scholarly journals Evidence of differential spreading events of grapevine pinot Gris virus in Italy using datamining as a tool

2021 ◽  
Author(s):  
Jean-Michel Hily ◽  
Véronique Komar ◽  
Nils Poulicard ◽  
Amandine Velt ◽  
Lauriane Renault ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
In Silico ◽  
Additional Data ◽  
Incomplete Knowledge ◽  
Sequence Read Archive ◽  
Emerging Virus ◽  
Grapevine Pinot Gris Virus

AbstractSince its identification in 2003, grapevine Pinot gris virus (GPGV, Trichovirus) has now been detected in most grape-growing countries. So far, little is known about the epidemiology of this newly emerging virus. In this work, we used datamining as a tool to monitor in-silico the sanitary status of three vineyards in Italy. All data used in the study were recovered from a work that was already published and for which data were publicly available as SRA (Sequence Read Archive, NCBI) files. While incomplete, knowledge gathered from this work was still important, with evidence of differential accumulation of the virus in grapevine according to year, location, and variety-rootstock association. Additional data regarding GPGV genetic diversity were collected. Some advantages and pitfalls of datamining are discussed.

scholarly journals Genetic diversity of Francisella tularensis subsp. holarctica in Kazakhstan

2021 ◽  
Vol 15 (5) ◽  
pp. e0009419
Author(s):  
Vladislav Shevtsov ◽  
Alma Kairzhanova ◽  
Alexandr Shevtsov ◽  
Alexandr Shustov ◽  
Ruslan Kalendar ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Francisella Tularensis ◽  
In Silico ◽  
Tandem Repeats ◽  
Migratory Bird ◽  
Time Interval ◽  
Whole Genome ◽  
Multiplex Pcr Assay ◽  
Strain Collection

Tularemia is a highly dangerous zoonotic infection due to the bacteria Francisella tularensis. Low genetic diversity promoted the use of polymorphic tandem repeats (MLVA) as first-line assay for genetic description. Whole genome sequencing (WGS) is becoming increasingly accessible, opening the perspective of a time when WGS might become the universal genotyping assay. The main goal of this study was to describe F. tularensis strains circulating in Kazakhstan based on WGS data and develop a MLVA assay compatible with in vitro and in silico analysis. In vitro MLVA genotyping and WGS were performed for the vaccine strain and for 38 strains isolated in Kazakhstan from natural water bodies, ticks, rodents, carnivores, and from one migratory bird, an Isabellina wheatear captured in a rodent burrow. The two genotyping approaches were congruent and allowed to attribute all strains to two F. tularensis holarctica lineages, B.4 and B.12. The seven tandem repeats polymorphic in the investigated strain collection could be typed in a single multiplex PCR assay. Identical MLVA genotypes were produced by in vitro and in silico analysis, demonstrating full compatibility between the two approaches. The strains from Kazakhstan were compared to all publicly available WGS data of worldwide origin by whole genome SNP (wgSNP) analysis. Genotypes differing at a single SNP position were collected within a time interval of more than fifty years, from locations separated from each other by more than one thousand kilometers, supporting a role for migratory birds in the worldwide spread of the bacteria.

scholarly journals Genome-Wide Novel Genic Microsatellite Marker Resource Development and Validation for Genetic Diversity and Population Structure Analysis of Banana

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1479
Author(s):  
Manosh Kumar Biswas ◽  
Mita Bagchi ◽  
Dhiman Biswas ◽  
Jennifer Ann Harikrishna ◽  
Yuxuan Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Comparative Mapping ◽  
In Silico ◽  
Large Scale ◽  
Crop Improvement ◽  
Musa Spp ◽  
Population Structure Analysis ◽  
A Genome ◽  
Development And Validation

Trait tagging through molecular markers is an important molecular breeding tool for crop improvement. SSR markers encoded by functionally relevant parts of a genome are well suited for this task because they may be directly related to traits. However, a limited number of these markers are known for Musa spp. Here, we report 35136 novel functionally relevant SSR markers (FRSMs). Among these, 17,561, 15,373 and 16,286 FRSMs were mapped in-silico to the genomes of Musa acuminata, M. balbisiana and M. schizocarpa, respectively. A set of 273 markers was validated using eight accessions of Musa spp., from which 259 markers (95%) produced a PCR product of the expected size and 203 (74%) were polymorphic. In-silico comparative mapping of FRSMs onto Musa and related species indicated sequence-based orthology and synteny relationships among the chromosomes of Musa and other plant species. Fifteen FRSMs were used to estimate the phylogenetic relationships among 50 banana accessions, and the results revealed that all banana accessions group into two major clusters according to their genomic background. Here, we report the first large-scale development and characterization of functionally relevant Musa SSR markers. We demonstrate their utility for germplasm characterization, genetic diversity studies, and comparative mapping in Musa spp. and other monocot species. The sequences for these novel markers are freely available via a searchable web interface called Musa Marker Database.

scholarly journals Genetic diversity of feline morbilliviruses isolated in Japan

2014 ◽  
Vol 95 (7) ◽  
pp. 1464-1468 ◽  
Author(s):  
Shoichi Sakaguchi ◽  
So Nakagawa ◽  
Rokusuke Yoshikawa ◽  
Chieko Kuwahara ◽  
Hiroko Hagiwara ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Urine Samples ◽  
Domestic Cats ◽  
Rt Pcr ◽  
N Protein ◽  
Virus Particles ◽  
Cytopathic Effects ◽  
Isolation And Characterization ◽  
Emerging Virus ◽  
Syncytia Formation

Feline morbillivirus (FmoPV) is an emerging virus in domestic cats and considered to be associated with tubulointerstitial nephritis. Although FmoPV was first described in China in 2012, there has been no report of the isolation of this virus in other countries. In this report, we describe the isolation and characterization of FmoPV from domestic cats in Japan. By using reverse transcription (RT)-PCR, we found that three of 13 urine samples from cats brought to veterinary hospitals were positive for FmoPV. FmoPV strains SS1 to SS3 were isolated from the RT-PCR-positive urine samples. Crandell-Rees feline kidney (CRFK) cells exposed to FmoPV showed cytopathic effects with syncytia formation, and FmoPV N protein was detected by indirect immunofluorescence assays. In addition, pleomorphic virus particles with apparent glycoprotein envelope spikes were observed by electron microscopy. By sequence analysis of FmoPV H and L genes, we found that FmoPVs showed genetic diversity; however, signatures of positive selection were not identified.

Incidence and Genetic Diversity of Grapevine Pinot gris Virus in California

2020 ◽  
pp. ajev.2020.20044
Author(s):  
Maher Al Rwahnih ◽  
Alfredo Diaz-Lara ◽  
Kari Arnold ◽  
Monica L. Cooper ◽  
Rhonda J. Smith ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Grapevine Pinot Gris Virus

In silico mining of microsatellites and analysis of genetic diversity among inter- and intra-generic aphids of the subfamily Aphidinae

2016 ◽  
Vol 160 (2) ◽  
pp. 179-187
Author(s):  
Sridhar Vaddi ◽  
Venkatesan Thiruvengadam ◽  
Sunil Joshi ◽  
Sushil Kumar Jalali ◽  
Lakshmana Reddy Dhoranalapalli Chinnappareddy ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
In Silico ◽  
In Silico Mining

scholarly journals Genetic diversity and species pattern of Trichoderma and Hypocrea in Manipur using in-silico analysis

2013 ◽  
Vol 9 (2) ◽  
pp. 106-111 ◽  
Author(s):  
Thongram Kamala ◽  
◽  
Sarangthem Indira Devi ◽  
Gourshyam Thingnam ◽  
Bharat Gopalrao Somkuwar
Keyword(s):  
Genetic Diversity ◽  
In Silico ◽  
In Silico Analysis ◽  
Species Pattern ◽  
Silico Analysis

scholarly journals Genetic diversity and epidemiology of accessory gene regulator loci in Clostridioides difficile

2020 ◽  
Vol 2 (7) ◽  
Author(s):  
Yuta Okada ◽  
Shu Okugawa ◽  
Mahoko Ikeda ◽  
Tatsuya Kobayashi ◽  
Ryoichi Saito ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
In Silico ◽  
Type Species ◽  
Clinical Samples ◽  
Pcr Analysis ◽  
Accessory Gene ◽  
Content Type ◽  
Link Type ◽  
Accessory Gene Regulator ◽  
Clostridioides Difficile

Quorum sensing is known to regulate bacterial virulence, and the accessory gene regulator (agr) loci is one of the genetic loci responsible for its regulation. Recent reports examining Clostridioides difficile show that two agr loci, agr1 and agr2, regulate toxin production, but the diversity of agr loci and their epidemiology is unknown. In our study, in silico analysis was performed to research genetic diversity of agr, and C. difficile isolates from clinical samples underwent multilocus sequence typing (MLST) and PCR analysis of agr loci. To reveal the distribution of agr among different strains, phylogenetic analysis was also performed. In our in silico analysis, two different subtypes, named agr2R and agr2M, were found in agr2, which were previously reported. PCR analysis of 133 C . difficile isolates showed that 131 strains had agr1, 61 strains had agr2R, and 26 strains had agr2M; agr2R was mainly found in clade 1 or clade 2 organisms, whereas agr2M was only found in clade 4. With rare exception, agr1-negative sequence types (STs) belonged to clade C-Ⅰ and C-Ⅲ, and one clade 4 strain had agr2R. Our study revealed subtypes of agr2 not previously recognized, and the distribution of several agr loci in C. difficile . These findings provide a foundation for further functional and clinical research of the agr loci.

In silico Prediction and Designing of Potential siRNAs to be Used as Antivirals Against SARS-CoV-2

2021 ◽  
Vol 27 ◽  
Author(s):  
Sayed Sartaj Sohrab ◽  
Sherif Aly El-Kafrawy ◽  
Aymn T. Abbas ◽  
Leena H. Bajrai ◽  
Esam Ibraheem Azhar
Keyword(s):  
Genetic Diversity ◽  
Sequence Analysis ◽  
Phylogenetic Relationships ◽  
In Silico ◽  
Full Genome ◽  
In Silico Prediction ◽  
High Sequence Identity ◽  
Minor Parent ◽  
Sequence Identity ◽  
The City

Background:: The unusual pneumonia outbreak that originated in the city of Wuhan, China in December 2019 was found to be caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), or COVID-19. Methods:: In this work, we have performed an in silico design and prediction of potential siRNAs based on genetic diversity and recombination patterns, targeting various genes of SARS-CoV-2 for antiviral therapeutics. We performed extensive sequence analysis to analyze the genetic diversity and phylogenetic relationships, and to identify the possible source of virus reservoirs and recombination patterns, and the evolution of the virus as well as we designed the siRNAs which can be used as antivirals against SARS-CoV-2. Results:: The sequence analysis and phylogenetic relationships indicated high sequence identity and closed clusters with many types of coronavirus. In our analysis, the full-genome of SARS-CoV-2 showed the highest sequence (nucleotide) identity with SARS-bat-ZC45 (87.7%). The overall sequence identity ranged from 74.3% to 87.7% with selected SARS viruses. The recombination analysis indicated the bat SARS virus is a potential recombinant and serves as a major and minor parent. We have predicted 442 siRNAs and finally selected only 19 functional, and potential siRNAs. Conclusions:: The siRNAs were predicted and selected based on their greater potency and specificity. The predicted siRNAs need to be validated experimentally for their effective binding and antiviral activity.

scholarly journals Use of a Plasmodium vivax genetic barcode for genomic surveillance and parasite tracking in Sri Lanka

2020 ◽  
Vol 19 (1) ◽  
Author(s):  
Rajika L. Dewasurendra ◽  
Mary Lynn Baniecki ◽  
Stephen Schaffner ◽  
Yamuna Siriwardena ◽  
Jade Moon ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sri Lanka ◽  
Plasmodium Vivax ◽  
In Silico ◽  
In Silico Analysis ◽  
Minor Allele ◽  
Allele Frequencies ◽  
Single Nucleotide ◽  
Parasite Populations ◽  
Silico Analysis

Abstract Background Sri Lanka was certified as a malaria-free nation in 2016; however, imported malaria cases continue to be reported. Evidence-based information on the genetic structure/diversity of the parasite populations is useful to understand the population history, assess the trends in transmission patterns, as well as to predict threatening phenotypes that may be introduced and spread in parasite populations disrupting elimination programmes. This study used a previously developed Plasmodium vivax single nucleotide polymorphism (SNP) barcode to evaluate the population dynamics of P. vivax parasite isolates from Sri Lanka and to assess the ability of the SNP barcode for tracking the parasites to its origin. Methods A total of 51 P. vivax samples collected during 2005–2011, mainly from three provinces of the country, were genotyped for 40 previously identified P. vivax SNPs using a high-resolution melting (HRM), single-nucleotide barcode method. Minor allele frequencies, linkage disequilibrium, pair-wise FST values, and complexity of infection (COI) were evaluated to determine the genetic diversity. Structure analysis was carried out using STRUCTURE software (Version 2.3.4) and SNP barcode was used to identify the genetic diversity of the local parasite populations collected from different years. Principal component analysis (PCA) was used to determine the clustering according to global geographic regions. Results The proportion of multi-clone infections was significantly higher in isolates collected during an infection outbreak in year 2007. The minor allele frequencies of the SNPs changed dramatically from year to year. Significant linkage was observed in sample sub-sets from years 2005 and 2007. The majority of the isolates from 2007 consisted of at least two genetically distinct parasite strains. The overall percentage of multi-clone infections for the entire parasite sample was 39.21%. Analysis using STRUCTURE software (Version 2.3.4) revealed the high genetic diversity of the sample sub-set from year 2007. In-silico analysis of these data with those available from other global geographical regions using PCA showed distinct clustering of parasite isolates according to geography, demonstrating the usefulness of the barcode in determining an isolate to be indigenous. Conclusions Plasmodium vivax parasite isolates collected during a disease outbreak in year 2007 were more genetically diverse compared to those collected from other years. In-silico analysis using the 40 SNP barcode is a useful tool to track the origin of an isolate of uncertain origin, especially to differentiate indigenous from imported cases. However, an extended barcode with more SNPs may be needed to distinguish highly clonal populations within the country.

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