scholarly journals Genetic characterization of Blueberry necrotic ring blotch virus, a novel RNA virus with unique genetic features

2013 ◽  
Vol 94 (6) ◽  
pp. 1426-1434 ◽  
Author(s):  
Diego F. Quito-Avila ◽  
Philip M. Brannen ◽  
William O. Cline ◽  
Philip F. Harmon ◽  
Robert R. Martin
Keyword(s):  
Rna Virus ◽  
Genetic Relationships ◽  
Double Stranded Rna ◽  
Coding Regions ◽  
Genetic Features ◽  
The Usa ◽  
Highbush Blueberries ◽  
Southern Highbush

A new disorder was observed on southern highbush blueberries in several south-eastern states in the USA. Symptoms included irregularly shaped circular spots or blotches with green centres on the upper and lower surfaces of leaves. Double-stranded RNA was extracted from symptomatic leaves suggesting the presence of virus(es) possibly involved in the disease. Sequencing revealed the presence of a novel RNA virus with a ~14 kb genome divided into four RNA segments. Sequence analyses showed that the virus, for which we propose the name Blueberry necrotic ring blotch virus (BNRBV), possesses protein domains conserved across RNA viruses in the alpha-virus-like supergroup. Phylogenetic inferences using different genes placed BNRBV in a clade that includes the Bromoviridae, the genus Cilevirus (CiLV) and the recently characterized Hibiscus green spot virus (HGSV). Despite the strong genetic relationships found among BNRBV, Cilevirus and HGSV, the genome of BNRBV contains three features that distinguish it significantly from its closest relatives: (i) the presence of two helicase domains with different evolutionary pathways, (ii) the existence of three conserved nucleotide stretches located at the 3′ non-coding regions of each RNA segment and (iii) the conservation of terminal nucleotide motifs across each segment. Furthermore, CiLV and HGSV possess poly(A)-tailed bipartite and tripartite genomes, respectively, whereas BNRBV has a quadra-partite genome lacking a poly(A) tail. Based on these genetic features a new genus is proposed for the classification of BNRBV.

scholarly journals Genetic characterization of Streptococcus pyogenes emm 89 strains isolated in Japan from 2011 to 2019

2020 ◽  
Author(s):  
Yujiro Hirose ◽  
Masaya Yamaguchi ◽  
Norihiko Takemoto ◽  
Tohru Miyoshi-Akiyama ◽  
Tomoko Sumitomo ◽  
...  
Keyword(s):  
Streptococcus Pyogenes ◽  
Genetic Characterization ◽  
Streptococcal Toxic Shock Syndrome ◽  
Toxic Shock ◽  
Gene Encoding ◽  
Serum Opacity Factor ◽  
Genetic Features ◽  
Fibronectin Binding Protein

Streptococcal toxic shock syndrome (STSS) caused by Streptococcus pyogenes emm 89 strains has been increasing in several countries and reported to be linked with a recently emerged clade of emm89 strains, designated clade 3. In Japan, epidemiological and genetic information for emm89 strains remains elusive. In this study, we utilized emm89 strains isolated from both STSS (89 isolates) and non-STSS (72 isolates) infections in Japan from 2011 to 2019, and conducted whole-genome sequencing and comparative analysis, which resulted in classification of a large majority into clade 3 regardless of disease severity. In addition, STSS-associated genes and SNPs were found in clade 3 strains, including mutations of streptokinase (Ska), control of virulence sensor (CovS), serum opacity factor (SOF), sortase (SrtB), and fibronectin-binding protein F1 (PrtF1), and absence of the hylP1 gene encoding hyaluronidase. These findings provide insights into notable genetic features of emm89 strains.

scholarly journals A discovery 70 years in the making: characterization of the Rose rosette virus

2011 ◽  
Vol 92 (7) ◽  
pp. 1727-1732 ◽  
Author(s):  
Alma G. Laney ◽  
Karen E. Keller ◽  
Robert R. Martin ◽  
Ioannis E. Tzanetakis
Keyword(s):  
Rna Virus ◽  
Causal Agent ◽  
Low Diversity ◽  
The Usa ◽  
Rose Rosette ◽  
Diversity Studies ◽  
The Rose ◽  
Negative Sense ◽  
Eastern Half

Rose rosette was first described in the early 1940s and it has emerged as one of the most devastating diseases of roses. Although it has been 70 years since the disease description, the rosette agent is yet to be characterized. In this communication, we identify and characterize the putative causal agent of the disease, a negative-sense RNA virus and new member of the genus Emaravirus. The virus was detected in 84/84 rose rosette-affected plants collected from the eastern half of the USA, but not in any of 30 symptomless plants tested. The strong correlation between virus and disease is a good indication that the virus, provisionally named Rose rosette virus, is the causal agent of the disease. Diversity studies using two virus proteins, p3 and p4, demonstrated that the virus has low diversity between isolates as they share nucleotide identities ranging from 97 to 99%.

scholarly journals Genetic Characterization of Cleveland Bay Horse Breed

Diversity ◽  
2019 ◽  
Vol 11 (10) ◽  
pp. 174 ◽  
Author(s):  
Khanshour ◽  
Hempsey ◽  
Juras ◽  
Cothran
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Genetic Similarity ◽  
Genetic Resource ◽  
Genetic Characterization ◽  
Genetic Relationships ◽  
Similarity Measures ◽  
Horse Breed ◽  
The Usa

The Cleveland Bay (CB) is the United Kingdom’s oldest established horse breed. In this study we analyzed the genetic variability in CB horses and investigated its genetic relationships with other horse breeds. We examined the genetic variability among 90 CB horses sampled in the USA compared to a total of 3447 horses from 59 other breeds. Analysis of the genetic diversity and population structure was carried out using 15 microsatellite loci. We found that genetic diversity in CB horses was less than that for the majority of other tested breeds. The genetic similarity measures showed no direct relationship between the CB and Thoroughbred but suggested the Turkman horses (likely in the lineage of ancestors of the Thoroughbred) as a possible ancestor. Our findings reveal the genetic uniqueness of the CB breed and indicate its need to be preserved as a genetic resource.

scholarly journals Coat protein gene of a PStV-Bm isolate from West Nusa Tenggara, Indonesia

2020 ◽  
Vol 21 (3) ◽  
Author(s):  
Nur Indah Julisaniah ◽  
SUHARJONO ◽  
RETNO MASTUTI ◽  
ESTRI LARAS ARUMINGTYAS
Keyword(s):  
Coat Protein ◽  
Coat Protein Gene ◽  
Genetic Similarity ◽  
Protein Gene ◽  
Rna Virus ◽  
Genetic Relationships ◽  
Cp Gene ◽  
Similar Cluster ◽  
Similar Index ◽  
The Usa

Abstract. Julisaniah NI, Suharjono, Mastuti R, Arumingtyas EL. 2020. Coat protein gene of a PStV-Bm isolate from West Nusa Tenggara, Indonesia. Biodiversitas 21: 903-909. Peanut stripe virus (PStV) is a single-stranded positive-sense RNA virus capable of infecting peanut plants. An isolate of PStV (PStV-Bm) was collected from a peanut field in the Bima District, West Nusa Tenggara Province, Indonesia and the coat protein (CP) gene of this virus (CP-PStV) was extracted from the viral RNA and analyzed using reverse transcription-polymerase chain reaction methods. The CP-PStV gene of PStV-Bm was aligned with several PStV genes deposited in the Genbank (http://www.ncbi.nml.nih.gov). Based on the nucleotide sequence of the CP gene, PStV-Bm was grouped into a similar cluster with other PStVs that originated from Indonesia with a similar index, ranging from 96.8% to 98.9%. Genetic similarity (about 96.1%) was also observed between PStV-Bm and PStV from the USA. This genetic similarity indicated that viruses from adjacent regions have high genetic relationships. Some amino acid differences were observed in PStV-Bm that may be typical of this strain.

Collection and characterization of maize and upland rice populations cropped by poor farmers in the uplands of Panama's Azuero region

2008 ◽  
Vol 7 (02) ◽  
pp. 105-112
Author(s):  
B. E. Love ◽  
S. Dreisigacker ◽  
D. Spaner
Keyword(s):  
Genetic Diversity ◽  
Latin America ◽  
Upland Rice ◽  
Genetic Relationships ◽  
Phenotypic Differences ◽  
Crop Genetic Diversity ◽  
Maize Populations ◽  
Modern Varieties

The conservation of crop genetic resources is an international priority and requires the continued collection and characterization of farmer varieties. We collected and characterized maize and upland rice populations cropped by farmers in Panama's Azuero region. The objective of our study was to evaluate the crop genetic diversity of farmer varieties of maize and upland rice grown by poor farmers in Panama. We found that: (1) farmers' naming practices only partially corresponded to genetic relationships and were the strongest for rice populations; (2) farmers' classification of populations as ‘modern’ or ‘traditional’ was reflected in phenotypic differences; (3) Panamanian maize populations were molecularly distinct from populations collected elsewhere in Latin America; and (4) heterogeneous rice populations were common and heterogeneity was often due to admixture of recognized farmer varieties. Our results indicate that poor farmers in Panama continue to farm ‘traditional’ varieties that harbour genetic diversity of interest. There has, however, been substantial adoption of ‘modern’ varieties.

Identification and molecular characterization of a new nonsegmented double-stranded RNA virus isolated from Culex mosquitoes in Japan

2011 ◽  
Vol 155 (1) ◽  
pp. 147-155 ◽  
Author(s):  
Haruhiko Isawa ◽  
Ryusei Kuwata ◽  
Keita Hoshino ◽  
Yoshio Tsuda ◽  
Kouji Sakai ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Rna Virus ◽  
Double Stranded Rna ◽  
Culex Mosquitoes

scholarly journals Characterization of a segmented double-stranded RNA virus inDrosophilaKccells

1983 ◽  
Vol 11 (11) ◽  
pp. 3665-3678 ◽  
Author(s):  
Julia T. Hsu ◽  
Marilyn M. Sanders
Keyword(s):  
Rna Virus ◽  
Double Stranded Rna

scholarly journals Structures of Capsular Polysaccharide Serotypes 35F and 35C of Streptococcus pneumoniae Determined by Nuclear Magnetic Resonance and Their Relation to Other Cross-Reactive Serotypes

2015 ◽  
Vol 197 (17) ◽  
pp. 2762-2769 ◽  
Author(s):  
C. Allen Bush ◽  
John O. Cisar ◽  
Jinghua Yang
Keyword(s):  
Streptococcus Pneumoniae ◽  
Magnetic Resonance ◽  
Capsular Polysaccharide ◽  
Genetic Relationships ◽  
Repeat Unit ◽  
Immune Selection ◽  
Comprehensive Description ◽  
Content Type ◽  
Genetic Features

ABSTRACTThe structures ofStreptococcus pneumoniaecapsular polysaccharides (CPSs) are essential for defining the antigenic as well as genetic relationships between CPS serotypes. The four serotypes that comprise CPS serogroup 35 (i.e., types 35F, 35A, 35B, and 35C) are known to cross-react with genetically related type 20, 29, 34, 42, or 47F. While the structures of CPS serotype 35A (CPS35A) and CPS35B are known, those of CPS35F and CPS35C are not. In the present study, the serotypes of CPS35F and CPS35C were characterized by high-resolution heteronuclear magnetic resonance (NMR) spectroscopy and glycosyl composition analyses to reveal the following repeat unit structures:where OAc indicates O-acetylated. Importantly, CPS35F, the immunizing serotype for the production of group 35 serum, more closely resembles CPS34 and CPS47F than other members of serogroup 35. Moreover, CPS35C is distinct from either CPS35F or CPS35B but closely related to CPS35A and identical to de-O-acetylated CPS42. The findings provide a comprehensive view of the structural and genetic relations that exist between the members of CPS serogroup 35 and other cross-reactive serotypes.IMPORTANCECross-reactions of diagnostic rabbit antisera withStreptococcus pneumoniaecapsular polysaccharide serotypes are generally limited to members of the same serogroup. Exceptions do, however, occur, most notably among a group of nonvaccine serotypes that includes the members of serogroup 35 (i.e., types 35F, 35A, 35B, and 35C) and other genetically related types. The presently determined structures ofS. pneumoniaeserotypes 35F and 35C complete the structural characterization of serogroup 35 and thereby provide the first comprehensive description of how different members of this serogroup are related to each other and to types 29, 34, 42, and 47F. The structural and genetic features of these serotypes suggest the existence of three distinct capsular polysaccharide subgroups that presumably emerged by immune selection in the human host.

Sign in / Sign up

Export Citation Format

Share Document