scholarly journals Pro197Thr Substitution in Ahas Gene Causing Resistance to Pyroxsulam Herbicide in Rigid Ryegrass (Lolium Rigidum Gaud.)

2021 ◽  
Vol 13 (12) ◽  
pp. 6648
Author(s):  
Barbara Kutasy ◽  
Zsolt Takács ◽  
Judit Kovács ◽  
Verëlindë Bogaj ◽  
Syafiq A. Razak ◽  
...  
Keyword(s):  
Amino Acid ◽  
De Novo ◽  
Acetohydroxyacid Synthase ◽  
Lolium Rigidum ◽  
High Genetic Diversity ◽  
Reading Frame ◽  
Rigid Ryegrass ◽  
High Level ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Lolium rigidum Gaud. is a cross-pollinated species characterized by high genetic diversity and it was detected as one of the most herbicide resistance-prone weeds, globally. Acetohydroxyacid synthase (AHAS) resistant populations cause significant problems in cereal production; therefore, monitoring the development of AHAS resistance is widely recommended. Using next-generation sequencing (NGS), a de novo transcriptome sequencing dataset was presented to identify the complete open reading frame (ORF) of AHAS enzyme in L. rigidum and design markers to amplify fragments consisting of all of the eight resistance-conferring amino acid mutation sites. Pro197Thr, Pro197Ala, Pro197Ser, Pro197Gln, and Trp574Leu amino acid substitutions have been observed in samples. Although the Pro197Thr amino acid substitution was already described in SU and IMI resistant populations, this is the first report to reveal that the Pro197Thr in AHAS enzyme confers a high level of resistance (ED50 3.569) to pyroxsulam herbicide (Triazolopyrimidine).

scholarly journals MET Amplification in Non-Small Cell Lung Cancer (NSCLC)—A Consecutive Evaluation Using Next-Generation Sequencing (NGS) in a Real-World Setting

Cancers ◽  
2021 ◽  
Vol 13 (19) ◽  
pp. 5023
Author(s):  
Christoph Schubart ◽  
Robert Stöhr ◽  
Lars Tögel ◽  
Florian Fuchs ◽  
Horia Sirbu ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Next Generation Sequencing ◽  
Small Cell Lung Cancer ◽  
Cell Lung Cancer ◽  
Resistance Mechanism ◽  
Small Cell ◽  
Small Cell Lung ◽  
High Level ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

In non-small cell lung cancer (NSCLC), approximately 1–3% of cases harbor an increased gene copy number (GCN) of the MET gene. This alteration can be due to de novo amplification of the MET gene or can represent a secondary resistance mechanism in response to targeted therapies. To date, the gold standard method to evaluate the GCN of MET is fluorescence in situ hybridization (FISH). However, next-generation sequencing (NGS) is becoming more relevant to optimize therapy by revealing the mutational profile of each NSCLC. Using evaluable n = 205 NSCLC cases of a consecutive cohort, this study addressed the question of whether an amplicon based NGS assay can completely replace the FISH method regarding the classification of MET GCN status. Out of the 205 evaluable cases, only n = 9 cases (43.7%) of n = 16 high-level MET amplified cases assessed by FISH were classified as amplified by NGS. Cases harboring a MET GCN > 10 showed the best concordance when comparing FISH versus NGS (80%). This study confirms that an amplicon-based NGS assessment of the MET GCN detects high-level MET amplified cases harboring a MET GCN > 10 but fails to detect the various facets of MET gene amplification in the context of a therapy-induced resistance mechanism.

scholarly journals High levels of unreported intraspecific diversity among RNA viruses in faeces of neonatal piglets with diarrhoea

2019 ◽  
Vol 15 (1) ◽  
Author(s):  
Martí Cortey ◽  
Ivan Díaz ◽  
Anna Vidal ◽  
Gerard Martín-Valls ◽  
Giovanni Franzo ◽  
...  
Keyword(s):  
Early Life ◽  
Rna Viruses ◽  
Intraspecific Diversity ◽  
Virus Species ◽  
Neonatal Piglets ◽  
Porcine Epidemic Diarrhoea Virus ◽  
Diarrhoea Virus ◽  
High Level ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract Background Diarrhoea is a major cause of death in neonate pigs and most of the viruses that cause it are RNA viruses. Next Generation Sequencing (NGS) deeply characterize the genetic diversity among rapidly mutating virus populations at the interspecific as well as the intraspecific level. The diversity of RNA viruses present in faeces of neonatal piglets suffering from diarrhoea in 47 farms, plus 4 samples from non-diarrhoeic piglets has been evaluated by NGS. Samples were selected among the cases submitted to the Veterinary Diagnostic Laboratories of Infectious Diseases of the Universitat Autònoma de Barcelona (Barcelona, Spain) and Universidad de León (León, Spain). Results The analyses identified the presence of 12 virus species corresponding to 8 genera of RNA viruses. Most samples were co-infected by several viruses. Kobuvirus and Rotavirus were more commonly reported, with Sapovirus, Astrovirus 3, 4 and 5, Enterovirus G, Porcine epidemic diarrhoea virus, Pasivirus and Posavirus being less frequently detected. Most sequences showed a low identity with the sequences deposited in GenBank, allowing us to propose several new VP4 and VP7 genotypes for Rotavirus B and Rotavirus C. Conclusions Among the cases analysed, Rotaviruses were the main aetiological agents of diarrhoea in neonate pigs. Besides, in a small number of cases Kobuvirus and Sapovirus may also have an aetiological role. Even most animals were co-infected in early life, the association with enteric disease among the other examined viruses was unclear. The NGS method applied successfully characterized the RNA virome present in faeces and detected a high level of unreported intraspecific diversity.

scholarly journals The effect of variant interference on de novo assembly for viral deep sequencing

2019 ◽  
Author(s):  
Christina J. Castro ◽  
Rachel L. Marine ◽  
Edward Ramos ◽  
Terry Fei Fan Ng
Keyword(s):  
Deep Sequencing ◽  
De Novo ◽  
Gc Content ◽  
Read Length ◽  
Viral Genomes ◽  
Minor Variant ◽  
Main Driver ◽  
Next Generation Sequencing Ngs ◽  
Viral Sequences ◽  
Generation Sequencing

AbstractViruses have high mutation rates and generally exist as a mixture of variants in biological samples. Next-generation sequencing (NGS) approach has surpassed Sanger for generating long viral sequences, yet how variants affect NGS de novo assembly remains largely unexplored. Our results from >15,000 simulated experiments showed that presence of variants can turn an assembly of one genome into tens to thousands of contigs. This “variant interference” (VI) is highly consistent and reproducible by ten most used de novo assemblers, and occurs independent of genome length, read length, and GC content. The main driver of VI is pairwise identities between viral variants. These findings were further supported by in silico simulations, where selective removal of minor variant reads from clinical datasets allow the “rescue” of full viral genomes from fragmented contigs. These results call for careful interpretation of contigs and contig numbers from de novo assembly in viral deep sequencing.

scholarly journals Genome size and identification of abundant repetitive sequences in Vallisneria spinulosa

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3982 ◽  
Author(s):  
RuiJuan Feng ◽  
Xin Wang ◽  
Min Tao ◽  
Guanchao Du ◽  
Qishuo Wang
Keyword(s):  
Genome Size ◽  
Aquatic Plant ◽  
Nuclear Dna ◽  
De Novo ◽  
Repetitive Sequences ◽  
Nuclear Dna Content ◽  
Ltr Retrotransposons ◽  
Sequencing Data ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Vallisneria spinulosa is a freshwater aquatic plant of ecological and economic importance. However, there is limited cytogenetic and genomics information on Vallisneria. In this study, we measured the nuclear DNA content of Vallisneria spinulosa by flow cytometry, performed a de novo assembly, and annotated repetitive sequences by using a combination of next-generation sequencing (NGS) and bioinformatics tools. The genome size of Vallisneria spinulosa is approximately 3,595 Mbp, in which nearly 60% of the genome consists of repetitive sequences. The majority of the repetitive sequences are LTR-retrotransposons comprising 43% of the genome. Although the amount of sequencing data used in this study was not sufficient for a whole-genome assembly, it could generate an overview of representative elements in the genome. These results will lay a new foundation for further studies on various species that belong to the Vallisneria genus.

scholarly journals High Genomic Variability in Equine Infectious Anemia Virus Obtained from Naturally Infected Horses in Pantanal, Brazil: An Endemic Region Case

Viruses ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 207 ◽  
Author(s):  
Camila Dantas Malossi ◽  
Eduardo Gorzoni Fioratti ◽  
Jedson Ferreira Cardoso ◽  
Angelo Jose Magro ◽  
Erna Geessien Kroon ◽  
...  
Keyword(s):  
Amino Acid ◽  
Equine Infectious Anemia Virus ◽  
Genomic Sequences ◽  
Endemic Region ◽  
Viral Genomes ◽  
Equine Infectious Anemia ◽  
Anemia Virus ◽  
Next Generation Sequencing Ngs ◽  
First Time ◽  
Generation Sequencing

Equine infectious anemia virus (EIAV) is a persistent lentivirus that causes equine infectious anemia (EIA). In Brazil, EIAV is endemic in the Pantanal region, and euthanasia is not mandatory in this area. All of the complete genomic sequences from field viruses are from North America, Asia, and Europe, and only proviral genomic sequences are available. Sequences from Brazilian EIAV are currently available only for gag and LTR regions. Thus, the present study aimed for the first time to sequence the entire EIAV genomic RNA in naturally infected horses from an endemic area in Brazil. RNA in plasma from naturally infected horses was used for next-generation sequencing (NGS), and gaps were filled using Sanger sequencing methodology. Complete viral genomes of EIAV from two horses were obtained and annotated (Access Number: MN560970 and MN560971). Putative genes were analyzed and compared with previously described genes, showing conservation in gag and pol genes and high variations in LTR and env sequences. Amino acid changes were identified in the p26 protein, one of the most common targets used for diagnosis, and p26 molecular modelling showed surface amino acid alterations in some epitopes. Brazilian genome sequences presented 88.6% nucleotide identity with one another and 75.8 to 77.3% with main field strains, such as EIAV Liaoning, Wyoming, Ireland, and Italy isolates. Furthermore, phylogenetic analysis suggested that this Brazilian strain comprises a separate monophyletic group. These results may help to better characterize EIAV and to overcome the challenges of diagnosing and controlling EIA in endemic regions.

scholarly journals Species-specific transcriptional profiles of the gut and gut microbiome of Ceratitis quilicii and Ceratitis rosa sensu stricto

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Fathiya M. Khamis ◽  
Paul O. Mireji ◽  
Fidelis L. O. Ombura ◽  
Anna R. Malacrida ◽  
Erick O. Awuoche ◽  
...  
Keyword(s):  
Sibling Species ◽  
Gut Microbiome ◽  
De Novo ◽  
Differential Expression Analysis ◽  
Fruit Fly ◽  
Sensu Stricto ◽  
Transcriptional Profiles ◽  
Species Specific ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

AbstractThe fruit fly species, Ceratitis rosa sensu stricto and Ceratitis quilicii, are sibling species restricted to the lowland and highland regions, respectively. Until recently, these sibling species were considered as allopatric populations of C. rosa with distinct bionomics. We used deep Next Generation Sequencing (NGS) technology on intact guts of individuals from the two sibling species to compare their transcriptional profiles and simultaneously understand gut microbiome and host molecular processes and identify distinguishing genetic differences between the two species. Since the genomes of both species had not been published previously, the transcriptomes were assembled de novo into transcripts. Microbe-specific transcript orthologs were separated from the assembly by filtering searches of the transcripts against microbe databases using OrthoMCL. We then used differential expression analysis of host-specific transcripts (i.e. those remaining after the microbe-specific transcripts had been removed) and microbe-specific transcripts from the two-sibling species to identify defining species-specific transcripts that were present in only one fruit fly species or the other, but not in both. In C. quilicii females, bacterial transcripts of Pectobacterium spp., Enterobacterium buttiauxella, Enterobacter cloacae and Klebsiella variicola were upregulated compared to the C. rosa s.s. females. Comparison of expression levels of the host transcripts revealed a heavier investment by C. quilicii (compared with C. rosa s.s.) in: immunity; energy production; cell proliferation; insecticide resistance; reproduction and proliferation; and redox reactions that are usually associated with responses to stress and degradation of fruit metabolites.

Zellfreie fetale DNA im mütterlichen Blut: neue Möglichkeiten in der pränatalen Diagnostik/Cell free fetal DNA in maternal blood: new possibilities in prenatal diagnosis

2012 ◽  
Vol 36 (5) ◽  
Author(s):  
Markus Stumm ◽  
Rolf-Dieter Wegner ◽  
Wera Hofmann
Keyword(s):  
Prenatal Diagnosis ◽  
Next Generation Sequencing ◽  
De Novo ◽  
Maternal Blood ◽  
Fetal Dna ◽  
Cell Free Fetal Dna ◽  
Next Generation Sequencing Ngs ◽  
Fetale Dna ◽  
Generation Sequencing ◽  
Zellfreie Fetale Dna

ZusammenfassungDie zellfreie fetale DNA (cff-DNA) im mütterlichen Blut bietet viele neue Möglichkeiten der pränatalen genetischen Diagnostik. Im Gegensatz zu den etablierten invasiven Techniken der Chorionzottenbiopsie (CVS) und der Amniozentese (AC), die beide mit einem spezifischen Risiko (0,5–1%) einer eingriffsbedingten Fehlgeburt einhergehen, ist die Grundlage für die Gewinnung der cff-DNA eine einfache venöse Blutentnahme der Mutter, die keinerlei Risiko für den Embryo oder Feten darstellt. Damit bietet die cff-DNA die Möglichkeit einer risikofreien genetischen Diagnostik von bestehenden Schwangerschaften. Molekulargenetische Techniken werden schon seit längerer Zeit zum qualitativen Nachweis von spezifischen fetalen Sequenzen, wie paternal vererbten oder neu entstandenen (de novo) Mutationen, eingesetzt. Durch den Einsatz digitaler PCR und Next-Generation-Sequencing (NGS) Technologien gelingt mittlerweile aber auch der sichere quantitative Nachweis von mutierten Allelen sowie von klinisch relevanten Aneuploidien (Trisomie 13, 18 und 21) aus fetaler DNA im mütterlichen Blut.

scholarly journals Isolation and Abiotic Stress Resistance Analyses of a Catalase Gene fromIpomoea batatas(L.) Lam

2017 ◽  
Vol 2017 ◽  
pp. 1-10 ◽  
Author(s):  
Bin Yong ◽  
Xiaoyan Wang ◽  
Pan Xu ◽  
Haiyan Zheng ◽  
Xueting Fei ◽  
...  
Keyword(s):  
Sweet Potato ◽  
Stress Responses ◽  
Reading Frame ◽  
Calmodulin Binding ◽  
C Terminus ◽  
Young Leaves ◽  
Quantitative Analyses ◽  
Encoding Gene ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

As an indicator of the antioxidant capability of plants, catalase can detoxify reactive oxygen species (ROS) generated by environmental stresses. Sweet potato is one of the top six most important crops in the world. However, its catalases remain largely unknown. In this study, a catalase encoding gene,IbCAT2(accession number: KY615708), was identified and cloned from sweet potato cv. Xushu 18. It contained a 1479 nucleotides’ open reading frame (ORF). S-R-L, Q-K-L, and a putative calmodulin binding domain were located at the C-terminus of IbCAT2, which suggests that IbCAT2 could be a peroxisomal catalase. Next-generation sequencing (NGS) based quantitative analyses showed thatIbCAT2was mainly expressed in young leaves and expanding tuberous roots under normal conditions. When exposed to 10% PEG6000 or 200 mmol/L NaCl solutions,IbCAT2was upregulated rapidly in the first 11 days and then downregulated, although different tissues showed different degree of change. Overexpression ofIbCAT2conferred salt and drought tolerance inEscherichia coliandSaccharomyces cerevisiae. The positive response ofIbCAT2to abiotic stresses suggested thatIbCAT2might play an important role in stress responses.

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