scholarly journals Identification and Characterization of a Garlic Virus E Genome in Garlic (Allium sativum L.) Using High-Throughput Sequencing from India

Plants ◽  
2022 ◽  
Vol 11 (2) ◽  
pp. 224
Author(s):  
Malyaj Prajapati ◽  
Aakansha Manav ◽  
Jitender Singh ◽  
Pankaj Kumar ◽  
Amit Kumar ◽  
...  
Keyword(s):  
High Throughput ◽  
Complete Genome ◽  
Allium Sativum ◽  
High Throughput Sequencing ◽  
Uttar Pradesh ◽  
Nucleic Acid Binding ◽  
Potential Yield ◽  
Northern India ◽  
Close Relationship ◽  
Garlic Virus

Garlic (Allium sativum L.) plants exhibiting mosaics, deformation, and yellow stripes symptoms were identified in Meerut City, Uttar Pradesh, India. To investigate the viruses in the garlic samples, the method of high-throughput sequencing (HTS) was used. Complete genome of the garlic virus E (GarV-E) isolate (NCBI accession No. MW925710) was retrieved. The virus complete genome comprises 8450 nucleotides (nts), excluding the poly (A) tail at the 3′ terminus, with 5′ and 3′ untranslated regions (UTRs) of 99 and 384 nts, respectively, and ORFs encoding replicase with a conserved motif for RNA-dependent RNA polymerase (RdRP), TGB1, TGB2, TGB3, serine-rich protein, coat protein, and nucleic acid binding protein (NABP). The sequence homology shared 83.49–90.40% and 87.48–92.87% with those of GarV-E isolates available in NCBI at the nucleotide and amino acid levels, respectively. Phylogenetic analysis showed a close relationship of this isolate from India (MW925710) with GarV-E isolate YH (AJ292230) from Zhejiang, China. The presence of GarV-E was also confirmed by RT-PCR. The present study is the first report of GarV-E in garlic cultivar Yamuna Safed-3 grown in northern India. However, further studies are needed to confirm its role in symptom development, nationwide distribution, genetic diversity, and potential yield loss to the garlic in India.

scholarly journals Complete genome sequence and genetic organization of a Garlic virus D infecting garlic (Allium sativum) from northern India

2020 ◽  
Vol 64 (04) ◽  
pp. 427-432
Author(s):  
J. Singh ◽  
T. Ngoc Truong, ◽  
D. An ◽  
M. R. Prajapati ◽  
A. Manav ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Allium Sativum ◽  
Genetic Organization ◽  
Northern India ◽  
Garlic Virus

Characterization and complete genome sequence of a panicovirus from Bermuda grass by high-throughput sequencing

2016 ◽  
Vol 162 (4) ◽  
pp. 1099-1102 ◽  
Author(s):  
Muhammad N. Tahir ◽  
Ben Lockhart ◽  
Samuel Grinstead ◽  
Dimitre Mollov
Keyword(s):  
Genome Sequence ◽  
High Throughput ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
High Throughput Sequencing ◽  
Bermuda Grass

scholarly journals Complete Genome Sequence of Vibrio alginolyticus ZJ-T

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Yiqin Deng ◽  
Chang Chen ◽  
Zhe Zhao ◽  
Xiaochun Huang ◽  
Yiying Yang ◽  
...  
Keyword(s):  
Genome Sequence ◽  
High Throughput ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
High Throughput Sequencing ◽  
Opportunistic Pathogen ◽  
Vibrio Alginolyticus ◽  
Negative Bacterium ◽  
Marine Animals ◽  
Gram Negative

Vibrio alginolyticus is a ubiquitous Gram-negative bacterium which is normally distributed in the coastal and estuarine environments. It has been suggested to be an opportunistic pathogen to both marine animals and humans, Here, the completed genome sequence of V. alginolyticus ZJ-T was determined by Illumina high-throughput sequencing.

scholarly journals First complete genome sequence of garlic virus X infecting Allium sativum- G282 from India

Genomics ◽  
2020 ◽  
Vol 112 (2) ◽  
pp. 1861-1865
Author(s):  
Jitender Singh ◽  
Manoj Kumar Singh ◽  
Koushlesh Ranjan ◽  
Amit Kumar ◽  
Pankaj Kumar ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Allium Sativum ◽  
Garlic Virus

scholarly journals A Survey Using High-Throughput Sequencing Suggests That the Diversity of Cereal and Barley Yellow Dwarf Viruses Is Underestimated

2021 ◽  
Vol 12 ◽  
Author(s):  
Merike Sõmera ◽  
Sébastien Massart ◽  
Lucie Tamisier ◽  
Pille Sooväli ◽  
Kanitha Sathees ◽  
...  
Keyword(s):  
High Throughput ◽  
Complete Genome ◽  
High Throughput Sequencing ◽  
Barley Yellow Dwarf Virus ◽  
Sequence Data ◽  
Yellow Dwarf ◽  
Dwarf Virus ◽  
Gene Block ◽  
Barley Yellow Dwarf ◽  
Yellow Dwarf Virus

Worldwide, barley/cereal yellow dwarf viruses (YDVs) are the most widespread and damaging group of cereal viruses. In this study, we applied high-throughput sequencing technologies (HTS) to perform a virus survey on symptomatic plants from 47 cereal fields in Estonia. HTS allowed the assembly of complete genome sequences for 22 isolates of cereal yellow dwarf virus RPS, barley yellow dwarf virus GAV, barley yellow dwarf virus PAS (BYDV-PAS), barley yellow dwarf virus PAV (BYDV-PAV), and barley yellow dwarf virus OYV (BYDV-OYV). We also assembled a near-complete genome of the putative novel species BYDV-OYV from Swedish samples of meadow fescue. Previously, partial sequencing of the central part of the coat protein gene indicated that BYDV-OYV represented a putative new species closely related to BYDV-PAV-CN, which currently is recognized as a subtype of BYDV-PAV. The present study found that whereas the 3′gene block of BYDV-OYV shares the closest relationship with BYDV-PAV-CN, the 5′gene block of BYDV-OYV shows the closest relationships to that of BYDV-PAS. Recombination detection analysis revealed that BYDV-OYV is a parental virus for both. Analysis of complete genome sequence data indicates that both BYDV-OYV and BYDV-PAV-CN meet the species criteria of genus Luteovirus. The study discusses BYDV phylogeny, and through a systematic in silico analysis of published primers for YDV detection, the existing gaps in current diagnostic practices for detection of YDVs, proposing primer pairs based on the most recent genomic information for the detection of different BYDV species. Thanks to the rising number of sequences available in databases, continuous updating of diagnostic primers can improve test specificity, e.g., inclusivity and exclusivity at species levels. This is needed to properly survey the geographical and host distribution of the different species of the YDV complex and their prevalence in cereal/barley yellow dwarf disease epidemics.

scholarly journals Assessing Illumina technology for the high-throughput sequencing of bacteriophage genomes

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2055 ◽  
Author(s):  
Branko Rihtman ◽  
Sean Meaden ◽  
Martha R.J. Clokie ◽  
Britt Koskella ◽  
Andrew D. Millard
Keyword(s):  
Experimental Data ◽  
High Throughput ◽  
In Silico ◽  
Complete Genome ◽  
High Throughput Sequencing ◽  
Bacterial Genomes ◽  
Bacterial Populations ◽  
Illumina Technology ◽  
Biological Entities

Bacteriophages are the most abundant biological entities on the planet, playing crucial roles in the shaping of bacterial populations. Phages have smaller genomes than their bacterial hosts, yet there are currently fewer fully sequenced phage than bacterial genomes. We assessed the suitability of Illumina technology for high-throughput sequencing and subsequent assembly of phage genomes. In silico datasets reveal that 30× coverage is sufficient to correctly assemble the complete genome of ˜98.5% of known phages, with experimental data confirming that the majority of phage genomes can be assembled at 30× coverage. Furthermore, in silico data demonstrate it is possible to co-sequence multiple phages from different hosts, without introducing assembly errors.

scholarly journals Nearly Complete Genome Sequence of a Novel Phlebovirus-Like Virus Detected in a Human Plasma Sample by High-Throughput Sequencing

2019 ◽  
Vol 8 (35) ◽  
Author(s):  
Florian Laubscher ◽  
Samuel Cordey ◽  
Mary-Anne Hartley ◽  
Gael Vieille ◽  
Noémie Boillat-Blanco ◽  
...  
Keyword(s):  
Adult Patient ◽  
High Throughput ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
High Throughput Sequencing ◽  
Plasma Sample ◽  
Initial Sample ◽  
United Republic ◽  
United Republic Of Tanzania ◽  
Virus Sequence

Here, we report a novel phlebovirus-like virus sequence detected in a plasma sample from a febrile adult patient collected in the United Republic of Tanzania in 2014. A nearly complete RNA sequence was generated by high-throughput sequencing on a HiSeq 2500 instrument and further confirmed after repeating the analysis, starting from the initial sample.

scholarly journals Genome Sequences of Microviruses Identified in Gila Monster Feces

2021 ◽  
Vol 10 (11) ◽  
Author(s):  
Courtney L. Collins ◽  
Dale F. DeNardo ◽  
Mellecha Blake ◽  
Jessica Norton ◽  
Kara Schmidlin ◽  
...  
Keyword(s):  
High Throughput ◽  
Complete Genome ◽  
High Throughput Sequencing ◽  
Genome Sequences ◽  
Fecal Samples ◽  
Gila Monster

ABSTRACT The complete genome sequences of 33 microviruses were determined from fecal samples collected from 14 Arizona-dwelling Gila monsters using high-throughput sequencing. These microviruses with genomes 4,383 to 6,782 nucleotides (nt) long were broadly distributed across the 14 samples.

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