scholarly journals Epidemiology, Genetic Characterization, and Evolution of Hunnivirus Carried by Rattus norvegicus and Rattus tanezumi: The First Epidemiological Evidence from Southern China

Pathogens ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 661
Author(s):  
Minyi Zhang ◽  
Qiushuang Li ◽  
Fei Wu ◽  
Zejin Ou ◽  
Yongzhi Li ◽  
...  
Keyword(s):  
Rattus Norvegicus ◽  
Southern China ◽  
Genome Structure ◽  
Single Species ◽  
Synonymous Substitution ◽  
Limited Information ◽  
Coding Regions ◽  
Rattus Tanezumi ◽  
Synonymous Substitution Rates ◽  
Potential Risks

Hunnivirus is a novel member of the family Picornaviridae. A single species, Hunnivirus A, is currently described. However, there is limited information on the identification of Hunnivirus to date, and thereby the circulation of Hunnivirus is not fully understood. Thus, the objective of this study was to investigate the prevalence, genomic characteristics, and evolution of rat hunnivirus in southern China. A total of 404 fecal samples were subjected to detection of Hunnivirus from urban rats (Rattus norvegicus and Rattus tanezumi) using PCR assay based on specific primers targeted to partial 3D regions, with the prevalence of 17.8% in Rattus norvegicus and 15.6% in Rattus tanezumi. An almost full-length rat hunnivirus sequence (RatHuV/YY12/CHN) and the genome structure were acquired in the present study. Phylogenetic analysis of the P1 coding regions suggested the RatHuV/YY12/CHN sequence was found to be within the genotype of Hunnivirus A4. The negative selection was further identified based on analysis of non-synonymous to synonymous substitution rates. The present findings suggest that hunniviruses are common in urban rats. Further research is needed for increased surveillance and awareness of potential risks to human health.

scholarly journals Epidemiology and genetic characteristics of murine kobuvirus from faecal samples of Rattus losea, Rattus tanezumi and Rattus norvegicus in southern China

2021 ◽  
Vol 102 (9) ◽  
Author(s):  
Minyi Zhang ◽  
Fangfei You ◽  
Fei Wu ◽  
Huan He ◽  
Qiushuang Li ◽  
...  
Keyword(s):  
Rattus Norvegicus ◽  
Southern China ◽  
Phylogenetic Analyses ◽  
Rodent Species ◽  
Limited Information ◽  
Genetic Characteristics ◽  
Murine Rodent ◽  
Faecal Samples ◽  
Rattus Tanezumi ◽  
Rodent Populations

Recently, murine kobuvirus (MuKV), a novel member of the family Picornaviridae, was identified in faecal samples of Rattus norvegicus in China. The limited information on the circulation of MuKV in other murine rodent species prompted us to investigate its prevalence and conduct a genetic characterization of MuKV in Rattus losea, Rattus tanezumi and Rattus norvegicus in China. Between 2015 and 2017, 243 faecal samples of these three murine rodent species from three regions in southern China were screened for the presence of MuKV. The overall prevalence was 23.0% (56/243). Three complete MuKV polyprotein sequences were acquired, and the genome organization was determined. Phylogenetic analyses suggested that our sequences were closely related to Chinese strains and belong to the species Aichivirus A in the genus Kobuvirus. Additional studies are required to understand the true prevalence of MuKV in murine rodent populations in China.

Pseudogenized Amelogenin Reveals Early Tooth Loss in True Toads (Anura: Bufonidae)

2021 ◽  
Author(s):  
John Shaheen ◽  
Austin B Mudd ◽  
Thomas G H Diekwisch ◽  
John Abramyan
Keyword(s):  
Tooth Loss ◽  
Tooth Enamel ◽  
Synonymous Substitution ◽  
Bufo Bufo ◽  
Molecular Dating ◽  
Bufo Gargarizans ◽  
The Family ◽  
Synonymous Substitution Rates ◽  
Mandibular Teeth ◽  
Early Tooth Loss

Abstract Extant anurans (frogs and toads) exhibit reduced dentition, ranging from a lack of mandibular teeth to complete edentulation, as observed in the true toads of the family Bufonidae. The evolutionary timeline of these reductions remains vague due to a poor fossil record. Previous studies have demonstrated an association between the lack of teeth in edentulous vertebrates and the pseudogenization of the major tooth enamel gene amelogenin (AMEL) through accumulation of deleterious mutations and the disruption of its coding sequence. In the present study we have harnessed the pseudogenization of AMEL as a molecular dating tool to correlate loss of dentition with genomic mutation patterns during the rise of the family Bufonidae. Specifically, we have utilized AMEL pseudogenes in three members of the family as a tool to estimate the putative date of edentulation in true toads. Comparison of AMEL sequences from Rhinella marina, Bufo gargarizans and Bufo bufo, with nine extant, dentulous frogs, revealed mutations confirming AMEL inactivation in Bufonidae. AMEL pseudogenes in modern bufonids also exhibited remarkably high 86–93% sequence identity among each other, with only a slight increase in substitution rate and relaxation of selective pressure, in comparison to functional copies in other anurans. Moreover, using selection intensity estimates and synonymous substitution rates, analysis of functional and pseudogenized AMEL resulted in an estimated inactivation window of 46-60 MYA in the lineage leading to modern true toads, a timeline that coincides with the rise of the family Bufonidae.

scholarly journals Comparing Patterns of Nucleotide Substitution Rates Among Chloroplast Loci Using the Relative Ratio Test

Genetics ◽  
1997 ◽  
Vol 146 (1) ◽  
pp. 393-399 ◽  
Author(s):  
Spencer V Muse ◽  
Brandon S Gaut
Keyword(s):  
Nucleotide Substitution ◽  
Nonsynonymous Substitution ◽  
Synonymous Substitution ◽  
Joint Analysis ◽  
Ratio Test ◽  
Substitution Rates ◽  
Chloroplast Genomes ◽  
Synonymous Substitution Rates ◽  
Nucleotide Substitution Rates ◽  
Evolutionary Lineages

Even when several genetic loci are used in molecular evolutionary studies, each locus is typically analyzed independently of the others. This type of approach makes it difficult to study mechanisms and processes that affect multiple genes. In this work we develop a statistical approach for the joint analysis of two or more loci. The tests we propose examine whether or not nucleotide substitution rates across evolutionary lineages have the same relative proportions at two loci. Theses procedures are applied to 33 genes from the chloroplast genomes of rice, tobacco, pine, and liverwort. With the exception of five clearly distinct loci, we find that synonymous substitution rates tend to change proportionally across genes. We interpret these results to be consistent with a “lineage effect” acting on the entire chloroplast genome. In contrast, nonsynonymous rates do not change proportionally across genes, suggesting that locus-specific evolutionary effects dominate patterns of nonsynonymous substitution.

scholarly journals The single-particle mixing state and cloud scavenging of black carbon at a high-altitude mountain site in southern China

2017 ◽  
Author(s):  
Guohua Zhang ◽  
Qinhao Lin ◽  
Long Peng ◽  
Xinhui Bi ◽  
Duohong Chen ◽  
...  
Keyword(s):  
Black Carbon ◽  
Single Particle ◽  
Southern China ◽  
Climate Impacts ◽  
Limited Information ◽  
Mixing State ◽  
Cloud Droplets ◽  
Mountain Site ◽  
Cloud Scavenging ◽  
Scavenging Efficiency

Abstract. In the present study, a ground-based counterflow virtual impactor (GCVI) was used to sample cloud droplet residual (cloud RES) particles, while a parallel PM2.5 inlet was used to sample cloud-free or cloud interstitial (cloud INT) particles. The mixing state of black carbon (BC)-containing particles in a size range of 0.1–1.6 µm and the mass concentrations of BC in the cloud-free, RES and INT particles were investigated using a single particle aerosol mass spectrometer (SPAMS) and two aethalometers, respectively, at a mountain site (1690 m a.s.l.) in southern China. The measured BC-containing particles were internally mixed extensively with sulfate, and were activated into cloud droplets to the same extent as all the measured particles. The results indicate the preferential activation of larger particles and/or that the production of secondary compositions shifts the BC-containing particles towards larger sizes. BC-containing particles with an abundance of both sulfate and organics were activated less than those with sulfate but limited organics, implying the importance of the mixing state on the incorporation of BC-containing particles into cloud droplets. The mass scavenging efficiency of BC with an average of 33 % was similar for different cloud events independent of the air mass. This is the first time that both the mixing state and cloud scavenging of BC in China have been reported. Since limited information on BC-containing particles in the free troposphere is available, the results also provide an important reference for the representation of BC concentrations, properties, and climate impacts in modeling studies.

scholarly journals Comparative Genomic Analysis and a Novel Set of Missense Mutation of the Leptospira weilii Serogroup Mini From the Urine of Asymptomatic Dogs in Thailand

2021 ◽  
Vol 12 ◽  
Author(s):  
Alongkorn Kurilung ◽  
Vincent Perreten ◽  
Nuvee Prapasarakul
Keyword(s):  
Molecular Mechanisms ◽  
Genome Structure ◽  
Ecological Niches ◽  
Comparative Genomic ◽  
Genomic Feature ◽  
Missense Mutations ◽  
Limited Information ◽  
High Genetic Diversity ◽  
Pan Genome ◽  
Pathogenesis Related

Leptospira weilii belongs to the pathogenic Leptospira group and is a causal agent of human and animal leptospirosis in many world regions. L. weilii can produce varied clinical presentations from asymptomatic through acute to chronic infections and occupy several ecological niches. Nevertheless, the genomic feature and genetic basis behind the host adaptability of L. weilii remain elusive due to limited information. Therefore, this study aimed to examine the complete circular genomes of two new L. weilii serogroup Mini strains (CUDO6 and CUD13) recovered from the urine of asymptomatic dogs in Thailand and then compared with the 17 genomes available for L. weilii. Variant calling analysis (VCA) was also undertaken to gain potential insight into the missense mutations, focusing on the known pathogenesis-related genes. Whole genome sequences revealed that the CUDO6 and CUD13 strains each contained two chromosomes and one plasmid, with average genome size and G+C content of 4.37 Mbp and 40.7%, respectively. Both strains harbored almost all the confirmed pathogenesis-related genes in Leptospira. Two novel plasmid sequences, pDO6 and pD13, were identified in the strains CUDO6 and CUD13. Both plasmids contained genes responsible for stress response that may play important roles in bacterial adaptation during persistence in the kidneys. The core-single nucleotide polymorphisms phylogeny demonstrated that both strains had a close genetic relationship. Amongst the 19 L. weilii strains analyzed, the pan-genome analysis showed an open pan-genome structure, correlated with their high genetic diversity. VCA identified missense mutations in genes involved in endoflagella, lipopolysaccharide (LPS) structure, mammalian cell entry protein, and hemolytic activities, and may be associated with host-adaptation in the strains. Missense mutations of the endoflagella genes of CUDO6 and CUD13 were associated with loss of motility. These findings extend the knowledge about the pathogenic molecular mechanisms and genomic evolution of this important zoonotic pathogen.

scholarly journals Homoeologous exchanges occur through intragenic recombination generating novel transcripts and proteins in wheat and other polyploids

2020 ◽  
pp. 202003505 ◽  
Author(s):  
Zhibin Zhang ◽  
Xiaowan Gou ◽  
Hongwei Xun ◽  
Yao Bian ◽  
Xintong Ma ◽  
...  
Keyword(s):  
Homologous Recombination ◽  
Molecular Mechanisms ◽  
Genome Structure ◽  
Whole Genome Sequence ◽  
Intragenic Recombination ◽  
Protein Fusion ◽  
Coding Regions ◽  
Recombination Hotspots ◽  
Widespread Phenomenon ◽  
Arabidopsis Suecica

Recombination between homeologous chromosomes, also known as homeologous exchange (HE), plays a significant role in shaping genome structure and gene expression in interspecific hybrids and allopolyploids of several plant species. However, the molecular mechanisms that govern HEs are not well understood. Here, we studied HE events in the progeny of a nascent allotetraploid (genome AADD) derived from two diploid progenitors of hexaploid bread wheat using cytological and whole-genome sequence analyses. In total, 37 HEs were identified and HE junctions were mapped precisely. HEs exhibit typical patterns of homologous recombination hotspots, being biased toward low-copy, subtelomeric regions of chromosome arms and showing association with known recombination hotspot motifs. But, strikingly, while homologous recombination preferentially takes place upstream and downstream of coding regions, HEs are highly enriched within gene bodies, giving rise to novel recombinant transcripts, which in turn are predicted to generate new protein fusion variants. To test whether this is a widespread phenomenon, a dataset of high-resolution HE junctions was analyzed for allopolyploid Brassica, rice, Arabidopsis suecica, banana, and peanut. Intragenic recombination and formation of chimeric genes was detected in HEs of all species and was prominent in most of them. HE thus provides a mechanism for evolutionary novelty in transcript and protein sequences in nascent allopolyploids.

A new species of Weiseronyssus Samsinak 1962 (Acari: Mesostigmata: Diplogyniidae) from Iran, with a key for genera

Zootaxa ◽  
2008 ◽  
Vol 1824 (1) ◽  
pp. 17 ◽  
Author(s):  
SHAHROOZ KAZEMI ◽  
HANS KLOMPEN ◽  
MARÍA L. MORAZA ◽  
KARIM KAMALI ◽  
ALIREZA SABOORI
Keyword(s):  
New Species ◽  
Southern China ◽  
Single Species ◽  
Generic Diagnosis ◽  
Northern Iran ◽  
Adult Females ◽  
A New Species

A new species of Weiseronyssus (Mesostigmata: Diplogyniidae) is described from adult females and males taken from Oryctes nasicornis (L.) (Coleoptera: Scarabaeidae) in northern Iran. The genus was previously known from a single species associated with an undetermined dynastine scarab from southern China. The generic diagnosis is updated and a key to the genera of Diplogyniidae is presented.

scholarly journals Can Green Algal Plastid Genome Size Be Explained by DNA Repair Mechanisms?

2020 ◽  
Vol 12 (2) ◽  
pp. 3797-3802 ◽  
Author(s):  
David Roy Smith
Keyword(s):  
Synonymous Substitution ◽  
Land Plant ◽  
Strand Breaks ◽  
Coding Regions ◽  
Green Algal ◽  
Mutational Pattern ◽  
Mutational Hotspots ◽  
Repair Mechanisms ◽  
Synonymous Sites ◽  
Break Induced Replication

Abstract A major finding in organelle biology over the past decade is that land plant mitochondrial genomes, which are the largest among eukaryotes, can have a “Jekyll and Hyde” mutational pattern: low for synonymous sites, high for intergenic ones. This has led to the theory that double-strand breaks (DSBs) in the intergenic DNA of plant mitogenomes are repaired by inaccurate mechanisms, such as break-induced replication, which can result in large insertions and, thus, could explain why these genomes are so prone to expansion. But how universal is this theory? Can it apply to other giant organelle DNAs, such as the massive plastid DNAs (ptDNAs) of chlamydomonadalean green algae? Indeed, it can. Analysis of the expanded plastomes from two distinct isolates of the unicellular chlamydomonadalean Chlorosarcinopsis eremi uncovered exceptionally low rates of synonymous substitution in the coding regions but high substitution rates, including frequent indels, in the noncoding ptDNA, mirroring the trend from land plant mitogenomes. Remarkably, nearly all of the substitutions and indels identified in the noncoding ptDNA of C. eremi occur adjacent to or within short inverted palindromic repeats, suggesting that these elements are mutational hotspots. Building upon earlier studies, I propose that these palindromic repeats are predisposed to DSBs and that error-prone repair of these breaks is contributing to genomic expansion. Short palindromic repeats are a common theme among bloated plastomes, including the largest one on record, meaning that these data could have wide-reaching implications for our understanding of ptDNA expansion.

scholarly journals Molecular Evolution of the Vertebrate FK506 Binding Protein 25

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Fei Liu ◽  
Xiao-Long Wei ◽  
Hao Li ◽  
Ji-Fu Wei ◽  
Yong-Qing Wang ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Nuclear Dna ◽  
Purifying Selection ◽  
Synonymous Substitution ◽  
Vertebrate Lineage ◽  
Gene Splicing ◽  
Fk506 Binding Protein ◽  
Ppiase Domain ◽  
Synonymous Substitution Rates ◽  
Peptidyl Prolyl Isomerases

FK506 binding proteins (FKBPs) belong to immunophilins with peptidyl-prolyl isomerases (PPIases) activity. FKBP25 (also known as FKBP3) is one of the nuclear DNA-binding proteins in the FKBPs family, which plays an important role in regulating transcription and chromatin structure. The calculation of nonsynonymous and synonymous substitution rates suggested that FKBP25 undergoes purifying selection throughout the whole vertebrate evolution. Moreover, the result of site-specific tests showed that no sites were detected under positive selection. Only one PPIase domain was detected by searching FKBP25 sequences at Pfam and SMART domain databases. Mammalian FKBP25 possess exon-intron conservation, although conservation in the whole vertebrate lineage is incomplete. The result of this study suggests that the purifying selection triggers FKBP25 evolutionary history, which allows us to discover the complete role of the PPIase domain in the interaction between FKBP25 and nuclear proteins. Moreover, intron alterations during FKBP25 evolution that regulate gene splicing may be involved in the purifying selection.

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