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Introduction: This study, conducted in China prior to RotaTeq's launch, examined the epidemiological, molecular, and evolutionary features of the G1P[8] genotype RVA in children admitted with diarrhea, to aid in evaluating its efficacy and impact on G1P[8] RVA in China. Methods: Data from the Chinese viral diarrhea surveillance network were collected from January 2016 to December 2018. RVA strains identified as the G1P[8] genotype were subjected to whole-genome sequencing. Neutralizing epitope, amino acid selection pressure, and evolution dynamics analyses on VP7 and VP4 were performed using BioEdit v.7.0.9.0 and PyMOL v.2.5.2, four algorithms (MEME, SLAC, FEL, and FUBAR) in the Datamonkey online software, and the MCMC model in BEAST v. 1.10.4, respectively. Phylogenetic and identity features of 11 genes were assessed by DNAStar and MEGA v.7. Results: Results showed that the detection rate of G1P[8] in China from 2016 to 2018 was generally low with significant seasonality. The whole genome of G1P[8] of four 2016 childhood diarrhea specimens was successfully sequenced. Phylogenetic and neutralizing epitope analysis showed that Rotavin-M1 might have better protection on G1P[8] prevalent in China than Rotarix and RotaTeq. Two conserved N-glycosylation sites on VP7 of Chinese G1P[8] might affect the protective effect of the vaccine. Evolution rate and selection pressure analysis identified the possibility of rapidly evolving and adapting to the new environment introduced by vaccines of G1P[8], whereas positive selection specific to VP4 indicated the potential tendency to select for dominant traits. Identity and phylogeny analysis showed that Chinese G1P[8] from before 2018 was generally stable with possible genetic recombination among local strains. Discussion: These findings not only are of great significance for predicting the prevalence of G1P [8] in China, but also provide data reference for evaluating rotavirus vaccine efficacy. [ABSTRACT FROM AUTHOR]

Background: Antimicrobial resistance presents a formidable challenge, yet its existence predates the introduction of antibiotics. Our study delves into the presence of antimicrobial resistance genes (ARGs) in ancient permafrost microbiomes, comparing them with contemporary soil and pristine environments. Majority of the samples are from regions around Beringia, encompassing parts of Russia and Alaska, with only one sample originating from the Tien Shan Mountain range in Kyrgyzstan. Results: From over 2.3 tera basepairs of raw metagenomic data, retrieved from samples ranging in age from approximately 7,000 years to 1.1 million years, we assembled about 1.3 billion metagenomic contigs and explored the prevalence of ARGs within them. Our findings reveal a diverse array of ARGs in ancient microbiomes, akin to contemporary counterparts. On average, we identified 2 ARGs per rRNA gene in ancient samples. Actinomycetota, Bacillota, and several thermophiles were prominent carriers of ARGs in Chukochi and Kamchatkan samples. Conversely, ancient permafrost from the Tien Shan Mountain range exhibited no Thermophiles or Actinomycetota carrying ARGs. Both ancient and contemporary microbiomes showcased numerous divergent ARGs, majority of which have identity between 40 and 60% to genes in antibiotic resistance gene databases. To study the selection pressure on ARGs, we performed dN/dS analysis specifically on antibiotic inactivation-type ARGs, which exhibited purifying selection compared to contemporary genes. Conclusion: Antibiotic resistance has existed throughout microbial evolution and will likely persist, as microbes have the capacity to develop and retain resistance genes through evolutionary processes. The classes of antimicrobial resistance genes profiled and the function of antibiotic-inactivating enzymes from ancient permafrost microbiomes do not seem to be very different from the genes found in the antibiotic era. Additionally, we retrieved 359 putative complete viruses from ancient microbiomes and none of them harboured any ARGs. [ABSTRACT FROM AUTHOR]

Why does the growth of most life forms exhibit a narrow range of optimal temperatures below 40°C? We hypothesize that the recently identified stable range of oceanic temperatures of ~5 to 37°C for more than two billion years of Earth history tightly constrained the evolution of prokaryotic thermal performance curves to optimal temperatures for growth to less than 40°C. We tested whether competitive mechanisms reproduced the observed upper limits of life's temperature optima using simple Lotka–Volterra models of interspecific competition between organisms with different temperature optima. Model results supported our proposition whereby organisms with temperature optima up to 37°C were most competitive. Model results were highly robust to a wide range of reasonable variations in temperature response curves of modeled species. We further propose that inheritance of prokaryotic genes and subsequent co‐evolution with microbial partners may have resulted in eukaryotes also fixing their temperature optima within this narrow temperature range. We hope this hypothesis will motivate considerable discussion and future work to advance our understanding of the remarkable consistency of the temperature dependence of life. [ABSTRACT FROM AUTHOR]

Wisteria vein mosaic virus (WVMV, Potyvirus wisteriae), a virus belonging to the genus Potyvirus, is responsible for Wisteria vein mosaic disease (WMD), a severe disease that affects Wisteria, a genus of garden plants acclaimed worldwide. Although probably originating in the Far East, WVMV infection was first reported in the US, and subsequently in numerous countries. Following the first molecular detection of an Italian isolate, WVMV Bari, its full-length genome was achieved using NGS barcoding technology. A PhyML phylogenetic analysis, supported by clustering algorithm validation, identified a clear separation between two phylogroups. One major clade comprised WVMV strains isolated from Wisteria spp. A second clade grouped three highly divergent strains, at the borderline species threshold, all found in non-wisteria hosts. Relying on a Relative Time Dated Tips (RTDT) molecular clock, the first emergence of WVMV clades has been traced back to around the 17th century. A network inference analysis confirmed the sharp separation between the two host-related phylogroups, also highlighting the presence of potential intermediate variants. Inter-population genetic parameters revealed a very high genetic differentiation in both populations, which was made reliable by statistically significant permutation tests. The migrant number (Nm) and fixation index (FST) evidenced a restricted gene flow and strong population structures. According to the dN/dS ratio and negative neutrality tests, it was derived that purifying selection at the expense of non-silent variants is underway within WVMV populations. Targeting WVMV evolutionary traits, the present effort raised interesting questions about the underestimated potential of this culpably neglected species to spread in economically relevant crops. The main intention of our study is, therefore, to propose an evolution-based analysis approach that serves as a case study to investigate how other potyviruses or newly emerging viruses may spread. [ABSTRACT FROM AUTHOR]

Understanding natural protein evolution and designing novel proteins are motivating interest in development of high-throughput methods to explore large sequence spaces. In this work, we demonstrate the application of multisite λ dynamics (MSλD), a rigorous free energy simulation method, and chemical denaturation experiments to quantify evolutionary selection pressure from sequence-stability relationships and to address questions of design. This study examines a mesophilic phylogenetic clade of ribonuclease H (RNase H), furthering its extensive characterization in earlier studies, focusing on E. coli RNase H (ecRNH) and a more stable consensus sequence (AncCcons) differing at 15 positions. The stabilities of 32,768 chimeras between these two sequences were computed using the MSλD framework. The most stable and least stable chimeras were predicted and tested along with several other sequences, revealing a designed chimera with approximately the same stability increase as AncCcons, but requiring only half the mutations. Comparing the computed stabilities with experiment for 12 sequences reveals a Pearson correlation of 0.86 and root mean squared error of 1.18 kcal/mol, an unprecedented level of accuracy well beyond less rigorous computational design methods. We then quantified selection pressure using a simple evolutionary model in which sequences are selected according to the Boltzmann factor of their stability. Selection temperatures from 110 to 168 K are estimated in three ways by comparing experimental and computational results to evolutionary models. These estimates indicate selection pressure is high, which has implications for evolutionary dynamics and for the accuracy required for design, and suggests accurate high-throughput computational methods like MSλD may enable more effective protein design.

AbstractDifferent animal groups with varying locomotion modes may have unique energy requirements. Mitochondria produce adenosine triphosphate (ATP) and reactive oxygen species via oxidative phosphorylation to support organisms energy requirements. The tribes Pteromyini (flying squirrels) and Sciurini (tree squirrels), two closely related taxa within the family Sciuridae, exhibit distinct locomotion modes, energy requirements, and likely face different selective pressures on mitochondrial protein-coding genes (PCGs). We analysed 13 mitochondrial genome sequences from species belonging to the tribe Pteromyini and 117 from species belonging to the tribe Sciurini. Phylogenetic analysis revealed Pteromyini and Sciurini formed a sister relationship within the family Sciuridae. Among the 13 PCGs, ATP8 exhibited the highest dN/dS values, while COX1 showed the lowest. The background selection ratio (ω2) values for six genes (ND1, ND2, ND4, ATP6, ND5, and COX3) in Pteromyini were lower than the foreground selection ratio (ω0) values observed in Sciurini. A RELAX analysis revealed that CYTB, ND4, ATP6, and COX3 genes experienced intensified in selection strength. BUSTED analysis identified stronger signatures of diversifying selection in CYTB and ATP6, highlighting amino acid changes. MEME identified episodic diversifying selection at specific sites among eight PCGs. These findings revealed distinct selective pressures on PCGs in flying and tree squirrels. [ABSTRACT FROM AUTHOR]

Simple Summary: The present study aimed to assemble and annotate the mitochondrial genome of Keenocardium buelowi and conducted an in-depth analysis to investigate the molecular features of this mitochondrial genome. Our findings established phylogenetic relationships within the Cardiidae family. Additionally, evidence of selection pressure on the cytochrome b gene was detected, suggesting its important role in the evolution of K. buelowi. The mitochondrial genome provides valuable data for phylogenetic analysis and evolutionary research. In this study, we sequenced, assembled, and annotated the mitochondrial genome of Keenocardium buelowi using the Illumina platform. The genome spanned 16,967 bp and included 13 protein-coding genes (PCGs), two ribosomal RNAs, and 22 transfer RNAs. All PCGs utilized standard ATN start codons and TAN stop codons. The phylogenetic tree based on maximum likelihood and Bayesian inference analyses revealed Clinocardiinae as the sister group to Trachycardiinae, with the estimated divergence time being 44.5 million years ago (MYA) between K. buelowi and Vasticardium flavum. Notably, the cytochrome b gene (cob) exhibited a positive selection signal. Our findings provide valuable insights into the evolutionary history and molecular phylogeny of K. buelowi. [ABSTRACT FROM AUTHOR]

As climate change intensifies heatwaves, quantifying associated mortality within ectothermic populations is crucial for effective conservation. Thermal tolerance landscape (TTL) models are useful predictive tools that assume exponentially decreasing survival durations in individuals with increasing temperatures. This assumption has been validated through regression analyses on data from constant temperature experiments, primarily focusing on adult‐stage individuals. However, this approach does not allow for direct model validation with data from dynamic, real‐world heatwave events and overlooks early recruitment stage vulnerabilities.This study aimed to address these gaps using the blue mussel Mytilus, a foundation species forming extensive reefs along temperate coasts, as a model organism. We monitored survival rates of mussels (juveniles and adults) under constant heatwave (CHW) conditions in a laboratory experiment and under dynamic heatwave (DHW) scenarios simulated in an outdoor mesocosm experiment. Post‐heatwaves, we also assessed recruitment rates within the mesocosms. TTL models were parametrised by employing Approximate Bayesian Computation with Sequential Monte Carlo (ABC‐SMC) on each dataset separately.The parameter distributions were similar across both experiments, and the ABC‐SMC model predictions closely matched the observed survival declines, validating these models. In comparison, we found a lower predictive performance when using a Bayesian regression approach. Additionally, our best‐fit model predicted that warming across the non‐fatal DHW regimes would increase sublethal effects on mussels. The observed impact on the recruitment stage was more pronounced, with the recruitment rate following an exponential decay as sublethal effects increased. Our model projected minor (<4%) sublethal effects in adult mussels during the century's five warmest summer temperature regimes, corresponding to 0%–32% declines in recruitment rates.Our research extends the TTL model validation, demonstrates the resilience of subtidal Baltic Mytilus to future extreme heatwaves and offers an approach to predict heatwave‐induced population mortalities, applicable to other species and sensitive systems. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

Duck hepatitis virus 1 (DHV-1) is a major threat to the global poultry industry, causing significant economic losses due to high mortality rates in young ducklings. To better understand the evolution and host adaptation strategies of DHV-1, we conducted a comprehensive codon usage analysis of DHV-1 genomes. Our phylogenetic analysis revealed three well-supported DHV-1 phylogroups (Ia, Ib, and II) with distinct genetic diversity patterns. Comparative analyses of the codon usage bias and dinucleotide abundance uncovered a strong preference for A/U-ended codons and a biased pattern of dinucleotide usage in the DHV-1 genome, with CG dinucleotides being extremely underrepresented. Effective number of codons (ENC) analysis indicated a low codon usage bias in the DHV-1 ORF sequences, suggesting adaptation to host codon usage preferences. PR2 bias, ENC plot, and neutrality analyses revealed that both mutation pressure and natural selection influence the codon usage patterns of DHV-1. Notably, the three DHV-1 phylogroups exhibited distinct evolutionary trends, with phylogroups Ia and Ib showing evidence of neutral evolution accompanied by selective pressure, while the phylogroup II evolution was primarily driven by random genetic drift. Comparative analysis of the codon usage indices (CAI, RCDI, and SiD) among the phylogroups highlighted significant differences between subgroups Ia and Ib, suggesting distinct evolutionary pressures or adaptations influencing their codon usage. These findings contribute to our understanding of DHV-1 evolution and host adaptation, with potential implications for the development of effective control measures and vaccines. [ABSTRACT FROM AUTHOR]

Climatic changes can affect species distributions, population abundance, and evolution. Such organismal responses could be determined by the amount and quality of available habitats, which can vary independently. In this study, we assessed changes in habitat quantity and quality independently to generate explicit predictions of the species' responses to climatic changes between Last Glacial Maximum (LGM) and present day. We built ecological niche models for genetic groups within 21 reptile, mammal, and plant taxa from the Baja California peninsula inhabiting lowland or highland environments. Significant niche divergence was detected for all clades within species, along with significant differences in the niche breadth and area of distribution between northern and southern clades. We quantified habitat quantity from the distribution models, and most clades showed a reduction in distribution area towards LGM. Further, niche marginality (used as a measure of habitat quality) was higher during LGM for most clades, except for northern highland species. Our results suggest that changes in habitat quantity and quality can affect organismal responses independently. This allows the prediction of genomic signatures associated with changes in effective population size and selection pressure that could be explicitly tested from our models. [ABSTRACT FROM AUTHOR]

The yellowtail snapper Ocyurus chrysurus Bloch, 1791 (Perciformes: Lutjanidae) is targeted by recreational or commercial fisheries across much of its range in the western Atlantic Ocean, from Massachusetts, USA, to São Paulo, Brazil. Genomic resources to support conservation of this species are needed. Here, we assembled, annotated and characterised in detail the mitochondrial genome of O. chrysurus. The mitochondrial genome of O. chrysurus is 16,502 bp in length and encodes 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNA), and two ribosomal RNA genes (rRNA). The putative control region, 827 bp in length, is located between the tRNA P and tRNA F genes. Most genes are encoded on the positive strand, while a single PCG (nad6) and six tRNA genes (in order from 5′ to 3′: tRNA N, tRNA P, tRNA E, tRNA Q, tRNA C and tRNA Y) are encoded on the negative strand. All tRNA have a typical 'cloverleaf' secondary structure except tRNA S1 (Serine1) that lacks the D arm. Calculated Ka/Ks values of all PCGs were <1, suggesting that these genes are under purifying selection. A maximum likelihood (ML) phylogenetic analysis confirmed monophyly of the family Lutjanidae and indicated that the genus Lutjanus is paraphyletic given that O. chrysurus clustered together with Lutjanus peru and L. guttatus in a strongly supported clade. Data published herein will inform conservation and management strategies for this fished snapper. [ABSTRACT FROM AUTHOR]

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A comprehensive and systematic examination of dengue virus (DENV) evolution is essential in Pakistan, where the virus poses a significant public health challenge due to its ability to adapt and evolve. To shed light on the intricate evolutionary patterns of all four DENV serotypes, we analyzed complete genome sequences (n = 43) and Envelope (E) gene sequences (n = 44) of all four DENV serotypes collected in Pakistan from 1994 to 2023, providing a holistic view of their genetic evolution. Our findings revealed that all four serotypes of DENV co-circulate in Pakistan with a close evolutionary relationship between DENV-1 and DENV-3. Among the genetically distinct serotypes DENV-2 and DENV-4, DENV-4 stands out as the most genetically different, while DENV-2 exhibits greater complexity due to the presence of multiple genotypes and the possibility of temporal fluctuations in genotype prevalence. Selective pressure analysis of the Envelope (E) gene revealed heterogeneity among sequences (n = 44), highlighting 46 codons in the genome experiencing selective pressure, characterized by a bias toward balancing selection, indicating genetic stability of the virus. Furthermore, our study suggested an intriguing evolutionary shift of DENV-4 toward the DENV-2 clade, potentially influenced by antibodies with cross-reactivity to multiple serotypes, providing a critical insight into the complex factors, shaping DENV evolution and contributing to the emergence of new serotypes. [ABSTRACT FROM AUTHOR]

【Objective】The study aimed to identify three NAC gene families of Castanea plants while analyzing of codon usage bias. It provided an important theoretical basis for further exploring the function of NAC gene family in chestnut plants.【Method】Using bioinformatics methods, the chromosome position, phyloevolutionary relationships, protein motif, selective pressure, codon usage bias were analyzed in the three Castanea plants.【Result】In the study, 333 Castanea NAC gene family members were identified with unequal distribution across different chromosomes. The evolutionary tree analysis revealed that it can be divided into five groups. Protein motif analysis revealed that the five groups all contained the conserved Motif 1- Motif 7. Collinearity analysis showed that it contained strong collinearity within and between the genome, and most of the collinear gene pairs were undergoing purifying selection pressure. The codon usage bias analysis showed a weak codon usage bias. Neutral mapping analysis and ENC-plot mapping analysis showed that their codon usage bias was more under natural selective pressure. The optimal codon analysis revealed that the NAC gene families of three Castanea plants together contained 11 optimal codons. For example, CAU, UAA, GUU, etc. Comparing the codon usage frequency with the comparative model plants, Arabidopsis thaliana, Nicotiana tabacum and Solanum lycopersicum were all suitable exogenous receptors for the three Castanea plants.【Conclusion】The study provides a comprehensive understanding of the evolutionary relationships, selection pressures, codon preference of NAC gene family members of Castanea plants. And the study lay a theoretical foundation for the later use of molecular biological means to improve the efficiency of NAC gene expression in Castanea plants. [ABSTRACT FROM AUTHOR]

Despite garlic (Allium sativum L.) being recognized as the second most important species in the Allium genus, a limited number of varieties are available worldwide. Aiming to develop new purple garlic varieties, a representative sample was used to determine the extent of phenotypic variability for commercially desirable characteristics. Initially, 360 bolting bulbs were selected based on their size and abundant external scales. After further assessment, 243 bulbs were discarded due to undesirable traits such as light purple color, numerous small cloves, or damage from Fusarium spp. and mites. Although garlic reproduces asexually, each bulb was considered to represent a distinct family. Thus, 117 families were planted in a randomized complete block design during the 2021–2022 growing season. Physiological, morphological, and phenological traits were assessed for each family, along with damages caused by pests and pathogens. As a result of these evaluations, 103 families were selected for a second trial the following season. Due to increased selection pressure, only 23 families remained in the program at the end of the second trial. High variability was observed for most traits, with a strong influence from family lineage. Environmental conditions significantly impacted the performance of the families, highlighting the need to evaluate them under diverse environments. The high variability within the selected sample indicates a strong potential for developing new garlic varieties. [ABSTRACT FROM AUTHOR]

Background: China is the hotspot of global freshwater crab diversity, but their wild populations are facing severe pressures associated with anthropogenic factors, necessitating the need to map their taxonomic and genetic diversity and design conservation policies. Results: Herein, we sequenced the mitochondrial genome of a Chinese freshwater crab species Bottapotamon fukienense, and found that it is fragmented into two chromosomes. We confirmed that fragmentation was not limited to a single specimen or population. Chromosome 1 comprised 15,111 base pairs (bp) and there were 26 genes and one pseudogene (pseudo-nad1) encoded on it. Chromosome 2 comprised 8,173 bp and there were 12 genes and two pseudogenes (pseudo-trnL2 and pseudo-rrnL) encoded on it. Combined, they comprise the largest mitogenome (23,284 bp) among the Potamidae. Bottapotamon was the only genus in the Potamidae dataset exhibiting rearrangements of protein-coding genes. Bottapotamon fukienense exhibited average rates of sequence evolution in the dataset and did not differ in selection pressures from the remaining Potamidae. Conclusions: This is the first experimentally confirmed fragmentation of a mitogenome in crustaceans. While the mitogenome of B. fukienense exhibited multiple signs of elevated mitogenomic architecture evolution rates, including the exceptionally large size, duplicated genes, pseudogenisation, rearrangements of protein-coding genes, and fragmentation, there is no evidence that this is matched by elevated sequence evolutionary rates or changes in selection pressures. [ABSTRACT FROM AUTHOR]

Whether in ant–aphid mutualism the ants exert evolutionary selection pressure on aphid morphology has not yet been fully tested. Here, we tested whether the long proboscises of Stomaphis yanonis (Aphididae Lachninae) aphids confer an advantage in preventing predation by the tending ants. Specifically, we tested the hypothesis that aphids with a shorter proboscis would excrete less honeydew, making them more likely to be preyed upon by ants. Our results showed that aphid individuals with a shorter proboscis took up less phloem sap and excreted less honeydew than individuals with a longer proboscis. In addition, among aphids with a similar body size, those with a shorter proboscis were more susceptible to predation by ants than those with a longer proboscis. These results suggest that predation by tending ants, by exerting selection pressure on aphid proboscis morphology, has caused the aphids to evolve longer proboscises. [ABSTRACT FROM AUTHOR]

IntroductionThis study, conducted in China prior to RotaTeq’s launch, examined the epidemiological, molecular, and evolutionary features of the G1P[8] genotype RVA in children admitted with diarrhea, to aid in evaluating its efficacy and impact on G1P[8] RVA in China.MethodsData from the Chinese viral diarrhea surveillance network were collected from January 2016 to December 2018. RVA strains identified as the G1P[8] genotype were subjected to whole-genome sequencing. Neutralizing epitope, amino acid selection pressure, and evolution dynamics analyses on VP7 and VP4 were performed using BioEdit v.7.0.9.0 and PyMOL v.2.5.2, four algorithms (MEME, SLAC, FEL, and FUBAR) in the Datamonkey online software, and the MCMC model in BEAST v. 1.10.4, respectively. Phylogenetic and identity features of 11 genes were assessed by DNAStar and MEGA v.7.ResultsResults showed that the detection rate of G1P[8] in China from 2016 to 2018 was generally low with significant seasonality. The whole genome of G1P[8] of four 2016 childhood diarrhea specimens was successfully sequenced. Phylogenetic and neutralizing epitope analysis showed that Rotavin-M1 might have better protection on G1P[8] prevalent in China than Rotarix and RotaTeq. Two conserved N-glycosylation sites on VP7 of Chinese G1P[8] might affect the protective effect of the vaccine. Evolution rate and selection pressure analysis identified the possibility of rapidly evolving and adapting to the new environment introduced by vaccines of G1P[8], whereas positive selection specific to VP4 indicated the potential tendency to select for dominant traits. Identity and phylogeny analysis showed that Chinese G1P[8] from before 2018 was generally stable with possible genetic recombination among local strains.DiscussionThese findings not only are of great significance for predicting the prevalence of G1P [8] in China, but also provide data reference for evaluating rotavirus vaccine efficacy.

Styrax japonicus is a medicinal and ornamental shrub belonging to the Styracaceae family. To explore the diversity and characteristics of the chloroplast genome of S. japonicus, we conducted sequencing and comparison of the chloroplast genomes of four naturally distributed S. japonicus. The results demonstrated that the four chloroplast genomes (157,914–157,962 bp) exhibited a typical quadripartite structure consisting of a large single copy (LSC) region, a small single copy (SSC) region, and a pair of reverse repeats (IRa and IRb), and the structure was highly conserved. DNA polymorphism analysis revealed that three coding genes (infA, psbK, and rpl33) and five intergene regions (petA-psbJ, trnC-petN, trnD-trnY, trnE-trnT, and trnY-trnE) were identified as mutation hotspots. These genetic fragments have the potential to be utilized as DNA barcodes for future identification purposes. When comparing the boundary genes, a small contraction was observed in the IR region of four S. japonicus. Selection pressure analysis indicated positive selection for ycf1 and ndhD. These findings collectively suggest the adaptive evolution of S. japonicus. The phylogenetic structure revealed conflicting relationships among several S. japonicus, indicating divergent evolutionary paths within this species. Our study concludes by uncovering the genetic traits of the chloroplast genome in the differentiation of S. japonicus variety, offering fresh perspectives on the evolutionary lineage of this species. [ABSTRACT FROM AUTHOR]

Megacarpaea megalocarpa, a perennial herbaceous species belonging to the Brassicaceae family, has potential medicinal value. We isolated and characterized the chloroplast (cp) genome of M. megalocarpa and compared it with closely related species. The chloroplast genome displayed a typical quadripartite structure, spanning 154,877 bp, with an overall guanine–cytosine (GC) content of 36.20%. Additionally, this genome contained 129 genes, 105 simple sequence repeats (SSRs), and 48 long repeat sequences. Significantly, the ycf1 gene exhibited a high degree of polymorphism at the small single copy (SSC) region and the inverted repeat a (IRa) boundary. Despite this polymorphism, relative synonymous codon usage (RSCU) values were found to be similar across species, and no large segment rearrangements or inversions were detected. The large single copy (LSC) and SSC regions showed higher sequence variations and nucleotide polymorphisms compared to the IR region. Thirteen distinct hotspot regions were identified as potential molecular markers. Our selection pressure analysis revealed that the protein-coding gene rpl20 is subjected to different selection pressures in various species. Phylogenetic analysis positioned M. megalocarpa within the expanded lineage II of the Brassicaceae family. The estimated divergence time suggests that M. megalocarpa diverged approximately 4.97 million years ago. In summary, this study provides crucial baseline information for the molecular identification, phylogenetic relationships, conservation efforts, and utilization of wild resources in Megacarpaea. [ABSTRACT FROM AUTHOR]

[Display omitted] • Whole-genome sequencing and comparative genomic analysis were performed on Cryptosporidium xiaoi. • Cryptosporidium xiaoi and the bovine-specific C. bovis have 96% genomic identity and undergo similar genome reduction. • The species-specific and divergent genes between C. xiaoi and C. bovis may contribute to their different host preferences. • These genes may be targets for in-depth study of Cryptosporidium biology. Cryptosporidium spp. are important diarrhea-associated pathogens in humans and livestock. Among the known species, Cryptosporidium xiaoi , which causes cryptosporidiosis in sheep and goats, was previously recognized as a genotype of the bovine-specific Cryptosporidium bovis based on their high sequence identity in the ssrRNA gene. However, the lack of genomic data has limited characterization of the genetic differences between the two closely related species. In this study, we sequenced the genomes of two C. xiaoi isolates and performed comparative genomic analysis to identify the sequence uniqueness of this ovine-adapted species compared with other Cryptosporidium spp. Our results showed that C. xiaoi is genetically related to C. bovis as shown by their 95.8% genomic identity and similar gene content. Consistent with this, both C. xiaoi and C. bovis appear to have fewer genes encoding mitochondrial metabolic enzymes and invasion-related protein families. However, they appear to possess several species-specific genes. Further analysis indicates that the sequence differences between these two Cryptosporidium spp. are mainly in 24 highly polymorphic genes, half of which are located in the subtelomeric regions. Some of these subtelomeric genes encode secretory proteins that have undergone positive selection. In addition, the genomes of two C. xiaoi isolates, identified as subtypes XXIIIf and XXIIIh, share 99.9% nucleotide sequence identity, with six highly divergent genes encoding putative secretory proteins. Therefore, these species-specific genes and sequence polymorphism in subtelomeric genes probably contribute to the different host preference of C. xiaoi and C. bovis. [ABSTRACT FROM AUTHOR]

Extensive use of carbapenems may lead to selection pressure for Stenotrophomonas maltophilia (SM) in hospital environments. The aim of our study was to assess the possible association between systemic antibiotic use and the incidence of SM. A retrospective, observational study was carried out in a tertiary-care hospital in Hungary, between January 1st 2010 and December 31st 2019. Incidence-density for SM and SM resistant to trimethoprim-sulfamethoxazole (SXT) was standardized for 1000 patient-days, while systemic antibiotic use was expressed as defined daily doses (DDDs) per 100 patient-days. Mean incidence density for SM infections was 0.42/1000 patient-days; 11.08% were were resistant to SXT, the mean incidence density for SXT-resistant SM was 0.047/1000 patient-days. Consumption rate for colistin, glycopeptides and carbapenems increased by 258.82, 278.94 and 372.72% from 2010 to 2019, respectively. Strong and significant positive correlations were observed with the consumption of carbapenems (r: 0.8759; P < 0.001 and r: 0.8968; P < 0.001), SXT (r: 0.7552; P = 0.011 and r: 0.7004; P = 0.024), and glycopeptides (r: 0.7542; P = 0.012 and r: 0.8138; P < 0.001) with SM and SXT-resistant SM incidence-density/1000 patient-days, respectively. Implementation of institutional carbapenem-sparing strategies are critical in preserving these life-saving drugs, and may affect the microbial spectrum of infections in clinical settings. [ABSTRACT FROM AUTHOR]

MYBs constitute the second largest transcription factor (TF) superfamily in flowering plants with substantial structural and functional diversity, which have been brought into focus because they affect flower colors by regulating anthocyanin biosynthesis. Up to now, the genomic data of several Chrysanthemum species have been released, which provides us with abundant genomic resources for revealing the evolution of the MYB gene family in Chrysanthemum species. In the present study, comparative analyses of the MYB gene family in six representative species, including C. lavandulifolium, C. seticuspe, C. ×morifolium, Helianthus annuus, Lactuca sativa, and Arabidopsis thaliana, were performed. A total of 1104 MYBs, which were classified into four subfamilies and 35 lineages, were identified in the three Chrysanthemum species (C. lavandulifolium, C. seticuspe, and C. ×morifolium). We found that whole-genome duplication and tandem duplication are the main duplication mechanisms that drove the occurrence of duplicates in CmMYBs (particularly in the R2R3-MYB subfamily) during the evolution of the cultivated chrysanthemums. Sequence structure and selective pressure analyses of the MYB gene family revealed that some of R2R3-MYBs were subjected to positive selection, which are mostly located on the distal telomere segments of the chromosomes and contain motifs 7 and 8. In addition, the gene expression analysis of CmMYBs in different organs and at various capitulum developmental stages of C. ×morifolium indicated that CmMYBS2, CmMYB96, and CmMYB109 might be the negative regulators for anthocyanin biosynthesis. Our results provide the phylogenetic context for research on the genetic and functional evolution of the MYB gene family in Chrysanthemum species and deepen our understanding of the regulatory mechanism of MYB TFs on the flower color of C. ×morifolium. [ABSTRACT FROM AUTHOR]

Abstract Goats have achieved global prominence as essential livestock since their initial domestication, primarily owing to their remarkable adaptability to diverse environmental and production systems. Differential selection pressures influenced by climate have led to variations in their physical attributes, leaving genetic imprints within the genomes of goat breeds raised in diverse agroecological settings. In light of this, our study pursued a comprehensive analysis, merging environmental data with single nucleotide polymorphism (SNP) variations, to unearth indications of selection shaped by climate-mediated forces in goats. Through the examination of 43,300 SNPs from 51 indigenous goat breeds adapting to different climatic conditions using four analytical methods: latent factor mixed models (LFMM), F-statistics (Fst), Extended haplotype homozygosity across populations (XPEHH), and spatial analysis method (SAM), A total of 74 genes were revealed to display clear signs of selection, which are believed to be influenced by climatic conditions. Among these genes, 32 were consistently identified by at least two of the applied methods, and three genes (DENND1A, PLCB1, and ITPR2) were confirmed by all four approaches. Moreover, our investigation yielded 148 Gene Ontology (GO) terms based on these 74 genes, underlining pivotal biological pathways crucial for environmental adaptation. These pathways encompass functions like vascular smooth muscle contraction, cellular response to heat, GTPase regulator activity, rhythmic processes, and responses to temperature stimuli. Of significance, GO terms about endocrine regulation and energy metabolic responses, key for local adaptation were also uncovered, including biological processes, such as cell differentiation, regulation of peptide hormone secretion, and lipid metabolism. These findings contribute to our knowledge of the genetic structure of climate-triggered adaptation across the goat genome and have practical implications for marker-assisted breeding in goats.

Abstract Background The mediator complex subunits (MED) constitutes a multiprotein complex, with each subunit intricately involved in crucial aspects of plant growth, development, and responses to stress. Nevertheless, scant reports pertain to the VunMED gene within the context of asparagus bean (Vigna unguiculata ssp. sesquipedialis). Establishing the identification and exploring the responsiveness of VunMED to cold stress forms a robust foundation for the cultivation of cold-tolerant asparagus bean cultivars. Results Within this study, a comprehensive genome-wide identification of VunMED genes was executed in the asparagus bean cultivar 'Ningjiang3', resulting in the discovery of 36 distinct VunMED genes. A phylogenetic analysis encompassing 232 MED genes from diverse species, including Arabidopsis, tomatoes, soybeans, mung beans, cowpeas, and asparagus beans, underscored the highly conserved nature of MED gene sequences. Throughout evolutionary processes, each VunMED gene underwent purification and neutral selection, with the exception of VunMED19a. Notably, VunMED9/10b/12/13/17/23 exhibited structural variations discernible across four cowpea species. Divergent patterns of temporal and spatial expression were evident among VunMED genes, with a prominent role attributed to most genes during early fruit development. Additionally, an analysis of promoter cis-acting elements was performed, followed by qRT-PCR assessments on roots, stems, and leaves to gauge relative expression after exposure to cold stress and subsequent recovery. Both treatments induced transcriptional alterations in VunMED genes, with particularly pronounced effects observed in root-based genes following cold stress. Elucidating the interrelationships between subunits involved a preliminary understanding facilitated by correlation and principal component analyses. Conclusions This study elucidates the pivotal contribution of VunMED genes to the growth, development, and response to cold stress in asparagus beans. Furthermore, it offers a valuable point of reference regarding the individual roles of MED subunits.

Wisteria vein mosaic virus (WVMV, Potyvirus wisteriae), a virus belonging to the genus Potyvirus, is responsible for Wisteria vein mosaic disease (WMD), a severe disease that affects Wisteria, a genus of garden plants acclaimed worldwide. Although probably originating in the Far East, WVMV infection was first reported in the US, and subsequently in numerous countries. Following the first molecular detection of an Italian isolate, WVMV Bari, its full-length genome was achieved using NGS barcoding technology. A PhyML phylogenetic analysis, supported by clustering algorithm validation, identified a clear separation between two phylogroups. One major clade comprised WVMV strains isolated from Wisteria spp. A second clade grouped three highly divergent strains, at the borderline species threshold, all found in non-wisteria hosts. Relying on a Relative Time Dated Tips (RTDT) molecular clock, the first emergence of WVMV clades has been traced back to around the 17th century. A network inference analysis confirmed the sharp separation between the two host-related phylogroups, also highlighting the presence of potential intermediate variants. Inter-population genetic parameters revealed a very high genetic differentiation in both populations, which was made reliable by statistically significant permutation tests. The migrant number (Nm) and fixation index (FST) evidenced a restricted gene flow and strong population structures. According to the dN/dS ratio and negative neutrality tests, it was derived that purifying selection at the expense of non-silent variants is underway within WVMV populations. Targeting WVMV evolutionary traits, the present effort raised interesting questions about the underestimated potential of this culpably neglected species to spread in economically relevant crops. The main intention of our study is, therefore, to propose an evolution-based analysis approach that serves as a case study to investigate how other potyviruses or newly emerging viruses may spread.

[Display omitted] • Strong mitonuclear discordance in phylogeny and evolutionary rates were found in Neodermata. • Polyopisthocotylea may have the fastest-evolving mtDNA sequences in Bilateria. • Polyopisthocotylea exhibits a long stem branch in the mtDNA, but not in the nDNA topology. • We found weak evidence of mitonuclear co-evolution and none for compensatory evolution. • A large (≈6.3 kb) numt in Diplorchis sp. exhibits signs of ncRNA expression. The genomic evolution of Polyopisthocotylea remains poorly understood in comparison to the remaining three classes of Neodermata: Monopisthocotylea, Cestoda, and Trematoda. Moreover, the evolutionary sequence of major events in the phylogeny of Neodermata remains unresolved. Herein we sequenced the mitogenome and transcriptome of the polyopisthocotylean Diplorchis sp., and conducted comparative evolutionary analyses using nuclear (nDNA) and mitochondrial (mtDNA) genomic datasets of Neodermata. We found strong mitonuclear discordance in the phylogeny of Neodermata. Polyopisthocotylea exhibited striking mitonuclear discordance in relative evolutionary rates: the fastest-evolving mtDNA in Neodermata and a comparatively slowly-evolving nDNA genome. This was largely attributable to its very long stem branch in mtDNA topologies, not exhibited by the nDNA data. We found indications that the fast evolution of mitochondrial genomes of Polyopisthocotylea may be driven both by relaxed purifying selection pressures and elevated levels of directional selection. We identified mitochondria-associated genes encoded in the nuclear genome: they exhibited unique evolutionary rates, but not correlated with the evolutionary rate of mtDNA, and there is no evidence for compensatory evolution (they evolved slower than the rest of the genome). Finally, there appears to exist an exceptionally large (≈6.3 kb) nuclear mitochondrial DNA segment (numt) in the nuclear genome of newly sequenced Diplorchis sp. A 3′-end segment of the 16S rRNA gene encoded by the numt was expressed, suggesting that this gene acquired novel, regulatory functions after the transposition to the nuclear genome. In conclusion, Polyopisthocotylea appears to be the lineage with the fastest-evolving mtDNA sequences among all of Bilateria, but most of the substitutions were accumulated deep in the evolutionary history of this lineage. As the nuclear genome does not exhibit a similar pattern, the circumstances underpinning this evolutionary phenomenon remain a mystery. [ABSTRACT FROM AUTHOR]

Invasive plants typically escape specialist herbivores but are often attacked by generalist herbivores in their introduced ranges. The shifting defense hypothesis suggests that this will cause invasive plants to evolve lower resistance against specialists, higher resistance against generalists, and greater tolerance to herbivore damage. However, the duration and direction of selective pressures can shape the evolutionary responses of resistance and tolerance for invasive plants. Two critical factors are (1) residence time (length of time that an invasive species has been in its introduced range) and (2) specialist herbivore reassociation (attack by purposely or accidentally introduced specialists). Yet, these two factors have not been considered simultaneously in previous quantitative syntheses. Here, we performed a meta-analysis with 367 effect sizes from 70 studies of 35 invasive plant species from native and invasive populations. We tested how the residence time of invasive plant species and specialist reassociation in their introduced ranges affected evolutionary responses of defenses against specialists and generalists, including herbivore resistance traits (physical barriers, digestibility reducers and toxins), resistance effects (performance of and damage caused by specialists or generalists) and tolerance to damage (from specialists or generalists). We found that residence time and specialist reassociation each significantly altered digestibility reducers, specialist performance, generalist damage, and tolerance to specialist damage. Furthermore, residence time and specialist reassociation strongly altered toxins and generalist performance, respectively. When we restricted consideration to invasive plant species with both longer residence times and no reassociation with specialists, invasive populations had lower resistance to specialists, similar resistance to generalists, and higher tolerance to damage from both herbivore types, compared with native populations. We conclude that the duration and direction of selective pressure shape the evolutionary responses of invasive plants. Under long-term (long residence time) and stable (no specialist reassociation) selective pressure, invasive plants generally decrease resistance to specialists and increase tolerance to generalist damage that provides mixed support for the shifting defense hypothesis. [ABSTRACT FROM AUTHOR]

Diospyros sutchuensis is a national protected wild plant species with narrow distribution and extremely small population in southwestern China. At present, the genomic information of this species is lacking and its phylogenetic relationships among Diospyros remain unclear. In this study, the chloroplast genome of D. sutchuensis was sequenced by Illumina platform, assembled and annotated by Getorganelle v1.7.3.4 and PGA, and analyzed by DnaSP 6.12.03 for sequence comparison, REPuter, Tandem Reapeats Finder, MISA for repetitive sequences, CodonW1.4 for codon usage bias, and EasyCodemL for selection pressure. Meanwhile, based on four different chloroplast genome sequence datasets, the phylogenetic relationships between D. sutchuensis and 11 Diospyros species were analyzed using IQtree. The results were as follows: (1) The chloroplast genome of D. sutchuensis was 157 917 bp in length, including two inverted repeats (IRs) of 26 111 bp, which was separated by large single copy (LSC) and short single copy (SSC) of 87 303 bp and 18 392 bp, respectively. The GC content was 37.4%. (2) The genome contained 113 genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. A total of 49 long repeats, 27 tandem repeats, and 34 simple sequence repeats were identified. There were 31 high-frequency codons in protein-coding genes, most of them ended in A or U, and the most used codons were the ones encoding leucine. The coding regions were more conserved than the non-coding ones, and 10 regions were identified as most divergent hotspots for potential molecular markers. There had been positive selection on ndhB, ndhG, ndhI, rbcL, rpoB, petB, petD and rps12 among protein-coding genes. (3) Phylogenetic analyses showed that D. sutchuensis was closely related to D. rhombifolia and D. cathayensis. Together with D. hainanensis, these four species formed a monophyletic group. The phylogenetic tree constructed from the chloroplast genomes had the highest support values, indicating that the chloroplast genomes with most variable and informative sites are more suitable for phylogenetic studies of Diospyros. The results provide useful chloroplast genomic resources for germplasm identification, genetic diversity conservation, repopulation, and phylogenetic analysis of D. sutchuensis as well as Diospyros.

The mitochondrial genome provides valuable data for phylogenetic analysis and evolutionary research. In this study, we sequenced, assembled, and annotated the mitochondrial genome of Keenocardium buelowi using the Illumina platform. The genome spanned 16,967 bp and included 13 protein-coding genes (PCGs), two ribosomal RNAs, and 22 transfer RNAs. All PCGs utilized standard ATN start codons and TAN stop codons. The phylogenetic tree based on maximum likelihood and Bayesian inference analyses revealed Clinocardiinae as the sister group to Trachycardiinae, with the estimated divergence time being 44.5 million years ago (MYA) between K. buelowi and Vasticardium flavum. Notably, the cytochrome b gene (cob) exhibited a positive selection signal. Our findings provide valuable insights into the evolutionary history and molecular phylogeny of K. buelowi.

Duck hepatitis virus 1 (DHV-1) is a major threat to the global poultry industry, causing significant economic losses due to high mortality rates in young ducklings. To better understand the evolution and host adaptation strategies of DHV-1, we conducted a comprehensive codon usage analysis of DHV-1 genomes. Our phylogenetic analysis revealed three well-supported DHV-1 phylogroups (Ia, Ib, and II) with distinct genetic diversity patterns. Comparative analyses of the codon usage bias and dinucleotide abundance uncovered a strong preference for A/U-ended codons and a biased pattern of dinucleotide usage in the DHV-1 genome, with CG dinucleotides being extremely underrepresented. Effective number of codons (ENC) analysis indicated a low codon usage bias in the DHV-1 ORF sequences, suggesting adaptation to host codon usage preferences. PR2 bias, ENC plot, and neutrality analyses revealed that both mutation pressure and natural selection influence the codon usage patterns of DHV-1. Notably, the three DHV-1 phylogroups exhibited distinct evolutionary trends, with phylogroups Ia and Ib showing evidence of neutral evolution accompanied by selective pressure, while the phylogroup II evolution was primarily driven by random genetic drift. Comparative analysis of the codon usage indices (CAI, RCDI, and SiD) among the phylogroups highlighted significant differences between subgroups Ia and Ib, suggesting distinct evolutionary pressures or adaptations influencing their codon usage. These findings contribute to our understanding of DHV-1 evolution and host adaptation, with potential implications for the development of effective control measures and vaccines.

Despite garlic (Allium sativum L.) being recognized as the second most important species in the Allium genus, a limited number of varieties are available worldwide. Aiming to develop new purple garlic varieties, a representative sample was used to determine the extent of phenotypic variability for commercially desirable characteristics. Initially, 360 bolting bulbs were selected based on their size and abundant external scales. After further assessment, 243 bulbs were discarded due to undesirable traits such as light purple color, numerous small cloves, or damage from Fusarium spp. and mites. Although garlic reproduces asexually, each bulb was considered to represent a distinct family. Thus, 117 families were planted in a randomized complete block design during the 2021–2022 growing season. Physiological, morphological, and phenological traits were assessed for each family, along with damages caused by pests and pathogens. As a result of these evaluations, 103 families were selected for a second trial the following season. Due to increased selection pressure, only 23 families remained in the program at the end of the second trial. High variability was observed for most traits, with a strong influence from family lineage. Environmental conditions significantly impacted the performance of the families, highlighting the need to evaluate them under diverse environments. The high variability within the selected sample indicates a strong potential for developing new garlic varieties.

Abstract Background Persistent high-risk human papillomavirus (HR-HPV) infection is an important factor in the development of cervical cancer, and human papillomavirus type 16 (HPV-16) is the most common HR-HPV type worldwide. The oncogenic potential of HPV-16 is closely related to viral sequence variation. Methods In order to clarify the variant characteristics of HPV-16 E6 and E7 genes in central China, E6 and E7 sequences of 205 HPV‐16 positive samples were amplified by polymerase chain reaction. PCR products of E6 and E7 genes were further sequenced and subjected to variation analysis, phylogenetic analysis, selective pressure analysis and B-cell epitope prediction. Results Twenty-six single nucleotide variants were observed in E6 sequence, including 21 non-synonymous and 5 synonymous variants. Twelve single nucleotide variants were identified in E7 sequence, including 6 non-synonymous and 6 synonymous variants. Four new variants were found. Furthermore, nucleotide variation A647G (N29S) in E7 was significantly related to the higher risk of HSIL and cervical cancer. Phylogenetic analysis showed that the E6 and E7 sequences were all distributed in A lineage. No positively selected site was found in HPV-16 E6 and E7 sequences. Non-conservative substitutions in E6, H31Y, D32N, D32E, I34M, L35V, E36Q, L45P, N65S and K75T, affected multiple B-cell epitopes. However, the variation of E7 gene had little impact on the corresponding B-cell epitopes (score

Abstract Background Echovirus 30 is prone to cause hand-foot-and-mouth disease in infants and children. However, molecular epidemiologic information on the spread of E30 in southwestern China remains limited. In this study, we determined and analyzed the whole genomic sequences of E30 strains isolated from the stools of patients with hand-foot-and-mouth disease in Yunnan Province, China, in 2019. Methods E30 isolates were obtained from fecal samples of HFMD patients. The whole genomes were sequenced by segmented PCR and analyzed for phylogeny, mutation and recombination. MEGA and DNAStar were used to align the present isolates with the reference strains. The VP1 sequence of the isolates were analyzed for selection pressure using datamonkey server. Results The complete genome sequences of four E30 were obtained from this virus isolation. Significant homologous recombination signals in the P2-3’UTR region were found in all four isolates with other serotypes. Phylogenetic analysis showed that the four E30 isolates belonged to lineage H. Comparison of the VP1 sequences of these four isolates with other E30 reference strains using three selection pressure analysis models FUBAR, FEL, and MEME, revealed a positive selection site at 133rd position. Conclusions This study extends the whole genome sequence of E30 in GenBank, in which mutations and recombinations have driven the evolution of E30 and further improved and enriched the genetic characteristics of E30, providing fundamental data for the prevention and control of diseases caused by E30. Furthermore, we demonstrated the value of continuous and extensive surveillance of enterovirus serotypes other than the major HFMD-causing viruses.

Turnip mosaic virus (TuMV) is the most important virus of brassica crops. In our study, we compare the genetic structure of two Czech TuMV populations sampled in the country's 25-year interval of virus presence. The 21 isolates, mainly infecting rutabaga and horseradish, were collected from four farms under organic production, and nearly complete genome sequences, 9 596-9 787 nt in length, were obtained using Sanger sequencing for all of them. The analysis of variability and polymorphism showed differences in genetic structure but the relative stability of both populations and moderate negative selection as a factor affecting the current TuMV population. The newly collected isolates are characterised by a relatively high frequency of intralineage recombinants; interlineage recombinants were not detected compared to the 25-year-old population. The phylogenetic analysis allowed the classification of all Czech isolates into world-B phylogroup, with the prevalence of isolates of subgroup B2. The spread of isolates belonging to the other phylogenetic groups posing higher phytopathological risk, which were present in the old population and some surrounding countries, was not found.

ABSTRACTIn the Staphylococcus aureus genome, a set of highly conserved two-component systems (TCSs) composed of histidine kinases (HKs) and their cognate response regulators (RRs) sense and respond to environmental stimuli, which drive the adaptation of the bacteria. This study investigates the complex interplay between TCSs in S. aureus USA300, a predominant methicillin-resistant S. aureus strain, revealing shared and unique virulence regulatory pathways and genetic variations mediating signal specificity within TCSs. Using TCS-related mutants from the Nebraska Transposon Mutant Library, we analyzed the effects of inactivated TCS HKs and RRs on the production of various virulence factors, in vitro infection abilities, and adhesion assays. We found that the TCSs’ influence on virulence determinants was not associated with their phylogenetic relationship, indicating divergent functional evolution. Using the co-crystallized structure of the DesK-DesR from Bacillus subtilis and the modeled structures of the four NarL TCSs in S. aureus, we identified interacting residues, revealing specificity determinants and conservation within the same TCS, even from different strain backgrounds. The interacting residues were highly conserved within strains but varied between species due to selection pressures and the coevolution of cognate pairs. This study unveils the complex interplay and divergent functional evolution of TCSs, highlighting their potential for future experimental exploration of phosphotransfer between cognate and non-cognate recombinant HK and RRs.IMPORTANCEGiven the widespread conservation of two-component systems (TCSs) in bacteria and their pivotal role in regulating metabolic and virulence pathways, they present a compelling target for anti-microbial agents, especially in the face of rising multi-drug-resistant infections. Harnessing TCSs therapeutically necessitates a profound understanding of their evolutionary trajectory in signal transduction, as this underlies their unique or shared virulence regulatory pathways. Such insights are critical for effectively targeting TCS components, ensuring an optimized impact on bacterial virulence, and mitigating the risk of resistance emergence via the evolution of alternative pathways. Our research offers an in-depth exploration of virulence determinants controlled by TCSs in S. aureus, shedding light on the evolving specificity determinants that orchestrate interactions between their cognate pairs.

ABSTRACTWe conducted an in silico analysis to better understand the potential factors impacting host adaptation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in white-tailed deer, humans, and mink due to the strong evidence of sustained transmission within these hosts. Classification models trained on single nucleotide and amino acid differences between samples effectively identified white-tailed deer-, human-, and mink-derived SARS-CoV-2. For example, the balanced accuracy score of Extremely Randomized Trees classifiers was 0.984 ± 0.006. Eighty-eight commonly identified predictive mutations are found at sites under strong positive and negative selective pressure. A large fraction of sites under selection (86.9%) or identified by machine learning (87.1%) are found in genes other than the spike. Some locations encoded by these gene regions are predicted to be B- and T-cell epitopes or are implicated in modulating the immune response suggesting that host adaptation may involve the evasion of the host immune system, modulation of the class-I major-histocompatibility complex, and the diminished recognition of immune epitopes by CD8+ T cells. Our selection and machine learning analysis also identified that silent mutations, such as C7303T and C9430T, play an important role in discriminating deer-derived samples across multiple clades. Finally, our investigation into the origin of the B.1.641 lineage from white-tailed deer in Canada discovered an additional human sequence from Michigan related to the B.1.641 lineage sampled near the emergence of this lineage. These findings demonstrate that machine-learning approaches can be used in combination with evolutionary genomics to identify factors possibly involved in the cross-species transmission of viruses and the emergence of novel viral lineages.IMPORTANCESevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible virus capable of infecting and establishing itself in human and wildlife populations, such as white-tailed deer. This fact highlights the importance of developing novel ways to identify genetic factors that contribute to its spread and adaptation to new host species. This is especially important since these populations can serve as reservoirs that potentially facilitate the re-introduction of new variants into human populations. In this study, we apply machine learning and phylogenetic methods to uncover biomarkers of SARS-CoV-2 adaptation in mink and white-tailed deer. We find evidence demonstrating that both non-synonymous and silent mutations can be used to differentiate animal-derived sequences from human-derived ones and each other. This evidence also suggests that host adaptation involves the evasion of the immune system and the suppression of antigen presentation. Finally, the methods developed here are general and can be used to investigate host adaptation in viruses other than SARS-CoV-2.

ABSTRACTThe spread of SARS-CoV-2 virus accompanied by public availability of abundant sequence data provides a window for the determination of viral evolutionary patterns. In this study, SARS-CoV-2 genome sequences were collected from seven countries in the period January 2020–December 2022. The sequences were classified into three phases, namely, pre-vaccination, post-vaccination, and recent period. Comparison was performed between these phases based on parameters like mutation rates, selection pressure (dN/dS ratio), and transition to transversion ratios (Ti/Tv). Similar comparisons were performed among SARS-CoV-2 variants. Statistical significance was tested using Graphpad unpaired t-test. The analysis showed an increase in the percent genomic mutation rates post-vaccination and in recent periods across all countries from the pre-vaccination sequences. Mutation rates were highest in NSP3, S, N, and NSP12b before and increased further after vaccination. NSP4 showed the largest change in mutation rates after vaccination. The dN/dS ratios showed purifying selection that shifted toward neutral selection after vaccination. N, ORF8, ORF3a, and ORF10 were under highest positive selection before vaccination. Shift toward neutral selection was driven by E, NSP3, and ORF7a in the after vaccination set. In recent sequences, the largest dN/dS change was observed in E, NSP1, and NSP13. The Ti/Tv ratios decreased with time. C→U and G→U were the most frequent transitions and transversions. However, U→G was the most frequent transversion in recent period. The Omicron variant had the highest genomic mutation rates, while Delta showed the highest dN/dS ratio. Protein-wise dN/dS ratio was also seen to vary across the different variants.IMPORTANCETo the best of our knowledge, there exists no other large-scale study of the genomic and protein-wise mutation patterns during the time course of evolution in different countries. Analyzing the SARS-CoV-2 evolutionary patterns in view of the varying spatial, temporal, and biological signals is important for diagnostics, therapeutics, and pharmacovigilance of SARS-CoV-2.

Paeonia delavayi var. lutea, Paeonia delavayi var. angustiloba, and Paeonia ludlowii are Chinese endemics that belong to the Paeoniaceae family and have vital medicinal and ornamental value. It is often difficult to classify Paeoniaceae plants based on their morphological characteristics, and the limited genomic information has strongly hindered molecular evolution and phylogenetic studies of Paeoniaceae. In this study, we sequenced, assembled, and annotated the chloroplast genomes of P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii. The chloroplast genomes of these strains were comparatively analyzed, and their phylogenetic relationships and divergence times were inferred. These three chloroplast genomes exhibited a typical quadripartite structure and were 152,687–152,759 bp in length. Each genome contains 126–132 genes, including 81–87 protein-coding genes, 37 transfer RNAs, and 8 ribosomal RNAs. In addition, the genomes had 61–64 SSRs, with mononucleotide repeats being the most abundant. The codon bias patterns of the three species tend to use codons ending in A/U. Six regions of high variability were identified (psbK-psbL, trnG-UCC, petN-psbM, psbC, rps8-rpl14, and ycf1) that can be used as DNA molecular markers for phylogenetic and taxonomic analysis. The Ka/Ks ratio indicates positive selection for the rps18 gene associated with self-replication. The phylogenetic analysis of 99 chloroplast genomes from Saxifragales clarified the phylogenetic relationships of Paeoniaceae and revealed that P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii are monophyletic groups and sisters to P. delavayi. Divergence time estimation revealed two evolutionary divergences of Paeoniaceae species in the early Oligocene and Miocene. Afterward, they underwent rapid adaptive radiation from the Pliocene to the early Pleistocene when P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii formed. The results of this study enrich the chloroplast genomic information of Paeoniaceae and reveal new insights into the phylogeny of Paeoniaceae. [ABSTRACT FROM AUTHOR]

Diospyros sutchuensis is a national protected wild plant species with narrow distribution and extremely small population in southwestern China. At present, the genomic information of this species is lacking and its phylogenetic relationships among Diospyros remain unclear. In this study, the chloroplast genome of D. sutchuensis was sequenced by Illumina platform, assembled and annotated by Getorganelle v1.7.3.4 and PGA, and analyzed by DnaSP 6.12.03 for sequence comparison, REPuter, Tandem Reapeats Finder, MISA for repetitive sequences, CodonW1.4 for codon usage bias, and EasyCodemL for selection pressure. Meanwhile, based on four different chloroplast genome sequence datasets, the phylogenetic relationships between D. sutchuensis and 11 Diospyros species were analyzed using IQtree. The results were as follows:(1)The chloroplast genome of D. sutchuensis was 157 917 bp in length, including two inverted repeats(IRs)of 26 111 bp, which was separated by large single copy(LSC)and short single copy(SSC)of 87 303 bp and 18 392 bp, respectively. The GC content was 37.4%.(2)The genome contained 113 genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. A total of 49 long repeats, 27 tandem repeats, and 34 simple sequence repeats were identified. There were 31 high-frequency codons in protein-coding genes, most of them ended in A or U, and the most used codons were the ones encoding leucine. The coding regions were more conserved than the non-coding ones, and 10 regions were identified as most divergent hotspots for potential molecular markers. There had been positive selection on ndhB, ndhG, ndhI, rbcL, rpoB, petB, petD and rps12 among protein-coding genes.(3)Phylogenetic analyses showed that D. sutchuensis was closely related to D. rhombifolia and D. cathayensis. Together with D. hainanensis, these four species formed a monophyletic group. The phylogenetic tree constructed from the chloroplast genomes had the highest support values, indicating that the chloroplast genomes with most variable and informative sites are more suitable for phylogenetic studies of Diospyros. The results provide useful chloroplast genomic resources for germplasm identification, genetic diversity conservation, repopulation, and phylogenetic analysis of D. sutchuensis as well as Diospyros. [ABSTRACT FROM AUTHOR]

Fujian province, an important tea-producing area in China, has abundant tea cultivars. To investigate the genetic relationships of tea plant cultivars in Fujian province and the characteristics of the tea plant varieties, a total of 70 tea cultivars from Fujian and other 12 provinces in China were subjected to restriction site-associated DNA sequencing (RAD-seq). A total of 60,258,975 single nucleotide polymorphism (SNP) sites were obtained. These 70 tea plant cultivars were divided into three groups based on analyzing the phylogenetic tree, principal component, and population structure. Selection pressure analysis indicated that nucleotide diversity was high in Southern China and genetically distinct from cultivars of Fujian tea plant cultivars, according to selection pressure analysis. The selected genes have significant enrichment in pathways associated with metabolism, photosynthesis, and respiration. There were ten characteristic volatiles screened by gas chromatography–mass spectrometry (GC–MS) coupled with multivariate statistical methods, among which the differences in the contents of methyl salicylate, 3-carene, cis-3-hexen-1-ol, (E)-4-hexen-1-ol, and 3-methylbutyraldehyde can be used as reference indicators of the geographical distribution of tea plants. Furthermore, a metabolome genome-wide association study (mGWAS) revealed that 438 candidate genes were related to the aroma metabolic pathway. Further analysis showed that 31 genes of all the selected genes were screened and revealed the reasons for the genetic differences in aroma among tea plant cultivars in Fujian and Southern China. These results reveal the genetic diversity in the Fujian tea plants as well as a theoretical basis for the conservation, development, and utilization of the Fujian highly aromatic tea plant cultivars. [ABSTRACT FROM AUTHOR]