SEGMENT 10 SEQUENCE BASED MOLECULAR CHARACTERIZATION OF BLUETONGUE VIRUS OF INDIAN ORIGIN

2016 ◽  
Vol 12 (1) ◽  
Author(s):  
Minakshi Prasad ◽  
Koushlesh Ranjan ◽  
Gaya Prasad
Keyword(s):  
Complete Genome ◽  
Sequence Data ◽  
Viral Disease ◽  
Spatial Spread ◽  
Ion Torrent Pgm ◽  
New Genes ◽  
Domestic Ruminants ◽  
Indian Origin ◽  
Geographical Regions ◽  
Bluetongue Disease

Bluetongue disease (BT) is an infectious but non-contagious viral disease of wild and domestic ruminants. The complete genome of BTV isolate K31-08/ABT/HSR was sequenced using Ion-Torrent PGM system. The sequence data were denovo assembled and contig sequences were prepared with reference to known sequences from GenBank. The segment 10 based analysis segregates BTV in five distinct topotypes. The segment 10 of K31-08/ABT/HSR isolate showed maximum identity of >99/99%, nucleotide/amino acid with BTV 16 isolates from India and placed under eastern topotype viruses from India and several other countries. The clustering of BTV isolates from different geographical regions into same group indicated the spatial spread of the segment 10 through introduction of new genes via trade or illegal live vaccine or reassortment. It also indicates the common origin of segment 10 irrespective of BTV serotype. The effect of reassortment and genetic drift on BTV can be predicted using complete genome sequencing technique.

scholarly journals Genome sequence of the banana aphid, Pentalonia nigronervosa Coquerel (Hemiptera: Aphididae) and its symbionts

2020 ◽  
Author(s):  
Thomas C. Mathers ◽  
Sam T. Mugford ◽  
Saskia A. Hogenhout ◽  
Leena Tripathi
Keyword(s):  
Complete Genome ◽  
Sequence Data ◽  
Low Cost ◽  
Viral Disease ◽  
Aphid Species ◽  
Phylogenomic Analysis ◽  
Sequencing Library ◽  
Major Pest ◽  
Genome Assemblies ◽  
Pentalonia Nigronervosa

AbstractThe banana aphid, Pentalonia nigronervosa Coquerel (Hemiptera: Aphididae), is a major pest of cultivated bananas (Musa spp., order Zingiberales), primarily due to its role as a vector of Banana bunchy top virus (BBTV), the most severe viral disease of banana worldwide. Here, we generated a highly complete genome assembly of P. nigronervosa using a single PCR-free Illumina sequencing library. Using the same sequence data, we also generated complete genome assemblies of the P. nigronervosa symbiotic bacteria Buchnera aphidicola and Wolbachia. To improve our initial assembly of P. nigronervos a we developed a k-mer based deduplication pipeline to remove genomic scaffolds derived from the assembly of haplotigs (allelic variants assembled as separate scaffolds). To demonstrate the usefulness of this pipeline, we applied it to the recently generated assembly of the aphid Myzus cerasi, reducing the duplication of conserved BUSCO genes by 25%. Phylogenomic analysis of P. nigronervos a, our improved M. cerasi assembly, and seven previously published aphid genomes, spanning three aphid tribes and two subfamilies, reveals that P. nigronervos a falls within the tribe Macrosiphini, but is an outgroup to other Macrosiphini sequenced so far. As such, the genomic resources reported here will be useful for understanding both the evolution of Macrosphini and for the study of P. nigronervosa. Furthermore, our approach using low cost, high-quality, Illumina short-reads to generate complete genome assemblies of understudied aphid species will help to fill in genomic black spots in the diverse aphid tree of life.

scholarly journals Genome Sequence of the Banana Aphid, Pentalonia nigronervosa Coquerel (Hemiptera: Aphididae) and Its Symbionts

2020 ◽  
Vol 10 (12) ◽  
pp. 4315-4321
Author(s):  
Thomas C. Mathers ◽  
Sam T. Mugford ◽  
Saskia A. Hogenhout ◽  
Leena Tripathi
Keyword(s):  
Complete Genome ◽  
Sequence Data ◽  
Low Cost ◽  
Viral Disease ◽  
Aphid Species ◽  
Phylogenomic Analysis ◽  
Sequencing Library ◽  
Major Pest ◽  
Genome Assemblies ◽  
Pentalonia Nigronervosa

The banana aphid, Pentalonia nigronervosa Coquerel (Hemiptera: Aphididae), is a major pest of cultivated bananas (Musa spp., order Zingiberales), primarily due to its role as a vector of Banana bunchy top virus (BBTV), the most severe viral disease of banana worldwide. Here, we generated a highly complete genome assembly of P. nigronervosa using a single PCR-free Illumina sequencing library. Using the same sequence data, we also generated complete genome assemblies of the P. nigronervosa symbiotic bacteria Buchnera aphidicola and Wolbachia. To improve our initial assembly of P. nigronervosa we developed a k-mer based deduplication pipeline to remove genomic scaffolds derived from the assembly of haplotigs (allelic variants assembled as separate scaffolds). To demonstrate the usefulness of this pipeline, we applied it to the recently generated assembly of the aphid Myzus cerasi, reducing the duplication of conserved BUSCO genes by 25%. Phylogenomic analysis of P. nigronervosa, our improved M. cerasi assembly, and seven previously published aphid genomes, spanning three aphid tribes and two subfamilies, reveals that P. nigronervosa falls within the tribe Macrosiphini, but is an outgroup to other Macrosiphini sequenced so far. As such, the genomic resources reported here will be useful for understanding both the evolution of Macrosphini and for the study of P. nigronervosa. Furthermore, our approach using low cost, high-quality, Illumina short-reads to generate complete genome assemblies of understudied aphid species will help to fill in genomic black spots in the diverse aphid tree of life.

scholarly journals Complete Genome Sequences of Dengue Virus Type 2 Strains from Kilifi, Kenya

2019 ◽  
Vol 8 (4) ◽  
Author(s):  
Everlyn Kamau ◽  
Charles N. Agoti ◽  
Joyce M. Ngoi ◽  
Zaydah R. de Laurent ◽  
John Gitonga ◽  
...  
Keyword(s):  
Dengue Virus ◽  
Virus Type ◽  
Complete Genome ◽  
Sequence Data ◽  
Dengue Infection ◽  
Clinical Samples ◽  
Genome Sequences ◽  
Coastal Kenya ◽  
Dengue Virus Type 2

Dengue infection remains poorly characterized in Africa and little is known regarding its associated viral genetic diversity. Here, we report dengue virus type 2 (DENV-2) sequence data from 10 clinical samples, including 5 complete genome sequences of the cosmopolitan genotype, obtained from febrile adults seeking outpatient care in coastal Kenya.

scholarly journals Complete Genome Sequence Data of Three Xylella fastidiosa subsp. multiplex Strains Isolated from Olive Trees in California, U.S.A.

2020 ◽  
Vol 110 (11) ◽  
pp. 1759-1762
Author(s):  
Michael L. O’Leary ◽  
Lindsey P. Burbank ◽  
Rodrigo Krugner ◽  
Drake C. Stenger
Keyword(s):  
Los Angeles ◽  
Complete Genome ◽  
Sequence Data ◽  
Xylella Fastidiosa ◽  
Prunus Dulcis ◽  
Assembly Method ◽  
Wide Range ◽  
Olive Trees ◽  
Genome Assemblies ◽  
Bacterial Plant Pathogen

Xylella fastidiosa is a xylem-limited bacterial plant pathogen that causes disease on numerous hosts. Additionally, X. fastidiosa asymptomatically colonizes a wide range of plant species. X. fastidiosa subsp. multiplex has been detected in olive (Olea europaea) trees grown in California, U.S.A., as well as in Europe. Strains of X. fastidiosa subsp. multiplex isolated from California olive trees are not known to cause disease on olive, although some can induce leaf-scorch symptoms on almond (Prunus dulcis). No genome assemblies currently exist for olive-associated X. fastidiosa subsp. multiplex strains; therefore, a hybrid assembly method was used to generate complete genome sequences for three X. fastidiosa subsp. multiplex strains (Fillmore, LM10, and RH1) isolated from olive trees grown in Ventura and Los Angeles counties of California.

scholarly journals Retroposed New Genes Out of the X in Drosophila

2002 ◽  
Vol 12 (12) ◽  
pp. 1854-1859
Author(s):  
Esther Betrán ◽  
Kevin Thornton ◽  
Manyuan Long
Keyword(s):  
Population Genetics ◽  
Molecular Mechanisms ◽  
Sequence Data ◽  
Evolutionary Process ◽  
Significant Excess ◽  
Link Type ◽  
New Genes ◽  
Asymmetric Pattern ◽  
Unpublished Information

New genes that originated by various molecular mechanisms are an essential component in understanding the evolution of genetic systems. We investigated the pattern of origin of the genes created by retroposition in Drosophila. We surveyed the wholeDrosophila melanogaster genome for such new retrogenes and experimentally analyzed their functionality and evolutionary process. These retrogenes, functional as revealed by the analysis of expression, substitution, and population genetics, show a surprisingly asymmetric pattern in their origin. There is a significant excess of retrogenes that originate from the X chromosome and retropose to autosomes; new genes retroposed from autosomes are scarce. Further, we found that most of these X-derived autosomal retrogenes had evolved a testis expression pattern. These observations may be explained by natural selection favoring those new retrogenes that moved to autosomes and avoided the spermatogenesis X inactivation, and suggest the important role of genome position for the origin of new genes.[The sequence data from this study have been submitted to GenBank under accession nos. AY150701–AY150797. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: M.-L. Wu, F. Lemeunier, and P. Gibert.]

scholarly journals Complete Genome Sequence of a Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus Variant

2012 ◽  
Vol 86 (16) ◽  
pp. 8906-8906 ◽  
Author(s):  
Chengbao Wang ◽  
Qin Zhao ◽  
Chao Liang ◽  
Lu Dang ◽  
Yuping Ma ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Causative Agent ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Sequence Data ◽  
Nonstructural Protein ◽  
Respiratory Syndrome Virus ◽  
Highly Pathogenic ◽  
Virus Variant ◽  
Accelerate Evolution

Following the 2006 outbreaks of the highly pathogenic porcine reproductive and respiratory syndrome, the causative agent was identified as the highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV). To investigate whether the HP-PRRSV variant continues circulating and accelerating evolution, we sequenced and analyzed the complete genome of the identified HP-PRRSV field strain SD16. The sequence data indicate that the HP-PRRSV variant continues to prevail and accelerate evolution, especially in the nonstructural protein.

scholarly journals Phylogenomics of two ST1 antibiotic-susceptible non-clinical Acinetobacter baumannii strains reveals multiple lineages and complex evolutionary history in global clone 1

2021 ◽  
Vol 7 (12) ◽  
Author(s):  
Jonathan Koong ◽  
Claire Johnson ◽  
Rayane Rafei ◽  
Monzer Hamze ◽  
Garry S. A. Myers ◽  
...  
Keyword(s):  
Acinetobacter Baumannii ◽  
Genome Sequence ◽  
Evolutionary History ◽  
Sequence Data ◽  
Opportunistic Pathogen ◽  
Outer Core ◽  
Content Type ◽  
Geographical Regions ◽  
Long Read ◽  
Complex Evolutionary History

Acinetobacter baumannii is an opportunistic pathogen that is difficult to treat due to its resistance to extreme conditions, including desiccation and antibiotics. Most strains causing outbreaks around the world belong to two main global lineages, namely global clones 1 and 2 (GC1 and GC2). Here, we used a combination of Illumina short read and MinION (Oxford Nanopore) long-read sequence data with a hybrid assembly approach to complete the genome sequence of two antibiotic-sensitive GC1 strains, Ex003 and Ax270, recovered in Lebanon from water and a rectal swab of a cat, respectively. Phylogenetic analysis of Ax270 and Ex003 with 186 publicly available GC1 genomes revealed two major clades, including five main lineages (L1–L5), and four single-isolate lineages outside of the two clades. Ax270 and Ex003, along with AB307-0294 and MRSN7213 (both predicted antibiotic-susceptible isolates) represent these individual lineages. Antibiotic resistance islands and transposons interrupting the comM gene remain important features in L1–L5, with L1 associated with the AbaR-type resistance islands, L2 with AbaR4, L3 strains containing either AbaR4 or its variants as well as Tn6022::ISAba42, and L4 and L5 associated with Tn6022 or its variants. Analysis of the capsule (KL) and outer core (OCL) polysaccharide loci further revealed a complex evolutionary history probably involving many recombination events. As more genomes become available, more GC1 lineages continue to emerge. However, genome sequence data from more diverse geographical regions are needed to draw a more accurate population structure of this globally distributed clone.

Detection and molecular characterization of porcine enterovirus G15 and teschovirus from India

2020 ◽  
Vol 78 (5) ◽  
Author(s):  
Pradeep Mahadev Sawant ◽  
Nitin Atre ◽  
Abhijeet Kulkarni ◽  
Varanasi Gopalkrishna
Keyword(s):  
Amino Acid ◽  
Complete Genome ◽  
Prototype Strain ◽  
Western India ◽  
Vp1 Gene ◽  
Reading Frame ◽  
Porcine Enterovirus ◽  
Geographical Regions ◽  
Porcine Teschovirus

ABSTRACT Porcine enterovirus G (EV-G) and teschovirus (PTV) generally cause asymptomatic infections. Although both viruses have been reported from various countries, they are rarely detected from India. To detect these viruses in Western India, fecal samples (n = 26) of diarrheic piglets aged below three months from private pig farms near Pune (Maharashtra) were collected. The samples were screened by reverse transcription-polymerase chain reaction using conserved enterovirus specific primers from 5′ untranslated region. For genetic characterization of detected EV-G strain, nearly complete genome, and for PTV, partial VP1 gene were sequenced. EV-G strain showed the highest identity in a VP1 gene at nucleotide (78.61%) and amino acid (88.65%) level with EV-G15, prototype strain. However, its complete genome was homologous with the nucleotide (78.38% identity) and amino acid (91.24% identity) level to Ishi-Ka2 strain (LC316832), unassigned EV-G genotype detected from Japan. The nearly complete genome of EV-G15 consisted of 7398 nucleotides excluding the poly(A) tail and has an open reading frame that encodes a 2170 amino acid polyprotein. Genetic analysis of the partial VP1 gene of teschovirus identified porcine teschovirus 4 (PTV-4) and putative PTV-17 genotype. To the best of our knowledge, this is the first report on nearly full genome characterization of EV-G15, and detection of PTV-4 and putative PTV-17 genotypes from India. Further, detection and characterization of porcine enteroviruses are needed for a comprehensive understanding of their genetic diversity and their association with symptomatic infections from other geographical regions of India.

scholarly journals Serological Investigations of Bluetongue Virus (BTV) among Sheep and Goats in Kassala State, Eastern Sudan

2020 ◽  
Vol 2020 ◽  
pp. 1-7
Author(s):  
Molhima M. Elmahi ◽  
Abdel Rahim E. Karrar ◽  
Amira M. Elhassan ◽  
Mohammed O. Hussien ◽  
Khalid A. Enan ◽  
...  
Keyword(s):  
Risk Factors ◽  
Winter Season ◽  
Viral Disease ◽  
Enzyme Linked Immunosorbent Assay ◽  
Serum Samples ◽  
Sheep And Goats ◽  
Domestic Ruminants ◽  
The Family ◽  
Vector Borne ◽  
Center Section

Bluetongue (BT) is an infectious, noncontagious, vector-borne viral disease of wild and domestic ruminants. BTV is a member of the Orbivirus genus of the family Reoviridae. The present study aimed to investigate the seroprevalence of BTV in sheep and goats in Kassala State, Sudan. It also aimed to determine risk factors associated with BTV infection. The study was carried out by a structured questionnaire survey, and a total of 809 serum samples were collected from sheep (n = 459) and goats (n = 350) from 9 different localities in Kassala state. These samples were analyzed using a competitive enzyme-linked immunosorbent assay (cELISA) for the detection of BTV antibodies. The overall seroprevalence of BTV was 91.2% (738/809). In goats, the prevalence of BTV antibodies was comparatively higher (100%) than in sheep (84.5%). The prevalence differed between localities and was the highest in the center section of Kassala and Western Kassala (100%). Animals aged 6–11 months were highly infected (93.9%) compared to 1-year-old (85.5%). Caprine species was more likely to be infected (100%) than ovine (84.5%), and females were highly infected (92.8%) than males (85.5%). BTV infections were higher in the winter season (91.4%). Risk factors that showed significant associations with cELISA positivity included locality and sex (p≤0.003) and species and age (p≤0.000). Factors significantly associated with cELISA positivity in multivariate analysis were localities, species, age, and sex. BTV infection is prevalent in sheep and goat populations in Kassala state.

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