scholarly journals Genomic constitution of diploid species of the genus Avena L. with A-genome according to the data of the next-generation sequencing (NGS)

2021 ◽  
Vol 20 (1) ◽  
pp. 333-335
Author(s):  
N. N. Nosov ◽  
A. A. Gnutikov ◽  
I. G. Loskutov ◽  
E. V. Blinova ◽  
A. V. Rodionov
Keyword(s):  
Next Generation Sequencing ◽  
Diploid Species ◽  
Rrna Gene ◽  
Next Generation ◽  
Illumina Platform ◽  
5.8S Rrna Gene ◽  
A Genome ◽  
5.8S Rrna ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

For diploid (2x) species with the A-genome, as well as for hexaploid (6x) from the genus Avena, a locus-specific next-generation sequencing (NGS) of the sequence of the region of the internal transcribed spacer ITS1 and the beginning of the 5.8S rRNA gene was carried out on the Illumina platform. The high diversity and heterogeneity of the genomes of diploid species are shown. It was revealed that the genomes of modern diploid oat species are relatively far removed from the hexaploid species. It was found that A. canariensis occupies an isolated position among other diploid species, and also takes only an insignificant role in the formation of hexaploid genomes.

The origin of Alopecurus × brachystylus Peterm. according to the results of next-generation sequencing (NGS)

2020 ◽  
Vol 19 (1) ◽  
pp. 5-7
Author(s):  
A. A. Gnutikov ◽  
N. N. Nosov ◽  
E. O. Punina ◽  
A. V. Rodionov
Keyword(s):  
Next Generation Sequencing ◽  
Phylogenetic Study ◽  
Rrna Gene ◽  
Next Generation ◽  
Illumina Platform ◽  
Its1 Sequence ◽  
Molecular Phylogenetic Study ◽  
Molecular Phylogenetic ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

A molecular phylogenetic study of the hybrid species Alopecurus × brachystylus Peterm. and somesupposed ancestral taxa was carried out. Next-generation sequencing (NGS) of the ITS1 sequence and the start of the5.8S rRNA gene was used on the Illumina platform. According to NGS sequencing, genome of the A. × brachystylusforms common subgenomes with representatives of the section Alopecurium: A. geniculatus and A. aequalis, as well asrepresentatives of the type section: A. pratensis, A. arundinaceus, and alpine A. vlassowii. In addition, it was found thatA. vlassowii (section Alopecurus) contains sequences identical to the species of another section, Alopecurium.

scholarly journals Molecular phylogenetic study of rare weed-field species of the genus Avena L.

2021 ◽  
Vol 20 (1) ◽  
pp. 108-111
Author(s):  
A. A. Gnutikov ◽  
N. N. Nosov ◽  
I. G. Loskutov ◽  
E. V. Blinova ◽  
A. V. Rodionov
Keyword(s):  
Phylogenetic Study ◽  
Rrna Gene ◽  
Its1 Sequence ◽  
5.8S Rrna Gene ◽  
Molecular Phylogenetic Study ◽  
5.8S Rrna ◽  
C Genome ◽  
Molecular Phylogenetic ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

A molecular phylogenetic study of weed-field species of the genus Avena L. using marker sequences ITS1–5.8S rRNA gene–ITS2 was undertaken. In addition, next-generation sequencing (NGS) was performed on the Illuminaplatform for the ITS1 sequence and the beginning of the gene 5.8S rRNA. Sanger sequencing results revealed the separateclade of microspecies with a good level of support and small level of difference between themselves. According to NGSsequencing data, the two most abundant subgenomes in terms of the number of sequences were identified. Among thecommon sequences of hexaploids, those associated with the C-genome were not found. The presence of unique ribotypeswas shown for A. persica and A. georgica.

scholarly journals Comparison of KRAS mutation analysis of colorectal cancer samples by standard testing and next-generation sequencing

2014 ◽  
Vol 67 (9) ◽  
pp. 764-767 ◽  
Author(s):  
Nishi Kothari ◽  
Michael J Schell ◽  
Jamie K Teer ◽  
Timothy Yeatman ◽  
David Shibata ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Next Generation Sequencing ◽  
Clinical Laboratory ◽  
Clinical Care ◽  
Next Generation ◽  
Illumina Platform ◽  
Kras Mutations ◽  
Standard Testing ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

AimsBased on KRAS testing, the subset of patients with metastatic colorectal cancer (CRC) that could benefit from anti-EGFR therapy can be better delineated. Though KRAS testing has become significantly more prevalent over the last few years, methods for testing remain heterogeneous and discordance has been reported between methods.MethodsIn this study, we examined a CRC patient population and compared KRAS testing done in Clinical Laboratory Improvement Amendments (CLIA) approved laboratories as part of standard clinical care and by next-generation sequencing (NGS) using the Illumina platform. Discordances were further evaluated with manual review of the NGS testing.ResultsOut of 468 CRC patient samples, 77 had KRAS testing done by both CLIA assay and NGS. There were concordant results between testing methodologies in 74 out of 77 patients, or 96% (95% CI 89% to 99%). There were three patient samples that showed discordant results between the two methods of testing. Upon further investigation of the NGS results for the three discordant cases, one sample showed a low level of the mutation seen in the standard testing, one sample showed low tumour fraction and a third did not show any evidence of the mutation that was found with the standard assay. Five patients had KRAS mutations not typically tested with standard testing.ConclusionsOverall there was a high concordance rate between NGS and standard testing for KRAS. However, NGS revealed mutations that are not tested for with standard KRAS assays that might have clinical impact with regards to the role for anti-EGFR therapy.

Progress Report: Next-Generation Sequencing (NGS), Multiplex Polymerase Chain Reaction (PCR), and Broad-Range Molecular Assays as Diagnostic Tools for Fever of Unknown Origin (FUO) Investigations in Adults

2021 ◽  
Author(s):  
William F Wright ◽  
Patricia J Simner ◽  
Karen C Carroll ◽  
Paul G Auwaerter
Keyword(s):  
Next Generation Sequencing ◽  
Fever Of Unknown Origin ◽  
Unknown Origin ◽  
Diagnostic Tools ◽  
Rrna Gene ◽  
Next Generation ◽  
Potential Cost ◽  
Microbial Identification ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract Even well into the 21st century, infectious diseases still account for most causes of fever of unknown origin (FUO). Advances in molecular technologies, including broad-range PCR of the 16S rRNA gene followed by Sanger sequencing, multiplex PCR assays, and more recently, next-generation sequencing (NGS) applications, have transitioned from research methods to more commonplace in some clinical microbiology laboratories. They have the potential to supplant traditional microbial identification methods and antimicrobial susceptibility testing. Despite the remaining challenges with these technologies, publications in the past decade justify excitement about the potential to transform FUO investigations. We discuss available evidence using these molecular methods for FUO evaluations, including potential cost-benefits and future directions.

scholarly journals Exotic airborne bacteria identified in urban resuspended dust by next generation sequencing

2019 ◽  
Vol 99 ◽  
pp. 04009
Author(s):  
Nora Kováts ◽  
Eszter Horváth ◽  
Katalin Hubai ◽  
András Hoffer ◽  
Beatrix Jancsek-Turóczi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Large Scale ◽  
Rrna Gene ◽  
Pathogenic Microorganisms ◽  
Next Generation ◽  
Culture Independent ◽  
Next Generation Sequencing Ngs ◽  
Siberian Permafrost ◽  
Generation Sequencing ◽  
Airborne Transport

The airborne transport of bacteria is a well-known phenomenon, making it possible to exchange species between ecosystems, but it also provides a tool for spreading of pathogenic microorganisms. As part of a large-scale study, microbial community of inhalable and respirable fractions (PM1-10) of resuspended dust collected in Budapest (Hungary) has been characterised by culture-independent next generation sequencing (NGS) of variable 16S rRNA gene regions. Apart from common, mostly ubiqituos soil and organic material-dwelling bacteria, exotic airborne species have been identified, such as Variovorax ginsengisoli, previously isolated from Korean ginseng fields or Exiguobacterium sibiricum, isolated from the Siberian permafrost.

scholarly journals Processive and stochastic CHH methylation by plant DRM2 and CMT2 revealed by single-read methylome analysis

2020 ◽  
Author(s):  
Keith D. Harris ◽  
Assaf Zemach
Keyword(s):  
Enzyme Activity ◽  
Next Generation Sequencing ◽  
Genome Browser ◽  
Next Generation ◽  
A Genome ◽  
Methylome Analysis ◽  
Average Methylation ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

AbstractCytosine methylome data is commonly generated through next-generation sequencing (NGS). Analyses of this data average methylation states of individual reads. We propose an alternate method of analysing single-read methylome data. Using this method, we identified patterns that relate to the mechanism of two plant non-CG methylating enzymes, DRM2 and CMT2: DRM2 has higher processivity than CMT2, and DRM2-methylated regions have higher variation among cells. Based on these patterns, we developed a classifier that predicts enzyme activity in different species and tissues. To facilitate further single-read analyses, we developed a genome browser optimised for visualising and analysing NGS data at single-read resolution.

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