Identification and full genomic sequence of nerine yellow stripe virus

AbstractEscherichia coliC forms more robust biofilms than the other laboratory strains. Biofilm formation and cell aggregation under a high shear force depends on temperature and salt concentrations. It is the last of fiveE. colistrains (C, K12, B, W, Crooks) designated as safe for laboratory purposes whose genome has not been sequenced. Here we present the complete genomic sequence of this strain in which we utilized both long-read PacBio-based sequencing and high resolution optical mapping to confirm a large inversion in comparison to the other laboratory strains. Notably, DNA sequence comparison revealed the absence of several genes thought to be involved in biofilm formation, including antigen 43,waaSBOJYZULfor LPS synthesis, andcpsBfor curli synthesis. The first main difference we identified that likely affects biofilm formation is the presence of an IS3-like insertion sequence in front of the carbon storage regulatorcsrAgene. This insertion is located 86 bp upstream of thecsrAstart codon inside the −35 region of P4 promoter and blocks the transcription from the sigma32and sigma70promoters P1-P3 located further upstream. The second is the presence of an IS5/IS1182 in front of thecsgDgene, which may drive its overexpression in biofilm. And finally,E. coliC encodes an additional sigma70subunit overexpressed in biofilm and driven by the same IS3-like insertion sequence. Promoter analyses using GFP gene fusions and total expression profiles using RNA-seq analyses comparing planktonic and biofilm envirovars provided insights into understanding this regulatory pathway inE. coli.IMPORTANCEBiofilms are crucial for bacterial survival, adaptation, and dissemination in natural, industrial, and medical environments. Most laboratory strains ofE. coligrown for decadesin vitrohave evolved and lost their ability to form biofilm, while environmental isolates that can cause infections and diseases are not safe to work with. Here, we show that the historic laboratory strain ofE. coliC produces a robust biofilm and can be used as a model organism for multicellular bacterial research. Furthermore, we ascertained the full genomic sequence as well as gene expression profiles of both the biofilm and planktonic envirovars of this classic strain, which provide for a base level of characterization and make it useful for many biofilm-based applications.

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A Comprehensive Analysis of cis-Acting RNA Elements in the SARS-CoV-2 Genome by a Bioinformatics Approach

Frontiers in Genetics ◽

10.3389/fgene.2020.572702 ◽

2020 ◽

Vol 11 ◽

Author(s):

Firoz Ahmed ◽

Monika Sharma ◽

Abdulsalam Abdullah Al-Ghamdi ◽

Sultan Muhammad Al-Yami ◽

Abdulaziz Musa Al-Salami ◽

...

Keyword(s):

Comparative Analysis ◽

Rna Structure ◽

Viral Genome ◽

Genomic Sequence ◽

Evolutionary Relationship ◽

Cis Acting ◽

Full Genomic Sequence ◽

Rna Elements ◽

Global Threat ◽

Genomic Regions

The emergence of a new coronavirus (CoV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for severe respiratory disease in humans termed coronavirus disease of 2019 (COVID-19), became a new global threat for health and the economy. The SARS-CoV-2 genome is about a 29,800-nucleotide-long plus-strand RNA that can form functionally important secondary and higher-order structures called cis-acting RNA elements. These elements can interact with viral proteins, host proteins, or other RNAs and be involved in regulating translation and replication processes of the viral genome and encapsidation of the virus. However, the cis-acting RNA elements and their biological roles in SARS-CoV-2 as well as their comparative analysis in the closely related viral genome have not been well explored, which is very important to understand the molecular mechanism of viral infection and pathogenies. In this study, we used a bioinformatics approach to identify the cis-acting RNA elements in the SARS-CoV-2 genome. Initially, we aligned the full genomic sequence of six different CoVs, and a phylogenetic analysis was performed to understand their evolutionary relationship. Next, we predicted the cis-acting RNA elements in the SARS-CoV-2 genome using the structRNAfinder tool. Then, we annotated the location of these cis-acting RNA elements in different genomic regions of SARS-CoV-2. After that, we analyzed the sequence conservation patterns of each cis-acting RNA element among the six CoVs. Finally, the presence of cis-acting RNA elements across different CoV genomes and their comparative analysis was performed. Our study identified 12 important cis-acting RNA elements in the SARS-CoV-2 genome; among them, Corona_FSE, Corona_pk3, and s2m are highly conserved across most of the studied CoVs, and Thr_leader, MAT2A_D, and MS2 are uniquely present in SARS-CoV-2. These RNA structure elements can be involved in viral translation, replication, and encapsidation and, therefore, can be potential targets for better treatment of COVID-19. It is imperative to further characterize these cis-acting RNA elements experimentally for a better mechanistic understanding of SARS-CoV-2 infection and therapeutic intervention.

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Complete Genomic Sequence and Phylogenomics Analysis of Agrobacterium Strain AB2/73: A New Rhizobium Species with a Unique mega-Ti Plasmid

10.21203/rs.3.rs-635723/v1 ◽

2021 ◽

Author(s):

Marjolein J.G. Hooykaas ◽

Paul J.J. Hooykaas

Keyword(s):

Comparative Genomics ◽

Host Range ◽

Genomic Sequence ◽

Ti Plasmid ◽

Virulence Determinants ◽

High Quality ◽

Agrobacterium Strain ◽

Total Size ◽

Full Genomic Sequence ◽

Comparative Genomics Analysis

Abstract Background: The Agrobacterium strain AB2/73 has a unique host range for the induction of crown gall tumors, and contains an exceptionally large, over 500 kbp mega Ti plasmid. We used whole genome sequencing to fully characterize and comparatively analyze the complex genome of strain AB2/73, including its Ti plasmid and virulence factors. Results: We obtained a high-quality, full genomic sequence of AB2/73 by a combination of short-read Illumina sequencing and long-read Nanopore sequencing. The AB2/73 genome has a total size of 7,266,754 bp with 59.5% GC for which 7,012 genes (6,948 protein coding sequences) are predicted. Phylogenetic and comparative genomics analysis revealed that strain AB2/73 does not belong to the genus Agrobacterium, but to a new species in the genus Rhizobium, which is most related to Rhizobium tropici. In addition to the chromosome, the genome consists of 6 plasmids of which the largest two, of more than 1 Mbp, have chromid-like properties. The mega Ti plasmid is 605 kbp in size and contains two, one of which is incomplete, repABC replication units and thus appears to be a cointegrate consisting of about 175 kbp derived from an unknown Ti plasmid linked to 430 kbp from another large plasmid. In pTiAB2/73 we identified a complete set of virulence genes and two T-DNAs. Besides the previously described T-DNA we found a larger, second T-DNA containing a 6b-like onc gene and the acs gene for agrocinopine synthase. Also we identified two clusters of genes responsible for opine catabolism, including an acc-operon for agrocinopine degradation, and genes putatively involved in ridéopine catabolism. The plasmid also harbours tzs, iaaM and iaaH genes for the biosynthesis of the plant growth regulators cytokinin and auxin. Conclusions: The comparative genomics analysis of the high quality genome of strain AB2/73 provided insight into the unusual phylogeny and genetic composition of the limited host range Agrobacterium strain AB2/73. The description of its unique genomic composition and of all the virulence determinants in pTiAB2/73 will be an invaluable tool for further studies into the special host range properties of this bacterium.

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Three previously characterized resistances to yellow rust are encoded by a single locus Wtk1

10.1101/2020.01.02.892968 ◽

2020 ◽

Author(s):

Valentyna Klymiuk ◽

Andrii Fatiukha ◽

Dina Raats ◽

Valeria Bocharova ◽

Lin Huang ◽

...

Keyword(s):

Gene Networks ◽

Genomic Sequence ◽

Triticum Turgidum ◽

Yellow Rust ◽

Natural Populations ◽

Single Locus ◽

Stripe Rust Resistance ◽

Dependent Manner ◽

Resistance Response ◽

Yellow Stripe

AbstractThe wild emmer wheat (Triticum turgidum ssp. dicoccoides; WEW) yellow (stripe) rust resistance genes Yr15, YrG303 and YrH52 were discovered in natural populations from different geographic locations. They all localize to chromosome 1B but were thought to be non-allelic based on differences in resistance response. We recently cloned Yr15 as a Wheat Tandem Kinase 1 (WTK1) and showed here that these three resistance loci co-segregate in fine-mapping populations and share identical full-length genomic sequence of functional Wtk1. Independent EMS mutagenized susceptible yrG303 and yrH52 lines carried single nucleotide mutations in Wtk1 that disrupted function. A comparison of the mutations for yr15, yrG303 and yrH52 mutants showed that while key conserved residues were intact, other conserved regions in critical kinase subdomains were frequently affected. Thus, we concluded that Yr15-, YrG303- and YrH52-mediated resistances to yellow rust are encoded by a single locus Wtk1. Introgression of Wtk1 into multiple genetic backgrounds resulted in variable phenotypic responses, confirming that Wtk1-mediated resistance is part of a complex immune response network. WEW natural populations subjected to natural selection and adaptation have potential to serve as a good source for evolutionary studies of different traits and multifaceted gene networks.HighlightWe demonstrate that Yr15, YrG303 and YrH52 resistances are encoded by the Wtk1 locus, but express variable resistance responses to yellow rust in a genetic background dependent manner.

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Monitoring West Nile virus (WNV) infection in wild birds in Serbia during 2012: first isolation and characterisation of WNV strains from Serbia

Eurosurveillance ◽

10.2807/1560-7917.es2013.18.44.20622 ◽

2013 ◽

Vol 18 (44) ◽

Cited By ~ 40

Author(s):

T Petrović ◽

A B Blázquez ◽

D Lupulović ◽

G Lazić ◽

E Escribano-Romero ◽

...

Keyword(s):

West Nile Virus ◽

Migratory Birds ◽

Genomic Sequence ◽

Wild Birds ◽

Enzyme Linked Immunosorbent Assay ◽

West Nile ◽

Tissue Samples ◽

Full Genomic Sequence ◽

Common Pheasant ◽

Mute Swans

West Nile virus (WNV), a neurovirulent mosquito-transmissible zoonotic virus, has caused recent outbreaks in Europe, including Serbia from August until October 2012. Although humans can be infected, birds are the main natural WNV reservoir. To assess WNV circulation in northern Serbia, 133 wild birds were investigated. These comprised resident and migratory birds, collected between January and September 2012 in the Vojvodina province. The birds belonged to 45 species within 27 families. Blood sera (n=92) and pooled tissues from respective birds (n=81) were tested by enzyme-linked immunosorbent assay (ELISA), plaque reduction neutralisation test (PRNT) and real-time reverse transcription-polymerase chain reaction (RT-qPCR). WNV antibodies were detected in seven (8%) sera: four from Mute Swans (Cygnus olor), two from White-tailed Eagles (Haliaeetus albicillas), and one from a Common Pheasant (Phasianus colchicus). Five sera neutralised WNV but not Usutu virus. For the first time in Serbia, WNV RNA was detected by RT-qPCR in pooled tissue samples of eight respective birds. WNV RNA was also derived from an additional bird, after a serum sample resulted infective in cell culture. The total nine WNV RNA positive birds included three Northern Goshawks (Accipiter gentilis), two White-tailed Eagles, one Legged Gull (Larus michahelis), one Hooded Crow (Corvus cornix), one Bearded Parrot-bill (Panarus biramicus), and one Common Pheasant. Phylogenetic analysis of partial E region sequences showed the presence of, at least, two lineage 2 Serbian clusters closely related to those responsible for recent human and animal outbreaks in Greece, Hungary and Italy. Full genomic sequence from a goshawk isolate corroborated this data. These results confirm WNV circulation in Serbia and highlight the risk of infection for humans and horses, pointing to the need for implementing WNV surveillance programmes.

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Full genomic sequence analysis of swine genotype 3 hepatitis E virus isolated from Shanghai

Virus Research ◽

10.1016/j.virusres.2009.04.009 ◽

2009 ◽

Vol 144 (1-2) ◽

pp. 290-293 ◽

Cited By ~ 6

Author(s):

Fu-sheng Si ◽

Yu-min Zhu ◽

Shi-juan Dong ◽

Shui-sheng Yu ◽

Rui-song Yu ◽

...

Keyword(s):

Sequence Analysis ◽

Hepatitis E Virus ◽

Genomic Sequence ◽

Hepatitis E ◽

Genotype 3 ◽

Full Genomic Sequence ◽

Genomic Sequence Analysis

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Genome rearrangements induce biofilm formation in Escherichia coli C – an old model organism with a new application in biofilm research

BMC Genomics ◽

10.1186/s12864-019-6165-4 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 2

Author(s):

Jarosław E. Król ◽

Donald C. Hall ◽

Sergey Balashov ◽

Steven Pastor ◽

Justin Sibert ◽

...

Keyword(s):

Escherichia Coli ◽

Biofilm Formation ◽

Insertion Sequence ◽

Genomic Sequence ◽

Model Organism ◽

Start Codon ◽

Bacterial Survival ◽

E Coli ◽

Full Genomic Sequence

Abstract Background Escherichia coli C forms more robust biofilms than other laboratory strains. Biofilm formation and cell aggregation under a high shear force depend on temperature and salt concentrations. It is the last of five E. coli strains (C, K12, B, W, Crooks) designated as safe for laboratory purposes whose genome has not been sequenced. Results Here we present the complete genomic sequence of this strain in which we utilized both long-read PacBio-based sequencing and high resolution optical mapping to confirm a large inversion in comparison to the other laboratory strains. Notably, DNA sequence comparison revealed the absence of several genes thought to be involved in biofilm formation, including antigen 43, waaSBOJYZUL for lipopolysaccharide (LPS) synthesis, and cpsB for curli synthesis. The first main difference we identified that likely affects biofilm formation is the presence of an IS3-like insertion sequence in front of the carbon storage regulator csrA gene. This insertion is located 86 bp upstream of the csrA start codon inside the − 35 region of P4 promoter and blocks the transcription from the sigma32 and sigma70 promoters P1-P3 located further upstream. The second is the presence of an IS5/IS1182 in front of the csgD gene. And finally, E. coli C encodes an additional sigma70 subunit driven by the same IS3-like insertion sequence. Promoter analyses using GFP gene fusions provided insights into understanding this regulatory pathway in E. coli. Conclusions Biofilms are crucial for bacterial survival, adaptation, and dissemination in natural, industrial, and medical environments. Most laboratory strains of E. coli grown for decades in vitro have evolved and lost their ability to form biofilm, while environmental isolates that can cause infections and diseases are not safe to work with. Here, we show that the historic laboratory strain of E. coli C produces a robust biofilm and can be used as a model organism for multicellular bacterial research. Furthermore, we ascertained the full genomic sequence of this classic strain, which provides for a base level of characterization and makes it useful for many biofilm-based applications.

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Characterization of a New Nepovirus Causing a Leaf Mottling Disease in Petunia hybrida

Plant Disease ◽

10.1094/pdis-12-16-1785-re ◽

2017 ◽

Vol 101 (6) ◽

pp. 1017-1021 ◽

Cited By ~ 1

Author(s):

Sara Bratsch ◽

Benham Lockhart ◽

Dimitre Mollov

Keyword(s):

Petunia Hybrida ◽

High Throughput Sequencing ◽

Genomic Sequence ◽

Phylogenetic Analyses ◽

Pcr Amplification ◽

Particle Morphology ◽

Reverse Transcription Pcr ◽

Full Genomic Sequence ◽

Chlorotic Mottle Virus ◽

Chlorotic Mottle

Icosahedral virus-like particles were isolated from Petunia hybrida cuttings with interveinal chlorotic mottling. The virus was transmitted by mechanical inoculation from infected to healthy P. hybrida, and was found to contain a bipartite RNA genome of 7.6 and 3.8 kilobases. Full genomic sequence was obtained by high-throughput sequencing combined with RACE amplification of the 5′-termini of RNAs 1 and 2, and reverse-transcription PCR amplification of the 3′-termini with oligo-dT and sequence specific primers. Based on particle morphology, genome organization, and phylogenetic analyses, it was concluded that the new virus is a member of the genus Nepovirus, subgroup A. This new virus causing a leaf mottling disease of petunia was provisionally named Petunia chlorotic mottle virus (PCMoV).

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ADAPTATION OF THE CORN EARWORM SINGLE NUCLEOCAPCIDE NUCLEOPOLYHEDROVIRUS (HELICOVERPA ZEA SNPV) FOR THE CONTROL OF THE COTTON BOLLWORM (HELICOVERPA ARMIGERA) POPULATION

Voprosy Virusologii ◽

10.18821/0507-4088-2017-62-3-134-137 ◽

2017 ◽

Vol 62 (3) ◽

pp. 134-137

Author(s):

A. V. Kolosov ◽

V. A. Ternovoy ◽

A. N. Shvalov ◽

A. A. Moiseeva ◽

A. S. Safatov ◽

...

Keyword(s):

Helicoverpa Armigera ◽

Helicoverpa Zea ◽

Genomic Sequence ◽

Ring Finger ◽

Corn Earworm ◽

Cotton Bollworm ◽

Base Substitutions ◽

Nucleotide Mutation ◽

Full Genomic Sequence ◽

Helicoverpa Armígera

Helicoverpa zea (Boddie, 1850) (Hz) single nucleocapcide nucleopolyhedrovirus (SNPV) was adapted to the cotton bollworm (Helicoverpa armigera, (Hübner, 1805) (Ha)) by five blind passages on larvae. The full genomic sequence of the resulting strain HS-18 has been determined (GenBank acc. №: KJ004000.1). Biological activity of the HS-18 strain is higher than the activity of all other Russian strains of NPV, as far as cotton bollworm strain HearSNPV-G4. HS-18-infected caterpillars at the 3-rd and 4-th ages died much faster than those infected with HearSNPV-G4 strain. A major difference of HS-18 genome is an 18 bp repeat in the RING-finger ORF that confirms high variability of this region. Three other insertions and seven base substitutions were observed earlier, while six base substitutions are new. Mutations are located at ORF42, lef-9, ORF58, VP39, PIF-4, P48, SOD, ORF111, ORF129 and ORF138 genes. Among all nucleotide mutation only one is synonymous. Thus we suppose the selective pressure to the virus. The resulting strain HS-18 is recommended as a biopesticide for controlling the number of cotton bollworm in cotton fields.

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NOVEL BIOINFORMATICS APPROACH DETECTS HUNDREDS OF PREVIOUSLY UNDETECTED SPLICED TRANSCRIPTS DISCOVERED FROM CAENORHABDITIS ELEGANS GENOME

Indian Journal of Medical Sciences ◽

10.18203/issn.0019-5359.indianjmedsci20163531 ◽

2016 ◽

Vol 68 (1) ◽

pp. 49

Author(s):

Kashyap Luv ◽

Kriti Shrivastava ◽

Aakriti Shrivastava ◽

Ugam Kumari Chauhan

Keyword(s):

Caenorhabditis Elegans ◽

Genomic Sequence ◽

Single Gene ◽

Genome Structure ◽

Chromosome 1 ◽

Soil Nematode ◽

C Elegans ◽

Full Genomic Sequence ◽

Depth Analysis ◽

Alternatively Spliced

CONTEXT: With the completion of genome sequence of several organisms including free-living soil nematode Caenorhabditis elegans, precise genome annotations of this sea of raw information are now of prime importance, as they allow the accurate definition of generic regions. Alternative splicing is seen in nearly all metazoan organisms as a means for producing functionally diverse polypeptides from a single gene. AIM: In this study, we performed a detailed and in-depth analysis of the full genomic sequence of one of the six chromosomes of C. elegans. MATERIALS AND METHODS: In this study, several bioinformatics tools including gene/exon prediction programs, ORF finders, blast analysis tools, and alignment programs were used to analyze the genes/exons encoded by chromosome 1 of C. elegans with special reference to alternatively spliced transcripts. CONCLUSION: Using these tools, we have predicted >200 new alternatively spliced hypothetical transcripts from the genes encoded by chromosome 1 in C. elegans. These new spliced transcripts were identified from unusually large untranslated (UTR) regions and large introns present at the 3’ and 5’ ends of the genes with a maximum number of transcripts predicted from 5’ UTR analysis. Further studies and subsequent confirmation of these alternatively spliced transcripts will enhance our understanding of the genome structure, expression, and in elucidating their role during the development of C. elegans.

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