scholarly journals Algal and cyanobacterial diversity in saline rivers of the Elton Lake Basin (Russia) studied via light microscopy and next-generation sequencing

2021 ◽  
Vol 29 (1) ◽  
pp. 59-66
Author(s):  
M. E. Ignatenko ◽  
E. A. Selivanova ◽  
Y. A. Khlopko ◽  
Y. A. Khlopko ◽  
T. N. Yatsenko-Stepanova
Keyword(s):  
Next Generation Sequencing ◽  
Species Diversity ◽  
Light Microscopy ◽  
Taxonomic Structure ◽  
Lake Basin ◽  
Next Generation ◽  
Saline Rivers ◽  
Tetraselmis Cordiformis ◽  
First Time ◽  
Generation Sequencing

Naturally saline rivers are known in various regions of the world. Saline rivers with a salinity gradient from the source to the mouth are particularly interesting, because the range of salinity is the structure-forming factor of the hydrobiont assemblage. Such rivers are represented by saline rivers of the Elton Lake Basin in Volgograd region of Russia (the Bolshaya Samoroda River and the Malaya Samoroda River). Herein, we analyzed taxonomic structure and species diversity of microalgae and Cyanobacteria of the saline rivers flowing into the Elton Lake by light microscopy and next-generation sequencing. The differences and possible causes of inconsistencies in the results obtained by these methods are discussed. In total, 91 taxa of microorganisms were identified by integrated approach in the assemblages of microalgae and Cyanobacteria in the middle course of the Bolshaya Samoroda River, and 60 taxa – in the river mouth. The species diversity of those assemblages in the hypersaline Malaya Samoroda River was lower: 27 taxa from the middle course and 23 taxa from the mouth. Next-generation sequencing allowed us to refine and expand the list of microalgae taxa in the studied saline rivers due to detection of species which were hard to identify, low-abundance taxa, as well as extremely small-cell forms. Some discrepancies between the data obtained by light microscopy and next-generation sequencing indicate the advantage of simultaneous use of both methods for study of the algae communities. Such a comprehensive approach provides the most accurate and correct list of taxa added with the morphological descriptions and 18S rRNA and 16S rRNA partial sequences. Generally, 18 taxa have been recorded for the first time in the Bolshaya Samoroda River, belonging to the phyla Chlorophyta (Borodinellopsis sp., Chlorochytrium lemnae Cohn, Caespitella sp., Halochlorococcum sp., Tetraselmis cordiformis (H. J. Carter) F. Stein), Ochrophyta (Pseudocharaciopsis ovalis (Chodat) D. J. Hibberd, Characiopsis sp., Poterioochromonas stipitata Scherffel, Chrysolepidomonas sp.), Euglenozoa (Euglena bucharica I. Kisselev, Lepocinclis tripteris (Dujardin) B. Marin & Melkonian, Phacus orbicularis K. Hübner, P. parvulus G. A. Klebs), Cryptophyta (Hemiselmis cryptochromatica C. E. Lane & J. M. Archibald, Rhodomonas sp., Hanusia phi J. A. Deane), Haptophyta (Pavlova sp.), Cyanobacteria (Johanseninema constrictum (Szafer) Hasler, Dvorák & Poulícková). Seven taxa have been detected for the first time in the algal and cyanobacterial assemblages of the Malaya Samoroda River from the phyla Chlorophyta (Tetraselmis cordiformis, T. arnoldii (Proschkina-Lavrenko) R. E. Norris, Hori & Chihara, T. tetrathele (West) Butcher, Pyrobotrys elongatus Korshikov), Cryptophyta (Hanusia phi), and Cyanobacteria (Synechococcus elongatus (Nägeli) Nägeli, Oscillatoria simplicissima Gomont).

scholarly journals Next-Generation Sequencing Combined With Conventional Sanger Sequencing Reveals High Molecular Diversity in Actinidia Virus 1 Populations From Kiwifruit Grown in China

2020 ◽  
Vol 11 ◽  
Author(s):  
Shaohua Wen ◽  
Guoping Wang ◽  
Zuokun Yang ◽  
Yanxiang Wang ◽  
Min Rao ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Sanger Sequencing ◽  
Molecular Diversity ◽  
Genome Structure ◽  
Viral Disease ◽  
Open Reading Frames ◽  
Next Generation ◽  
Next Generation Sequencing Ngs ◽  
First Time ◽  
Generation Sequencing

Kiwifruit (Actinidia spp.) is native to China. Viral disease–like symptoms are common on kiwifruit plants. In this study, six libraries prepared from total RNA of leaf samples from 69 kiwifruit plants were subjected to next-generation sequencing (NGS). Actinidia virus 1 (AcV-1), a tentative species in the family Closteroviridae, was discovered in the six libraries. Two full-length and two near-full genome sequences of AcV-1 variants were determined by Sanger sequencing. The genome structure of these Chinese AcV-1 variants was identical to that of isolate K75 and consisted of 12 open reading frames (ORFs). Analyses of these sequences together with the NGS-derived contig sequences revealed high molecular diversity in AcV-1 populations, with the highest sequence variation occurring at ORF1a, ORF2, and ORF3, and the available variants clustered into three phylogenetic clades. For the first time, our study revealed different domain compositions in the viral ORF1a and molecular recombination events among AcV-1 variants. Specific reverse transcriptase–polymerase chain reaction assays disclosed the presence of AcV-1 in plants of four kiwifruit species and unknown Actinidia spp. in seven provinces and one city.

scholarly journals New Genotypes and Phenotypes in Patients with 3 Subtypes of Waardenburg Syndrome Identified by Diagnostic Next-Generation Sequencing

2019 ◽  
Vol 2019 ◽  
pp. 1-12 ◽  
Author(s):  
Wu Li ◽  
Lingyun Mei ◽  
Hongsheng Chen ◽  
Xinzhang Cai ◽  
Yalan Liu ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
De Novo ◽  
Waardenburg Syndrome ◽  
Next Generation ◽  
Single Nucleotide Variants ◽  
Number Variation ◽  
First Time ◽  
Generation Sequencing

Background. Waardenburg syndrome (WS) is one of the most common forms of syndromic deafness with heterogeneity of loci and alleles and variable expressivity of clinical features. Methods. The technology of single-nucleotide variants (SNV) and copy number variation (CNV) detection was developed to investigate the genotype spectrum of WS in a Chinese population. Results. Ninety WS patients and 24 additional family members were recruited for the study. Fourteen mutations had not been previously reported, including c.808C>G, c.117C>A, c.152T>G, c.803G>T, c.793-3T >G, and c.801delT on PAX3; c.642_650delAAG on MITF; c.122G>T and c.127C>T on SOX10; c.230C>G and c.365C>T on SNAI2; and c.481A>G, c.1018C>G, and c.1015C>T on EDNRB. Three CNVs were de novo and first reported in our study. Five EDNRB variants were associated with WS type 1 in the heterozygous state for the first time, with a detection rate of 22.2%. Freckles occur only in WS type 2. Yellow hair, amblyopia, congenital ptosis, narrow palpebral fissures, and pigmentation spots are rare and unique symptoms in WS patients from China. Conclusions. EDNRB should be considered as another prevalent pathogenic gene in WS type 1. Our study expanded the genotype and phenotype spectrum of WS, and diagnostic next-generation sequencing is promising for WS.

scholarly journals Next-generation sequencing in childhood disorders

2013 ◽  
Vol 99 (3) ◽  
pp. 284-290 ◽  
Author(s):  
Ricardo Parolin Schnekenberg ◽  
Andrea H Németh
Keyword(s):  
Clinical Practice ◽  
Next Generation Sequencing ◽  
Applied Research ◽  
New Technologies ◽  
Clinical Diagnostics ◽  
Next Generation ◽  
Genetic Syndromes ◽  
Childhood Disorders ◽  
First Time ◽  
Generation Sequencing

Genetics has been revolutionised by recent technologies. The latest addition to these advances is next-generation sequencing, which is set to transform clinical diagnostics in every branch of medicine. In the research arena this has already been instrumental in identifying hundreds of novel genetic syndromes, making a molecular diagnosis possible for the first time in numerous refractory cases. However, the pace of change has left many clinicians bewildered by new terminology and the implications of next-generation sequencing for their clinical practice. The rapid developments have also left many diagnostic laboratories struggling to implement these new technologies with limited resources. This review explains the basic concepts of next-generation sequencing, gives examples of its role in clinically applied research and examines the challenges of its introduction into clinical practice.

scholarly journals Identification of tick-borne pathogens by metagenomic next-generation sequencing in Dermacentor nuttalli and Ixodes persulcatus in Inner Mongolia, China

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Jun Jiao ◽  
Zhiyu Lu ◽  
Yonghui Yu ◽  
Yangxuan Ou ◽  
Mengjiao Fu ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Inner Mongolia ◽  
Human Infection ◽  
Ixodes Persulcatus ◽  
Next Generation ◽  
Nested Polymerase Chain Reaction ◽  
Hard Ticks ◽  
Animal Pathogens ◽  
First Time ◽  
Generation Sequencing

Abstract Background Hard ticks act as arthropod vectors in the transmission of human and animal pathogens and are widely distributed in northern China. The aim of this study is to screen the important tick-borne pathogens (TBPs) carried by hard ticks in Inner Mongolia using metagenomic next-generation sequencing (mNGS) and to estimate the risk of human infection imposed by tick bites. Methods The adult Dermacentor nuttalli (n = 203) and Ixodes persulcatus (n = 36) ticks feeding on cattle were collected. The pooled DNA samples prepared from these ticks were sequenced as the templates for mNGS to survey the presence of TBPs at the genus level. Individual tick DNA samples were detected by genus--specific or group-specific nested polymerase chain reaction (PCR) of these TBPs and combined with DNA sequencing assay to confirm the results of mNGS. Results R. raoultii (45.32%, 92/203), Candidatus R. tarasevichiae (5.42%, 11/203), Anaplasma sp. Mongolia (26.60%, 54/203), Coxiella-like endosymbiont (CLE) (53.69%, 109/203), and Babesia venatorum (7.88%, 16/203) were detected in D. nuttalli, while R. raoultii (30.56%, 11/36), Anaplasma sp. Mongolia (27.80%, 10/36), and CLE (27.80%, 10/36) were detected in I. persulcatus. The double- and triple-pathogen/endosymbiont co-infections were detected in 40.39% of D. nuttalli and 13.89% of I. persulcatus, respectively. The dual co-infection with R. raoultii and CLE (14.29%, 29/203) and triple co-infection with R. raoultii, Anaplasma sp. Mongolia, and CLE (13.79%, 28/203) were most frequent in D. nuttalli. Conclusions This study provides insight into the microbial diversity of D. nuttalli and I. persulcatus in Inner Mongolia, China, reporting for the first time that Candidatus R. tarasevichiae had been found in D. nuttalli in China, and for the first time in the world that Anaplasma sp. Mongolia has been detected in I. persulcatus. This study proves that various vertically transmitted pathogens co-inhabit D. nuttalli and I. persulcatus, and indicates that cattle in Inner Mongolia are exposed to several TBPs. Graphic Abstract

Periodontal disease: From the lenses of light microscopy to the specs of proteomics and next-generation sequencing

2019 ◽  
pp. 263-290 ◽  
Author(s):  
Nagihan Bostanci ◽  
Kai Bao ◽  
David Greenwood ◽  
Angelika Silbereisen ◽  
Georgios N. Belibasakis
Keyword(s):  
Next Generation Sequencing ◽  
Periodontal Disease ◽  
Light Microscopy ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Mitochondrial m.13513G>A Point Mutation in ND5 in a 16-Year-Old Man with Leber Hereditary Optic Neuropathy Detected by Next-Generation Sequencing

2019 ◽  
Vol 08 (04) ◽  
pp. 231-234
Author(s):  
Daniel Vázquez-Justes ◽  
Lidia Carreño-Gago ◽  
Elena García-Arumi ◽  
Alicia Traveset ◽  
Julio Montoya ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Optic Neuropathy ◽  
Nadh Dehydrogenase ◽  
Deoxyribonucleic Acid ◽  
Next Generation ◽  
Leber Hereditary Optic Neuropathy ◽  
Next Generation Sequencing Ngs ◽  
First Time ◽  
Generation Sequencing ◽  
Hereditary Optic Neuropathy

AbstractThis article reports a Leber hereditary optic neuropathy (LHON) case associated for the first time with mitochondrial m.13513G>A mutation. We present a 16-year-old man who complained of subacute, painless, visual loss. Ocular examination showed optic nerve atrophy, papillary pseudoedema, and optic disc pallor. Extraocular manifestations included hypertrophic myocardiopathy and myopathy. Initial genetic analysis excluded the three most common LHON mutations. Sanger sequencing of the whole mitochondrial deoxyribonucleic acid showed no mutation. Next-generation sequencing (NGS) revealed m.13513G>A mutation in the NADH dehydrogenase (ND5) subunit gene (MT-ND5). The m.13513G>A mutation has never been associated with LHON phenotype without Leigh/mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes features. NGS techniques should be considered when this diagnosis is strongly suspected.

scholarly journals Reference Mapping Considering Swaps of Adjacent Bases

2021 ◽  
Vol 11 (11) ◽  
pp. 5038
Author(s):  
Youngho Kim ◽  
Munseong Kang ◽  
Ju-Hui Jeong ◽  
Dae Woong Kang ◽  
Soo Jun Park ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Sequence Information ◽  
Drosophila Genome ◽  
Computer Algorithms ◽  
Next Generation ◽  
Mapping Algorithm ◽  
Sequencing Method ◽  
The Cost ◽  
First Time ◽  
Generation Sequencing

Since the time of the HGP, research into next-generation sequencing, which can reduce the cost and time of sequence analysis using computer algorithms, has been actively conducted. Mapping is a next-generation sequencing method that identifies sequences by aligning short reads with a reference genome for which sequence information is known. Mapping can be applied to tasks such as SNP calling, motif searches, and gene identification. Research on mapping that utilizes BWT and GPU has been undertaken in order to obtain faster mapping. In this paper, we propose a new mapping algorithm with additional consideration for base swaps. The experimental results demonstrate that when the penalty score for swaps was −1, −2, and −3 in paired-end alignment, for the human whole genome, SOAP3-swap aligned 4667, 2318, and 972 more read pairs, respectively, than SOAP3-dp, and for the drosophila genome, SOAP3-swap aligned 1253, 454, and 129 more read pairs, respectively, than SOAP3-dp. SOAP3-swap has the same functionality as that of SOAP3-dp and also improves the alignment ratio by taking biologically significant swaps into account for the first time.

scholarly journals Swine viral detection by adapted Next-Generation Sequencing (NGS) for RNA and DNA species reveals first detection of porcine circovirus type 3 (PCV3) in Chile

2020 ◽  
Author(s):  
Paulina S. Rubilar ◽  
Javier Tognarelli ◽  
Jorge Fernández ◽  
Cristóbal Valdés ◽  
Felipe Broitman ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Porcine Circovirus Type ◽  
Porcine Circovirus ◽  
Next Generation ◽  
Animal Pathogens ◽  
Next Generation Sequencing Ngs ◽  
Type 3 ◽  
First Time ◽  
Generation Sequencing ◽  
Rna And Dna

AbstractThe outbreak and propagation of COVID-19 have posed a significant challenge to our society, highlighting the relevance of epidemiological monitoring of animal pathogens closely related to humans due to potential zoonosis. To find previously undetected viruses inside Chilean swine farms, we collected non-invasive samples from animals suspected to undergo any viral disease. After screening by Next Generation Sequencing (NGS) adapted to identify viral species with RNA and DNA genomes simultaneously, different viral species were successfully detected. Among viruses with an RNA genome, Porcine Rotavirus A (RVA), Porcine Astrovirus type 5 (PAstV-5) and Porcine Feces-Associated IASV-like virus (PfaIV) were identified; whereas among viruses with DNA genome, Porcine Parvovirus 1 (PPV1), Porcine Circovirus type 1 (PCV1) and Porcine Circovirus type 3 (PCV3) were found. PCV3, a recently described pathogenic virus, was detected for the first time in Chile in different samples from mummified tissue of stillbirths. The whole genome sequence of PCV3 was completed using conventional PCR and Sanger sequencing and compared with previously reported genomes. To the best of our knowledge, this is the first time that an adapted NGS system is used for the screening of DNA and RNA viral species simultaneously inside the Chilean swine industry. This adapted NGS system might be useful for the detection of swine viral emerging diseases worldwide.

scholarly journals Yield of Rare Variants Detected by Targeted Next-Generation Sequencing in a Cohort of Romanian Index Patients with Hypertrophic Cardiomyopathy

Diagnostics ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1061
Author(s):  
Miruna Mihaela Micheu ◽  
Nicoleta-Monica Popa-Fotea ◽  
Nicoleta Oprescu ◽  
Stefan Bogdan ◽  
Monica Dan ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Hypertrophic Cardiomyopathy ◽  
Rare Variants ◽  
Causal Variant ◽  
Next Generation ◽  
Targeted Next Generation Sequencing ◽  
Novel Variants ◽  
Next Generation Sequencing Ngs ◽  
First Time ◽  
Generation Sequencing

Background: The aim of this study was to explore the rare variants in a cohort of Romanian index cases with hypertrophic cardiomyopathy (HCM). Methods: Forty-five unrelated probands with HCM were screened by targeted next generation sequencing (NGS) of 47 core and emerging genes connected with HCM. Results: We identified 95 variants with allele frequency < 0.1% in population databases. MYBPC3 and TTN had the largest number of rare variants (17 variants each). A definite genetic etiology was found in 6 probands (13.3%), while inconclusive results due to either known or novel variants were established in 31 cases (68.9%). All disease-causing variants were detected in sarcomeric genes (MYBPC3 and MYH7 with two cases each, and one case in TNNI3 and TPM1 respectively). Multiple variants were detected in 27 subjects (60%), but no proband carried more than one causal variant. Of note, almost half of the rare variants were novel. Conclusions: Herein we reported for the first time the rare variants identified in core and putative genes associated with HCM in a cohort of Romanian unrelated adult patients. The clinical significance of most detected variants is yet to be established, additional studies based on segregation analysis being required for definite classification.

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