD), and pancreatitis, and is a heavy burden on public health. However, CVB3 has not been systematically analyzed with regard to whole-genome diversity and recombination. Therefore, this study was undertaken to systematically examine the genetic characteristics of CVB3 based on its whole genome. Methods We combined CVB3 isolates from our national HFMD surveillance and global sequences retrieved from GenBank. Phylogenetic analysis was performed to examine the whole genome variety and recombination forms of CVB3 in China and worldwide. Results Phylogenetic analysis showed that CVB3 strains isolated worldwide could be classified into groups A–E based on the sequence of the entire VP1 region. The predominant CVB3 strains in China belonged to group D, whereas group E CVB3 might be circulated globally compared to other groups. The average nucleotide substitution rate in the P1 region of CVB3 was 4.82 × 10−3 substitutions/site/year. Myocarditis was more common with group A. Groups C and D presented more cases of acute flaccid paralysis, and group D may be more likely to cause HFMD. Multiple recombination events were detected among CVB3 variants, and there were twenty-three recombinant lineages of CVB3 circulating worldwide. Conclusions Overall, this study provides full-length genomic sequences of CVB3 isolates with a wide geographic distribution over a long-term time scale in China, which will be helpful for understanding the evolution of this pathogen. Simultaneously, continuous surveillance of CVB3 is indispensable to determine its genetic diversity in China as well as worldwide.

Genetic Characterizations and Molecular Evolution of the Measles Virus Genotype B3’s Hemagglutinin (H) Gene in the Elimination Era

Measles virus (MeV) genotype B3 is one globally significant circulating genotype. Here, we present a systematic description of long-term evolutionary characterizations of the MeV genotype B3’s hemagglutinin (H) gene in the elimination era. Our results show that the B3 H gene can be divided into two main sub-genotypes, and the highest intra-genotypic diversity was observed in 2004. MeV genotype B3’s H gene diverged in 1976; its overall nucleotide substitution rate is estimated to be 5.697 × 10−4 substitutions/site/year, and is slowing down. The amino acid substitution rate of genotype B3’s H gene is also decreasing, and the mean effective population size has been in a downward trend since 2000. Selection pressure analysis only recognized a few sites under positive selection, and the number of positive selection sites is getting smaller. All of these observations may reveal that genotype B3’s H gene is not under strong selection pressure, and is becoming increasingly conservative. MeV H-gene or whole-genome sequencing should be routine, so as to better elucidate the molecular epidemiology of MeV in the future.

Molecular evolution and genetic analysis of Mesta yellow vein mosaic virus and associated betasatellites

Mesta yellow vein mosaic disease (MYVMD), one of the major diseases circulating mesta growing regions of Indian sub-continent, is responsible for serious yield loss in mesta crops. A complex of monopartite begomovirus, Mesta yellow vein mosaic virus (MYVMV) and associated betasatellite, is reported in several studies as the causal agent of MYVMD. However, all-inclusive molecular evolutionary analysis of so far available MYVMVs and associated betasatellites disseminating in this region is still lacking. In this study, by estimating and analyzing various indexes of population genetics and evolutionary parameters, we discussed the sources of genetic variations, population dynamics and different forces acting on the evolution of MYVMVs and associated betasatellites. The study finds recombination as a vital force in the evolution and diversification of begomovirus complexes in different geographic locations however, betasatellites were found to be exposed to more diverse recombination events compared to MYVMVs. Indian isolates are reported to have high frequency of polymorphism in this study which suggests a balancing selection or expansion occurring in Indian populations of begomoviruses. Higher degree of genetic differentiation and lower rate of gene flow calculated between the viral populations of Bangladesh and Pakistan is justified by the relatively far geographical distance between these two countries. Although the study detects overall purifying selection, the degrees of constraints acting on individual gene tested are found different. Coat protein (AV1) is estimated with very high nucleotide substitution rate which is very likely to result from the strongest purifying selection pressure (dN/dS = 0.131) calculated in this study on coat protein. The findings of this study on different evolutionary forces that shape the emergence and diversification of MYVMVs and associated betasatellites may provide directions towards future evolutionary trend analysis and development of comprehensive disease control strategies for begomoviruses.

Genomic comparison of non-photosynthetic plants from the family Balanophoraceae with their photosynthetic relatives

The plant family Balanophoraceae consists entirely of species that have lost the ability to photosynthesize. Instead, they obtain nutrients by parasitizing other plants. Recent studies have revealed that plastid genomes of Balanophoraceae exhibit a number of interesting features, one of the most prominent of those being a highly elevated AT content of nearly 90%. Additionally, the nucleotide substitution rate in the plastid genomes of Balanophoraceae is an order of magnitude greater than that of their photosynthetic relatives without signs of relaxed selection. Currently, there are no definitive explanations for these features. Given these unusual features, we hypothesised that the nuclear genomes of Balanophoraceae may also provide valuable information in regard to understanding the evolution of non-photosynthetic plants. To gain insight into these genomes, in the present study we analysed the transcriptomes of two Balanophoraceae species (Rhopalocnemis phalloides and Balanophora fungosa) and compared them to the transcriptomes of their close photosynthetic relatives (Daenikera sp., Dendropemon caribaeus, and Malania oleifera). Our analysis revealed that the AT content of the nuclear genes of Balanophoraceae did not markedly differ from that of the photosynthetic relatives. The nucleotide substitution rate in the genes of Balanophoraceae is, for an unknown reason, several-fold larger than in the genes of photosynthetic Santalales; however, the negative selection in Balanophoraceae is likely stronger. We observed an extensive loss of photosynthesis-related genes in the Balanophoraceae family members. Additionally, we did not observe transcripts of several genes whose products function in plastid genome repair. This implies their loss or very low expression, which may explain the increased nucleotide substitution rate and AT content of the plastid genomes.

A time irreversible model of nucleotide substitution for the coronavirus evolution

SARS-CoV-2 is the cause of the worldwide epidemic of severe acute respiratory syndrome. Evolutionary studies of the virus genome will provide a predictor of the fate of COVID-19 in the near future. Recent studies of the virus genomes have shown that C to U substitutions are overrepresented in the genome sequences of SARS-CoV-2. Traditional time-reversible substitution models cannot be applied to the evolution of SARS-CoV-2 sequences. Therefore, in this study, I propose a new time-irreversible model and a new method for estimating the nucleotide substitution rate of SARS-CoV-2. Computer simulations showed that that the new method gives good estimates. I applied the new method to estimate nucleotide substitution rates of SARS-CoV-2 sequences. The result suggests that the rate of C to U substitution of SARS-Cov-2 is ten times higher than other types of substitutions.

Evolutionary Shift from Purifying Selection towards Divergent Selection of SARS-CoV2 Favors its Invasion into Multiple Human Organs

SARS-CoV2 virus is believed to be originated from a closely related bat Coronavirus RaTG13 lineage after gaining insertions of RBD of spike (S) protein by exchanged recombination with pangolin virus Pan_SL_COV_GD. SARSCoV2 uses its entry-point key residues in S1 protein to attach with human ACE2 receptor. SARS-CoV2 evolution comprises any of these possibilities: it entered human from bat with its poorly developed entry-point residues much before its known appearance with slower mutation rate; or recently with efficiently developed entry-point residues having more infective power with higher mutation rate; or through an intermediate host. RaTG13 has 96.3% identity with SARS-CoV2 genome implying that it substituted ~1106 nucleotides to evolute as present-day virus. Temporal analysis of SARS-CoV2 genome from December 2019 shows that its nucleotide substitution rate is as low as 27nt/year with an evolutionary rate of 9x10-4 /site/year, which is a little less than other retrovirus (10-4 to 10-6 /site/year). Estimation of TMRCA of SARS-CoV2 from bat RaTG13 lineage appears to be in between 9-14 years. Furthermore, evolution of a critical entry-point residue Y493Q needs two substitutions with an intermediate virus carrying Y493H (Y>H>Q), although such an intermediate virus has not been identified in known twenty-nine bat CoV virus. Genetic codon analysis indicates that SARS-CoV2 evolution from RaTG13 lineage strictly follows neutral evolution with strong purifying selection whereas its propagation in human disobeys neutral evolution as nonsynonymous mutations surpasses synonymous mutations with the increase of ω (dn/ds) signifying its proceedings towards divergent selection predictably for its infection power to evade multiple organs.

High nucleotide substitution rates associated with retrotransposon proliferation drive dynamic secretome evolution in smut pathogens

Transposable elements (TEs) play a pivotal role in shaping diversity in eukaryotic genomes. The covered smut pathogen on barley, Ustilago hordei, encountered a recent genome expansion. Using long reads, we assembled genomes of 6 U. hordei strains and 3 sister species, to study this genome expansion. We found that larger genome sizes can mainly be attributed to long terminal repeat retrotransposons (LTR-RTs) of the Copia and Gypsy superfamilies. From the studied smuts, LTR-RTs proliferated the most recently and to the furthest extent in the U. hordei genome, in which they make up for 19.5% of the genome. Interestingly, the extent of TE proliferation in different smut species is positively correlated to the mating-type locus size, which is largest in U. hordei with up to ~560 kb. TE transposition within the mating-type loci and their flanking regions are mating-type specific, which is likely due to the very low recombination activity in this region. Furthermore, LTR-RT proliferation was found to be associated with higher nucleotide substitution levels, as genes in genome regions that are rich in dynamic LTR-RTs display higher nucleotide substitution levels. The high nucleotide substitution rate particularly affected the evolution of genes encoding secreted proteins as substitutions more frequently led to amino acid alterations. The mechanism behind this increase in nucleotide substitution rate remains elusive, but seems not to be a consequence of the repeat-induced point mutation (RIP) mechanism, as genes and LTR-RTs did not display typical RIP substitutions.

Coxsackievirus B4: a Undervalued Pathogen that Associated with Hand, Foot and Mouth Disease Outbreak

Objectives: This study was conducted to discover the causes of Coxsackievirus B4 (CVB4) -induced hand, foot, and mouth disease (HFMD) outbreaks and its evolutionary characteristics.Methods: In this study, we sequenced isolates obtained during the outbreak for comparative analyses with previously sequenced strains. Phylogenetic analysis and evolutionary dynamics were performed to illustrate the genetic characteristics of CVB4 in China and worldwide.Results: The nucleotide sequence of CVB4 isolated during the outbreak in 2011 was more similar to that of CVB4 isolated in Shandong Province, China in 2010 (95.7–99.4%) than to other CVB4 isolated in China (90.9–98.8%). A phylogenetic analysis showed that CVB4 originated from a common ancestor in Shandong. CVB4 strains isolated worldwide could be classified into genotypes A–E according to the VP1 region. All CVB4 strains in China belonged to genotype E. The global population diversity of CVB4 fluctuated substantially over time, and CVB4 isolated from China accounted for a significant increase in diversity of CVB4. The average nucleotide substitution rate in VP1 of Chinese CVB4 (5.20 × 10-3 substitutions/site/year) was slightly higher than that of global CVB4 (4.82 × 10-3 substitutions/site/year). Conclusions: These findings explain both the 2011 outbreak and a global increase in CVB4 diversity. In addition to improving our understanding of a major outbreak, these findings provide a basis for the development of surveillance strategies.