scholarly journals Comparative analysis of freshwater phytoplankton communities in two lakes of Burabay National Park using morphological and molecular approaches

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Dmitry V. Malashenkov ◽  
Veronika Dashkova ◽  
Kymbat Zhakupova ◽  
Ivan A. Vorobjev ◽  
Natasha S. Barteneva
Keyword(s):  
National Park ◽  
Phytoplankton Assemblages ◽  
Freshwater Phytoplankton ◽  
Molecular Approaches ◽  
Phytoplankton Communities ◽  
Total Phytoplankton ◽  
Next Generation Sequencing Ngs ◽  
Taxonomic Characterization ◽  
Generation Sequencing

AbstractWe analyzed phytoplankton assemblages’ variations in oligo-mesotrophic Shchuchie and Burabay lakes using traditional morphological and next-generation sequencing (NGS) approaches. The total phytoplankton biodiversity and abundance estimated by both microscopy and NGS were significantly higher in Lake Burabay than in Lake Shchuchie. NGS of 16S and 18S rRNA amplicons adequately identify phytoplankton taxa only on the genera level, while species composition obtained by microscopic examination was significantly larger. The limitations of NGS analysis could be related to insufficient coverage of freshwater lakes phytoplankton by existing databases, short algal sequences available from current instrumentation, and high homology of chloroplast genes in eukaryotic cells. However, utilization of NGS, together with microscopy allowed us to perform a complete taxonomic characterization of phytoplankton lake communities including picocyanobacteria, often overlooked by traditional microscopy. We demonstrate the high potential of an integrated morphological and molecular approach in understanding the processes of organization in aquatic ecosystem assemblages.

scholarly journals Characterization of Unknown Orthobunya-Like Viruses from India

Viruses ◽  
2018 ◽  
Vol 10 (9) ◽  
pp. 451 ◽  
Author(s):  
Shannon Whitmer ◽  
Pragya Yadav ◽  
Prasad Sarkale ◽  
Gouri Chaubal ◽  
Alicia Francis ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Febrile Illness ◽  
Geographic Region ◽  
Emerging Viruses ◽  
Simbu Serogroup ◽  
Isolation And Characterization ◽  
Karnataka State ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Next-generation sequencing (NGS) of agents causing idiopathic human diseases has been crucial in the identification of novel viruses. This study describes the isolation and characterization of two novel orthobunyaviruses obtained from a jungle myna and a paddy bird from Karnataka State, India. Using an NGS approach, these isolates were classified as Cat Que and Balagodu viruses belonging to the Manzanilla clade of the Simbu serogroup. Closely related viruses in the Manzanilla clade have been isolated from mosquitos, humans, birds, and pigs across a wide geographic region. Since Orthobunyaviruses exhibit high reassortment frequency and can cause acute, self-limiting febrile illness, these data suggest that human and livestock infections of the Oya/Cat Que/Manzanilla virus may be more widespread and/or under-reported than anticipated. It therefore becomes imperative to identify novel and unknown viruses in order to understand their role in human and animal pathogenesis. The current study is a step forward in this regard and would act as a prototype method for isolation, identification and detection of several other emerging viruses.

scholarly journals Caracterización Molecular de la Diversidad Fúngica de los Bosques Llucud y Palictahua: Potencialidades en Control Biológico/Molecular Characterization of Diversity Fungic of the Llucud and Palictahua Forests: Potential in Biological Control

2020 ◽  
Author(s):  
N. S. Erazo Sandoval ◽  
J. C. Manzano Ocaña ◽  
B. D. Patiño Castillo
Keyword(s):  
Biological Control ◽  
Natural Ecosystem ◽  
Metarhizium Robertsii ◽  
Killer Activity ◽  
Pests And Diseases ◽  
Palabras Clave ◽  
Next Generation Sequencing Ngs ◽  
Chemical Pesticides ◽  
Generation Sequencing

Dentro de los microorganismos más abundantes que se pueden encontrar en formaciones ecosistémicas naturales como los bosques andinos del Ecuador se encuentran los hongos microscópicos, los cuales desempeñan funciones cruciales en dichos ecosistemas. Por lo cual el objetivo de esta investigación fue caracterizar molecularmente la diversidad de hongos presentes en los bosques nativos Llucud y Palictahua, estableciendo sus potencialidades de uso en el control biológico de plagas y enfermedades que afectan a los cultivos agrícolas y cuyo control en su mayoría se lo realiza con plaguicidas químicos. Mediante secuenciación de próxima generación (NGS por sus siglas en inglés) de las muestras compuestas de suelo tomadas del horizonte “A” (rizósfera) de cada bosque, se identificaron 56 especies de hongos en Palictahua y 38 en Llucud, presentándose en ambos bosques un total de 6 hongos con importantes potencialidades para su uso en el control biológico, dentro de las cuales se encontraron: Brachyphoris oviparasitica (nematófago), Simplicillium (entomopatógeno y micoparásito), Hamamotoa lignophila (levadura con actividad Killer) en Llucud, y Metarhizium robertsii (entomopatógeno), Brachyphoris oviparasitica (nematófago) y Paraphaeosphaeria parmeliae (micoparásito) en Palictahua. El Bosque Palictahua presentó mayor diversidad de hongos que el bosque Llucud, sin embargo es importante cuidar ambos bosques, pues poseen una gran riqueza microbiana con un sinnúmero de posibilidades de uso en la medicina, industria, biotecnología y otros campos. Among the most abundant microorganisms that can be found in natural ecosystem formations such as the Andean forests of Ecuador are microscopic fungi, which play crucial roles in these ecosystems. So that the objective of this research was to molecularly characterize the diversity of fungi present in the native forests Llucud and Palictahua, establishing their potential for use in the biological control of pests and diseases that affect agricultural crops and whose control is mostly carried out with chemical pesticides. Through next-generation sequencing (NGS for its acronym in English) of compound samples of soil took from “A” horizon (rhizosphere). 56 species of fungi were identified in Palictahua and 38 in Llucud, presenting in both forests a total of 6 fungi with significant potential for use in biological control, among which were found: Brachyphoris oviparasitica (nematophagous), Simplicillium sp. (entomopathogen and mycoparasite), Hamamotoa lignophila (yeast with Killer activity) in Llucud, and Metarhizium robertsii (entomopathogen), Brachyphoris oviparasitica (nematophagous) and Paraphaeosphaeria parmeliae (mycoparasite) in Palictahua. The Palictahua forest presented greater diversity of fungi than the Llucud forest, however it is important to take care of both forests, since they have a great microbial richness with a myriad of possibilities of use in medicine, industry, biotechnology and other fields. Palabras clave: Biodiversidad, Microbiota, Plaguicidas. Keywords: Biodiversity, Microbiota, Pesticides.

scholarly journals Characterization of the Complete Mitochondrial Genome of Basidiomycete Yeast Hannaella oryzae: Intron Evolution, Gene Rearrangement, and Its Phylogeny

2021 ◽  
Vol 12 ◽  
Author(s):  
Qiang Li ◽  
Lijiao Li ◽  
Huiyu Feng ◽  
Wenying Tu ◽  
Zhijie Bao ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Intron Loss ◽  
Gene Arrangement ◽  
Total Size ◽  
Next Generation Sequencing Ngs ◽  
Different Origins ◽  
Generation Sequencing

In this study, the mitogenome of Hannaella oryzae was sequenced by next-generation sequencing (NGS) and successfully assembled. The H. oryzae mitogenome comprised circular DNA molecules with a total size of 26,444 bp. We found that the mitogenome of H. oryzae partially deleted the tRNA gene transferring cysteine. Comparative mitogenomic analyses showed that intronic regions were the main factors contributing to the size variations of mitogenomes in Tremellales. Introns of the cox1 gene in Tremellales species were found to have undergone intron loss/gain events, and introns of the H. oryzae cox1 gene may have different origins. Gene arrangement analysis revealed that H. oryzae contained a unique gene order different from other Tremellales species. Phylogenetic analysis based on a combined mitochondrial gene set resulted in identical and well-supported topologies, wherein H. oryzae was closely related to Tremella fuciformis. This study represents the first report of mitogenome for the Hannaella genus, which will allow further study of the population genetics, taxonomy, and evolutionary biology of this important phylloplane yeast and other related species.

scholarly journals Advances in Omic Studies Drive Discoveries in the Biology of Anisakid Nematodes

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 801 ◽  
Author(s):  
Stefano D’Amelio ◽  
Fabrizio Lombardo ◽  
Antonella Pizzarelli ◽  
Ilaria Bellini ◽  
Serena Cavallero
Keyword(s):  
Diagnostic Tools ◽  
Parasitic Diseases ◽  
Pathogenic Potential ◽  
Marine Parasites ◽  
Causative Agents ◽  
Biological Aspects ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Anisakid Nematodes

Advancements in technologies employed in high-throughput next-generation sequencing (NGS) methods are supporting the spread of studies that, combined with advances in computational biology and bioinformatics, have greatly accelerated discoveries within basic and biomedical research for many parasitic diseases. Here, we review the most updated “omic” studies performed on anisakid nematodes, a family of marine parasites that are causative agents of the fish-borne zoonosis known as anisakiasis or anisakidosis. Few deposited data on Anisakis genomes are so far available, and this still hinders the deep and highly accurate characterization of biological aspects of interest, even as several transcriptomic and proteomic studies are becoming available. These have been aimed at discovering and characterizing molecules specific to peculiar developmental parasitic stages or tissues, as well as transcripts with pathogenic potential as toxins and allergens, with a broad relevance for a better understanding of host–pathogen relationships and for the development of reliable diagnostic tools.

scholarly journals Current and New Approaches in GMO Detection: Challenges and Solutions

2015 ◽  
Vol 2015 ◽  
pp. 1-22 ◽  
Author(s):  
Marie-Alice Fraiture ◽  
Philippe Herman ◽  
Isabel Taverniers ◽  
Marc De Loose ◽  
Dieter Deforce ◽  
...  
Keyword(s):  
Genetically Modified Organisms ◽  
Digital Pcr ◽  
Detection Methods ◽  
Gmo Detection ◽  
Freedom Of Choice ◽  
Next Generation Sequencing Ngs ◽  
Detection Strategies ◽  
Generation Sequencing ◽  
Accurate Quantification

In many countries, genetically modified organisms (GMO) legislations have been established in order to guarantee the traceability of food/feed products on the market and to protect the consumer freedom of choice. Therefore, several GMO detection strategies, mainly based on DNA, have been developed to implement these legislations. Due to its numerous advantages, the quantitative PCR (qPCR) is the method of choice for the enforcement laboratories in GMO routine analysis. However, given the increasing number and diversity of GMO developed and put on the market around the world, some technical hurdles could be encountered with the qPCR technology, mainly owing to its inherent properties. To address these challenges, alternative GMO detection methods have been developed, allowing faster detections of single GM target (e.g., loop-mediated isothermal amplification), simultaneous detections of multiple GM targets (e.g., PCR capillary gel electrophoresis, microarray, and Luminex), more accurate quantification of GM targets (e.g., digital PCR), or characterization of partially known (e.g., DNA walking and Next Generation Sequencing (NGS)) or unknown (e.g., NGS) GMO. The benefits and drawbacks of these methods are discussed in this review.

scholarly journals Genetic and Antigenetic Characterization of the Novel Kotalahti Bat Lyssavirus (KBLV)

Viruses ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 69
Author(s):  
Sten Calvelage ◽  
Niina Tammiranta ◽  
Tiina Nokireki ◽  
Tuija Gadd ◽  
Elisa Eggerbauer ◽  
...  
Keyword(s):  
Novel Species ◽  
Reservoir Host ◽  
The Novel ◽  
Ion Torrent ◽  
Sequence Analyses ◽  
Cross Neutralization ◽  
Next Generation Sequencing Ngs ◽  
Demarcation Criteria ◽  
Generation Sequencing

There is a growing diversity of bat-associated lyssaviruses in the Old World. In August 2017, a dead Brandt’s bat (Myotis brandtii) tested positive for rabies and based on partial sequence analysis, the novel Kotalahti bat lyssavirus (KBLV) was identified. Because the bat was in an autolyzed state, isolation of KBLV was neither successful after three consecutive cell passages on cells nor in mice. Next generation sequencing (NGS) was applied using Ion Torrent ™ S5 technology coupled with target enrichment via hybridization-based capture (myBaits®) was used to sequence 99% of the genome, comprising of 11,878 nucleotides (nt). KBLV is most closely related to EBLV-2 (78.7% identity), followed by KHUV (79.0%) and BBLV (77.6%), supporting the assignment as phylogroup I lyssavirus. Interestingly, all of these lyssaviruses were also isolated from bat species of the genus Myotis, thus supporting that M. brandtii is likely the reservoir host. All information on antigenic and genetic divergence fulfil the species demarcation criteria by ICTV, so that we recommend KBLV as a novel species within the Lyssavirus genus. Next to sequence analyses, assignment to phylogroup I was functionally corroborated by cross-neutralization of G-deleted RABV, pseudotyped with KBLV-G by sera from RABV vaccinated humans. This suggests that conventional RABV vaccines also confer protection against the novel KBLV.

scholarly journals Molecular variants of Grapevine rupestris stem pitting-associated virus infecting grapevines (Vitis spp.) in Brazil

2017 ◽  
Vol 47 (11) ◽  
Author(s):  
Thor Vinícius Martins Fajardo ◽  
Aléxis Cardama Kin ◽  
Osmar Nickel
Keyword(s):  
Cp Gene ◽  
Multiple Alignments ◽  
Molecular Variants ◽  
Complete Sequences ◽  
Next Generation Sequencing Ngs ◽  
Rupestris Stem Pitting ◽  
Rugose Wood Complex ◽  
Stem Pitting ◽  
Generation Sequencing

ABSTRACT: Grapevine rupestris stem pitting-associated virus (GRSPaV) is one of the most common viruses of grapevine. It is involved in the graft-transmissible disease rupestris stem pitting of the rugose wood complex. The objective of the research was to perform the molecular characterization of the coat protein (CP) gene of sixteen Brazilian GRSPaV isolates aiming to determine the occurrence of molecular variants (strains) of this virus. Nine grapevine samples were evaluated, from which dsRNA was extracted. Nucleotide sequences were generated by Next generation sequencing (NGS). Fifteen complete sequences of the GRSPaV CP gene were obtained and phylogenetically analyzed. Multiple alignments of the sequences showed identities of nucleotides ranging from 82% to 99%, suggesting high variability among the CPs of Brazilian isolates. The study revealed that genetic variability of GRSPaV comprising three molecular variants is also present in Brazilian grapevine genotypes.

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