scholarly journals A Pilot Study Investigating the Dynamics of Pigeon Circovirus Recombination in Domesticated Pigeons Housed in a Single Loft

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 964
Author(s):  
Anthony Khalifeh ◽  
Simona Kraberger ◽  
Daria Dziewulska ◽  
Arvind Varsani ◽  
Tomasz Stenzel
Keyword(s):  
Evolutionary Dynamics ◽  
Cloacal Swab ◽  
Common Mechanism ◽  
Cold Spot ◽  
Coding Region ◽  
Genome Sequences ◽  
Pairwise Identity ◽  
Protein Coding ◽  
Genome Wide ◽  
Recombination Dynamics

Pigeon circovirus (PiCV) infects pigeon populations worldwide and has been associated with immunosuppression in younger pigeons. Recombination is a common mechanism of evolution that has previously been shown in various members of the Circoviridae family, including PiCV. In this study, three groups of pigeons acquired from separate lofts were screened for PiCV, and their genome sequence was determined. Following this, they were housed in a single loft for 22 days, during which blood and cloacal swab samples were taken. From these blood and cloacal swabs, PiCV genomes were determined with the aim to study the spread and recombination dynamics of PiCV in the birds. Genome sequences of PiCV were determined from seven pigeons (seven tested PiCV positive) before they were housed together in a loft (n = 58 sequences) and thereafter from the ten pigeons from blood and cloacal swabs (n = 120). These 178 PiCV genome sequences represent seven genotypes (98% pairwise identity genotype demarcation), and they share >88% genome-wide pairwise identity. Recombination analysis revealed 13 recombination events, and a recombination hotspot spanning the 3′ prime region, the replication-associated protein (rep) gene and the intergenic region. A cold spot in the capsid protein-coding region of the genome was also identified. The majority of the recombinant regions were identified in the rep coding region. This study provides insights into the evolutionary dynamics of PiCV in pigeons kept under closed rearing systems.

scholarly journals Genome-wide sexually antagonistic variants reveal longstanding constraints on sexual dimorphism in the fruitfly

2017 ◽  
Author(s):  
Filip Ruzicka ◽  
Mark S. Hill ◽  
Tanya M. Pennell ◽  
Ilona Flis ◽  
Fiona C. Ingleby ◽  
...  
Keyword(s):  
Sexual Dimorphism ◽  
Evolutionary Dynamics ◽  
Genome Wide Association Study ◽  
Balancing Selection ◽  
Sexual Antagonism ◽  
Protein Coding ◽  
Genome Wide ◽  
Genomic Location ◽  
Classic Theory ◽  
A Genome

The evolution of sexual dimorphism is constrained by a shared genome, leading to ‘sexual antagonism’ where different alleles at given loci are favoured by selection in males and females. Despite its wide taxonomic incidence, we know little about the identity, genomic location and evolutionary dynamics of antagonistic genetic variants. To address these deficits, we use sex-specific fitness data from 202 fully sequenced hemiclonal D. melanogaster fly lines to perform a genome-wide association study of sexual antagonism. We identify ~230 chromosomal clusters of candidate antagonistic SNPs. In contradiction to classic theory, we find no clear evidence that the X chromosome is a hotspot for sexually antagonistic variation. Characterising antagonistic SNPs functionally, we find a large excess of missense variants but little enrichment in terms of gene function. We also assess the evolutionary persistence of antagonistic variants by examining extant polymorphism in wild D. melanogaster populations. Remarkably, antagonistic variants are associated with multiple signatures of balancing selection across the D. melanogaster distribution range, indicating widespread and evolutionarily persistent (>10,000 years) genomic constraints. Based on our results, we propose that antagonistic variation accumulates due to constraints on the resolution of sexual conflict over protein coding sequences, thus contributing to the long-term maintenance of heritable fitness variation.

scholarly journals Novel Circoviruses Detected in Feces of Sonoran Felids

Viruses ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 1027
Author(s):  
Natalie Payne ◽  
Simona Kraberger ◽  
Rafaela S Fontenele ◽  
Kara Schmidlin ◽  
Melissa H Bergeman ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Negative Impact ◽  
Puma Concolor ◽  
Phylogenetic Analyses ◽  
Emerging Diseases ◽  
Lynx Rufus ◽  
Anthropogenic Factors ◽  
Pairwise Identity ◽  
Invasive Approach ◽  
Genome Wide

Sonoran felids are threatened by drought and habitat fragmentation. Vector range expansion and anthropogenic factors such as habitat encroachment and climate change are altering viral evolutionary dynamics and exposure. However, little is known about the diversity of viruses present in these populations. Small felid populations with lower genetic diversity are likely to be most threatened with extinction by emerging diseases, as with other selective pressures, due to having less adaptive potential. We used a metagenomic approach to identify novel circoviruses, which may have a negative impact on the population viability, from confirmed bobcat (Lynx rufus) and puma (Puma concolor) scats collected in Sonora, Mexico. Given some circoviruses are known to cause disease in their hosts, such as porcine and avian circoviruses, we took a non-invasive approach using scat to identify circoviruses in free-roaming bobcats and puma. Three circovirus genomes were determined, and, based on the current species demarcation, they represent two novel species. Phylogenetic analyses reveal that one circovirus species is more closely related to rodent associated circoviruses and the other to bat associated circoviruses, sharing highest genome-wide pairwise identity of approximately 70% and 63%, respectively. At this time, it is unknown whether these scat-derived circoviruses infect felids, their prey, or another organism that might have had contact with the scat in the environment. Further studies should be conducted to elucidate the host of these viruses and assess health impacts in felids.

scholarly journals Genome-Wide Mining, Characterization and Development of miRNA-SSRs in Arabidopsis thaliana

2017 ◽  
Author(s):  
Anuj Kumar ◽  
Aditi Chauhan ◽  
Mansi Sharma ◽  
Sai Kumar Kompelli ◽  
Vijay Gahlaut ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Dna Sequences ◽  
Tandem Repeats ◽  
Full Length ◽  
Coding Region ◽  
Protein Coding ◽  
Coding Regions ◽  
Mirna Genes ◽  
Genome Wide ◽  
Varying Length

AbstractSimple Sequence Repeats (SSRs), also known as microsatellites are short tandem repeats of DNA sequences that are 1-6 bp long. In plants, SSRs serve as a source of important class of molecular markers because of their hypervariabile and co-dominant nature, making them useful both for the genetic studies and marker-assisted breeding. The SSRs are widespread throughout the genome of an organism, so that a large number of SSR datasets are available, most of them from either protein-coding regions or untranslated regions. It is only recently, that their occurrence within microRNAs (miRNA) genes has received attention. As is widely known, miRNA themselves are a class of non-coding RNAs (ncRNAs) with varying length of 19-22 nucleotides (nts), which play an important role in regulating gene expression in plants under different biotic and abiotic stresses. In this communication, we describe the results of a study, where miRNA-SSRs in full length pre-miRNA sequences of Arabidopsis thaliana were mined. The sequences were retrieved by annotations available at EnsemblPlants using BatchPrimer3 server with miRNA-SSR flanking primers found to be well distributed. Our analysis shows that miRNA-SSRs are relatively rare in protein-coding regions but abundant in non-coding region. All the observed 147 di-, tri-, tetra-, penta- and hexanucleotide SSRs were located in non-coding regions of all the 5 chromosomes of A. thaliana. While we confirm that miRNA-SSRs were commonly spread across the full length pre-miRNAs, we envisage that such studies would allow us to identify newly discovered markers for breeding studies.

scholarly journals Novel Circoviruses Detected in Feces of Sonoran Felids

2020 ◽  
Author(s):  
Natalie Payne ◽  
Simona Kraberger ◽  
Rafaela S Fontenele ◽  
Kara Schmidlin ◽  
Melissa H Bergeman ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Negative Impact ◽  
Puma Concolor ◽  
Phylogenetic Analyses ◽  
Emerging Diseases ◽  
Lynx Rufus ◽  
Anthropogenic Factors ◽  
Pairwise Identity ◽  
Invasive Approach ◽  
Genome Wide

Sonoran felids are threatened by drought and habitat fragmentation. Vector range expansion and anthropogenic factors such as habitat encroachment and climate change are altering viral evolutionary dynamics and exposure. However, little is known about the diversity of viruses present in these populations. Small felid populations with lower genetic diversity are likely to be most threatened with extinction by emerging diseases, as with other selective pressures, due to having less adaptive potential. We used a metagenomic approach to identify novel circoviruses, which may have a negative impact on the population viability, from confirmed bobcat (Lynx rufus) and puma (Puma concolor) scats collected in Sonora, Mexico. Given some circoviruses are known to cause disease in their hosts, such as porcine and avian circoviruses, we took a non-invasive approach using scat to identify circoviruses in free-roaming bobcats and puma. Three circovirus genomes were determined, and, based on the current species demarcation, they represent two novel species. Phylogenetic analyses reveal that one circovirus species is more closely related to rodent associated circoviruses and the other to bat associated circoviruses, sharing the highest genome-wide pairwise identity of approximately 70% and 63%, respectively. At this time, it is unknown whether these scat-derived circoviruses infect felids, their prey, or another organism that might have had contact with the scat in the environment. Further studies should be conducted to elucidate the host of these viruses and assess health impacts in felids.

scholarly journals Genome-wide features of introns are evolutionary decoupled among themselves and from genome size throughout Eukarya

2018 ◽  
Author(s):  
Irma Lozada-Chávez ◽  
Peter F. Stadler ◽  
Sonja J. Prohaska
Keyword(s):  
Genome Size ◽  
Evolutionary Dynamics ◽  
Protein Coding ◽  
Specific Level ◽  
Spliceosomal Introns ◽  
Major Mechanism ◽  
Genome Wide ◽  
A Genome ◽  
Eukaryotic Gene ◽  
The Impact

AbstractThe impact of spliceosomal introns on genome and organismal evolution remains puzzling. Here, we investigated the correlative associations among genome-wide features of introns from protein-coding genes (e.g., size, density, genome-content, repeats), genome size and multicellular complexity on 461 eukaryotes. Thus, we formally distinguished simple from complex multicellular organisms (CMOs), and developed the program GenomeContent to systematically estimate genomic traits. We performed robust phylogenetic controlled analyses, by taking into account significant uncertainties in the tree of eukaryotes and variation in genome size estimates. We found that changes in the variation of some intron features (such as size and repeat composition) are only weakly, while other features measuring intron abundance (within and across genes) are not, scaling with changes in genome size at the broadest phylogenetic scale. Accordingly, the strength of these associations fluctuates at the lineage-specific level, and changes in the length and abundance of introns within a genome are found to be largely evolving independently throughout Eukarya. Thereby, our findings are in disagreement with previous estimations claiming a concerted evolution between genome size and introns across eukaryotes. We also observe that intron features vary homogeneously (with low repetitive composition) within fungi, plants and stramenophiles; but they vary dramatically (with higher repetitive composition) within holozoans, chlorophytes, alveolates and amoebozoans. We also found that CMOs and their closest ancestral relatives are characterized by high intron-richness, regardless their genome size. These patterns contrast the narrow distribution of exon features found across eukaryotes. Collectively, our findings unveil spliceosomal introns as a dynamically evolving non-coding DNA class and strongly argue against both, a particular intron feature as key determinant of eukaryotic gene architecture, as well as a major mechanism (adaptive or non-adaptive) behind the evolutionary dynamics of introns over a large phylogenetic scale. We hypothesize that intron-richness is a pre-condition to evolve complex multicellularity.

scholarly journals Elucidation of Genome Polymorphisms in Emerging SARS-CoV-2

2020 ◽  
Author(s):  
Manisha Ray ◽  
Saurav Sarkar ◽  
Surya Narayan Rath ◽  
Mukund Namdev Sable
Keyword(s):  
Genome Wide Association Study ◽  
Specific Treatment ◽  
Case Fatality ◽  
Distinct Species ◽  
Phylogenetic Study ◽  
Genome Sequences ◽  
Multiple Sequence ◽  
Protein Coding ◽  
Genome Wide ◽  
Genomic Regions

AbstractThe COVID-19 pandemic is having a devastating effect on the healthcare system and the economy of the world. The unavailability of a specific treatment regime and a candidate vaccine yet opens up scope for new approaches and discoveries of drugs for mitigation of the sufferings of humankind due to the disease. The present isolated whole-genome sequences of SARS-CoV-2 from 11 different nations subjected to evolutionary study and genome-wide association study through in silico approaches including multiple sequence alignment, phylogenetic study through MEGA7 and have been analyzed through DNAsp respectively. These investigations recognized the nucleotide varieties and single nucleotide mutations/polymorphisms on the genomic regions as well as protein-coding regions. The resulted mutations have diversified the genomic contents of SARS-CoV-2 according to the altered nucleotides found in 11 genome sequences. India and Nepal have found to have progressively more distinct species of SARS-CoV-2 with variations in Spike protein and Nucleocapsid protein-coding sites. These genomic variations might be the explanation behind the less case fatality rate of India and Nepal dependent on the populaces. The anticipated idea of this investigation upgrades the information about genomic medication and might be useful in the planning of antibodies against SARS-CoV-2.

scholarly journals Trends of Mutation Accumulation across Global SARS-CoV-2 Genomes: Implications for the Ecology and Evolution of the Novel Coronavirus

2020 ◽  
Author(s):  
Chayan Roy ◽  
Santi M Mandal ◽  
Suresh K Mondol ◽  
Shriparna Mukherjee ◽  
Wriddhiman Ghosh ◽  
...  
Keyword(s):  
Point Mutations ◽  
Phylogenomic Analysis ◽  
Whole Genome ◽  
The Novel ◽  
Structural Protein ◽  
Genome Sequences ◽  
Protein Coding ◽  
Pan Genome ◽  
Genome Wide ◽  
Novel Coronavirus

The all-pervasiveness and dynamic nature of the COVID-19 pandemic warrants comprehensive and constant surveillance of the numerous mutations that are accumulating in global SARS-CoV-2 genomes and contributing to the microevoution of the various lineages of the novel coronavirus. This would help us gain insights into the evolving pathogenicity of the virus, and thereby improvise our control and therapeutic strategies. This study explores the genome-wide frequency, gene-wise distribution, and molecular nature, of the large repertoire of point mutations detected across the global dataset of 3,608 SARS-CoV-2 RNA-genomes short-listed from a total 5,485 whole genome sequences deposited in GenBank till 4 June 2020 using a download filter that eliminated all incomplete/gapped sequences. Phylogenomic analysis involving all existing SARS-CoV-2 lineages, represented by 3,740 whole genome sequences from human-source (out of a total of 63,894 sequences stored in the GISAID repository, as on 15 July, 2020), illustrated that the two major-lineages of the virus contributed almost equivalently to the pandemic. However, entities belonging to the early lineages are still mostly spread over Asian countries, whereas those affiliated to recently-derived lineages have a relatively more global distribution. Mutation frequency in the SARS-CoV-2 pan genome was found to be 2.27 × 10-5 nucleotide positions mutated per nucleotide analyzed. An overwhelming majority (count: 1797) of the total 2452 instances of single nucleotide substitution detected (in the SARS-CoV-2 pan genome) were found to be transition mutations with cytidine to uridine (CàU) as the most ubiquitous molecular-type (count: 987). Of the 655 instances of transversion detected, the guanosine to uridine (GàU) variant was most widespread (count: 367). All transcribed and untranscribed loci of the pan genome were found to contain mutation(s). nsp3, and S, N and orf3a, were the most point-mutation-ridden non-structural and structural protein-coding genes, respectively, with 435, 300, 171 and 128 total mutations; 349/86, 192/108, 107/64 and 76/52 transitions/transversions; and 189/48, 106/55, 59/42 and 43/31 CàU/GàU substitutions respectively. Potential mechanistic backgrounds were envisaged for the molecular bias of mutations observed in SARS-CoV-2.

scholarly journals Synonymous genome recoding: a tool to explore microbial biology and new therapeutic strategies

2019 ◽  
Vol 47 (20) ◽  
pp. 10506-10519 ◽  
Author(s):  
Miguel Angel Martínez ◽  
Ana Jordan-Paiz ◽  
Sandra Franco ◽  
Maria Nevot
Keyword(s):  
Regulation Of Gene Expression ◽  
Biological Properties ◽  
Microbial Interactions ◽  
Coding Region ◽  
Protein Coding ◽  
Temporal Regulation ◽  
Synonymous Mutations ◽  
Synthetic Genome ◽  
Genome Wide ◽  
Inhibitory Signaling

Abstract Synthetic genome recoding is a new means of generating designed organisms with altered phenotypes. Synonymous mutations introduced into the protein coding region tolerate modifications in DNA or mRNA without modifying the encoded proteins. Synonymous genome-wide recoding has allowed the synthetic generation of different small-genome viruses with modified phenotypes and biological properties. Recently, a decreased cost of chemically synthesizing DNA and improved methods for assembling DNA fragments (e.g. lambda red recombination and CRISPR-based editing) have enabled the construction of an Escherichia coli variant with a 4-Mb synthetic synonymously recoded genome with a reduced number of sense codons (n = 59) encoding the 20 canonical amino acids. Synonymous genome recoding is increasing our knowledge of microbial interactions with innate immune responses, identifying functional genome structures, and strategically ameliorating cis-inhibitory signaling sequences related to splicing, replication (in eukaryotes), and complex microbe functions, unraveling the relevance of codon usage for the temporal regulation of gene expression and the microbe mutant spectrum and adaptability. New biotechnological and therapeutic applications of this methodology can easily be envisaged. In this review, we discuss how synonymous genome recoding may impact our knowledge of microbial biology and the development of new and better therapeutic methodologies.

scholarly journals Coding-Complete Genome Sequences and Mutation Profiles of Nine SARS-CoV-2 Strains Detected from COVID-19 Patients in Bangladesh

2021 ◽  
Vol 10 (10) ◽  
Author(s):  
Nihad Adnan ◽  
Mohib Ullah Khondoker ◽  
M. Shaminur Rahman ◽  
M. Firoz Ahmed ◽  
Shahana Sharmin ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Complete Genome ◽  
Spike Protein ◽  
Escape Mutation ◽  
Coding Region ◽  
Genome Sequences ◽  
Protein Coding

ABSTRACT Here, we report the coding-complete genome sequences of nine clinical severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and their mutations. The samples were collected from nine Bangladeshi coronavirus disease 2019 (COVID-19) patients. We have identified the E484K escape mutation and the S359T mutation within the spike protein coding region of the sequenced genomes.

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