scholarly journals Complete genome analysis identifies Tvärminne avian virus as a candidate new species within the genus Orthoreovirus

2014 ◽  
Vol 95 (4) ◽  
pp. 898-904 ◽  
Author(s):  
Eszter Dandár ◽  
Eili Huhtamo ◽  
Szilvia L. Farkas ◽  
Miklós Oldal ◽  
Ferenc Jakab ◽  
...  
Keyword(s):  
Neurological Disorders ◽  
Phylogenetic Analyses ◽  
Virus Species ◽  
Sea Lion ◽  
Avian Virus ◽  
Semiconductor Sequencing ◽  
Avian Origin ◽  
Complete Genome Analysis ◽  
Strain Genome

Orthoreoviruses have been associated with a variety of diseases in domesticated poultry and wild-living birds. In 2002, a reovirus strain named Tvärminne avian virus (TVAV), was identified in Finland in a crow showing neurological disorders. The objective of this study was the molecular characterization of this novel reovirus strain. Genome sequencing was performed by combining semiconductor sequencing and traditional capillary sequencing. Sequence and phylogenetic analyses showed that TVAV shares low nucleotide sequence identity with other reoviruses (range for each gene, 31–72 %) including strains belonging to the species Avian orthoreovirus. The most closely related reovirus strain was an isolate identified in Steller sea lion. Our data indicate that TVAV is a divergent reovirus of avian origin that may be the first representative of a distinct virus species within the genus Orthoreovirus.

scholarly journals Grapevine virus L: a Novel Vitivirus in Grapevine

2018 ◽  
Author(s):  
Humberto Debat ◽  
Diego Zavallo ◽  
Reid Soltero Brisbane ◽  
Darko Vončina ◽  
Rodrigo P.P. Almeida ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Phylogenetic Analyses ◽  
Protein A ◽  
Virus Species ◽  
Nucleic Acid Binding ◽  
Grapevine Virus ◽  
Rnaseq Data ◽  
Virus Sequence ◽  
Novel Virus

AbstractVitivirus are ssRNA(+) viruses in the family Betaflexiviridae (subfamily Trivirinae). There are currently ten ICTV recognized virus species in the genus; nevertheless, the extended use of NGS technologies is rapidly expanding their diversity and six more have been proposed recently. Here, we present the characterization of a novel virus from grapevines, which fits the genomic architecture and evolutionary constraints to be classifiable within the Vitivirus genus. The detected virus sequence is 7,607 nt long, including a typical genome organization of ORFs encoding a replicase (RP), a 22 kDa protein, a movement protein, a coat protein (CP) and a nucleic acid binding protein. Here, we present the characterization of a novel virus from grapevines. Phylogenetic analyses based on the predicted RP and CP protein unequivocally places the new virus within the Vitivirus genus. Multiple independent RNAseq data confirmed the presence of the detected virus in berries at diverse developmental stages. Additionally, we detected, confirmed, and assembled virus sequences from grapevine samples of distinct cultivars from America, Europe, Asia and Oceania, sharing 74.9%-97.9% nt identity, suggesting that the identified virus is widely distributed and diverse. We propose the name grapevine virus L (GVL) to the detected Vitivirus.

scholarly journals Functional and Molecular Characterization of the Halomicrobium sp. IBSBa Inulosucrase

2021 ◽  
Vol 9 (4) ◽  
pp. 749
Author(s):  
Gülbahar Abaramak ◽  
Jaime Ricardo Porras-Domínguez ◽  
Henry Christopher Janse van Rensburg ◽  
Eveline Lescrinier ◽  
Ebru Toksoy Öner ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Phylogenetic Analyses ◽  
Halophilic Archaea ◽  
Maximum Activity ◽  
Physiological Relevance ◽  
Health Related ◽  
Specific Alternative ◽  
Binding Groove ◽  
Native Host

Fructans are fructose-based (poly)saccharides with inulin and levan being the best-known ones. Thanks to their health-related benefits, inulin-type fructans have been under the focus of scientific and industrial communities, though mostly represented by plant-based inulins, and rarely by microbial ones. Recently, it was discovered that some extremely halophilic Archaea are also able to synthesize fructans. Here, we describe the first in-depth functional and molecular characterization of an Archaeal inulosucrase from Halomicrobium sp. IBSBa (HmcIsc). The HmcIsc enzyme was recombinantly expressed and purified in Escherichia coli and shown to synthesize inulin as proven by nuclear magnetic resonance (NMR) analysis. In accordance with the halophilic lifestyle of its native host, the enzyme showed maximum activity at very high NaCl concentrations (3.5 M), with specific adaptations for that purpose. Phylogenetic analyses suggested that Archaeal inulosucrases have been acquired from halophilic bacilli through horizontal gene transfer, with a HX(H/F)T motif evolving further into a HXHT motif, together with a unique D residue creating the onset of a specific alternative acceptor binding groove. This work uncovers a novel area in fructan research, highlighting unexplored aspects of life in hypersaline habitats, and raising questions about the general physiological relevance of inulosucrases and their products in nature.

scholarly journals Molecular Characterization of PGC-1β (PPAR Gamma Coactivator 1β) and its Roles in Mitochondrial Biogenesis in Blunt Snout Bream (Megalobrama amblycephala)

2020 ◽  
Vol 21 (6) ◽  
pp. 1935 ◽  
Author(s):  
Kangle Lu ◽  
Tomas Policar ◽  
Xiaojun Song ◽  
Samad Rahimnejad
Keyword(s):  
Molecular Characterization ◽  
Mitochondrial Biogenesis ◽  
Phylogenetic Analyses ◽  
Ppar Gamma ◽  
Megalobrama Amblycephala ◽  
Fat Intake ◽  
High Fat ◽  
Blunt Snout Bream ◽  
Mitochondria Biogenesis

This study aimed at achieving the molecular characterization of peroxisome proliferator-activated receptor-gamma coactivator 1β (PGC-1β) and exploring its modulatory roles in mitochondria biogenesis in blunt snout bream (Megalobrama amblycephala). A full-length cDNA of PGC-1β was cloned from liver which covered 3110 bp encoding 859 amino acids. The conserved motifs of PGC-1β family proteins were gained by MEME software, and the phylogenetic analyses showed motif loss and rearrangement of PGC-1β in fish. The function of PGC-1β was evaluated through overexpression and knockdown of PGC-1β in primary hepatocytes of blunt snout bream. We observed overexpression of PGC-1β along with enhanced mitochondrial transcription factor A (TFAM) expression and mtDNA copies in hepatocytes, and its knockdown led to slightly reduced NRF1 expression. However, knockdown of PGC-1β did not significantly influence TFAM expression or mtDNA copies. The alterations in mitochondria biogenesis were assessed following high-fat intake, and the results showed that it induces downregulation of PGC-1β. Furthermore, significant decreases in mitochondrial respiratory chain activities and mitochondria biogenesis were observed by high-fat intake. Our findings demonstrated that overexpression of PGC-1β induces the enhancement of TFAM expression and mtDNA amount but not NRF-1. Therefore, it could be concluded that PGC-1β is involved in mitochondrial biogenesis in blunt snout bream but not through PGC-1β/NRF-1 pathway.

scholarly journals Diversity unearthed by the estimated molecular phylogeny and ecologically quantitative characteristics of uncultured Ehrlichia bacteria in Haemaphysalis ticks, Japan

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hongru Su ◽  
Eri Onoda ◽  
Hitoshi Tai ◽  
Hiromi Fujita ◽  
Shigetoshi Sakabe ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Core Genome ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Housekeeping Genes ◽  
Pcr Screening ◽  
Taxonomic Profiling ◽  
Quantitative Characteristics

AbstractEhrlichia species are obligatory intracellular bacteria transmitted by arthropods, and some of these species cause febrile diseases in humans and livestock. Genome sequencing has only been performed with cultured Ehrlichia species, and the taxonomic status of such ehrlichiae has been estimated by core genome-based phylogenetic analysis. However, many uncultured ehrlichiae exist in nature throughout the world, including Japan. This study aimed to conduct a molecular-based taxonomic and ecological characterization of uncultured Ehrlichia species or genotypes from ticks in Japan. We first surveyed 616 Haemaphysalis ticks by p28-PCR screening and analyzed five additional housekeeping genes (16S rRNA, groEL, gltA, ftsZ, and rpoB) from 11 p28-PCR-positive ticks. Phylogenetic analyses of the respective genes showed similar trees but with some differences. Furthermore, we found that V1 in the V1–V9 regions of Ehrlichia 16S rRNA exhibited the greatest variability. From an ecological viewpoint, the amounts of ehrlichiae in a single tick were found to equal approx. 6.3E+3 to 2.0E+6. Subsequently, core-partial-RGGFR-based phylogenetic analysis based on the concatenated sequences of the five housekeeping loci revealed six Ehrlichia genotypes, which included potentially new Ehrlichia species. Thus, our approach contributes to the taxonomic profiling and ecological quantitative analysis of uncultured or unidentified Ehrlichia species or genotypes worldwide.

New perspectives on Aspersentis Megarhynchus (Acanthocephala: Heteracanthocephalidae) from Notothenia Coriiceps Richardson (Nototheniidae) in the West Antarctic, with emended generic diagnosis

2021 ◽  
Vol 95 ◽  
Author(s):  
O.M. Amin ◽  
R.A. Heckmann ◽  
S. Dallarés ◽  
M. Constenla ◽  
N.Yu. Rubtsova ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Original Description ◽  
Generic Diagnosis ◽  
West Antarctica ◽  
Dorsal Wall ◽  
West Antarctic ◽  
Notothenia Coriiceps ◽  
The Many ◽  
Dorsal Position

Abstract A number of variable descriptive accounts of Aspersentis megarhynchus (von Linstow, 1892) Golvan, 1960 have been reported from specimens collected from many species of fish in various locations off Antarctic islands. We have described a new population from Notothenia coriiceps Richardson (Nototheniidae) off Galindez Island, West Antarctica, and features not previously reported, resolved the taxonomic controversies and nomenclature, and emended and updated the generic diagnosis taking into account the newly observed structures. These are depicted in microscopic images and include the outer spiral wall of the proboscis receptacle, the thicker dorsal wall of the receptacle compared to the ventral wall, parts of the female reproductive system, the separate cement gland ducts, the dorsal position of the male gonopore and more detail of proboscis hooks and trunk spines. It is surprising that the newly observed features were missed from the many descriptions of A. megarhynchus created since the original description. The variability in A. megarhynchus is noted with a comparison of the morphometrics of our specimens vs. those in six other descriptions. We also analysed the metal composition of hooks and spines using energy-dispersive X-ray analysis and concluded a molecular characterization of the species based on 18S DNA gene, with related phylogenetic analyses.

scholarly journals Mealybug Transmission of Grapevine Leafroll Viruses: An Analysis of Virus–Vector Specificity

2010 ◽  
Vol 100 (8) ◽  
pp. 830-834 ◽  
Author(s):  
Chi-Wei Tsai ◽  
Adib Rowhani ◽  
Deborah A. Golino ◽  
Kent M. Daane ◽  
Rodrigo P. P. Almeida
Keyword(s):  
Plant Pathogens ◽  
Phylogenetic Analyses ◽  
Virus Vector ◽  
Disease Spread ◽  
Virus Species ◽  
Vector Species ◽  
Vector Transmission ◽  
Planococcus Ficus ◽  
Grapevine Leafroll Disease ◽  
Leafroll Disease

To understand ecological factors mediating the spread of insect-borne plant pathogens, vector species for these pathogens need to be identified. Grapevine leafroll disease is caused by a complex of phylogenetically related closteroviruses, some of which are transmitted by insect vectors; however, the specificities of these complex virus–vector interactions are poorly understood thus far. Through biological assays and phylogenetic analyses, we studied the role of vector-pathogen specificity in the transmission of several grapevine leafroll-associated viruses (GLRaVs) by their mealybug vectors. Using plants with multiple virus infections, several virus species were screened for vector transmission by the mealybug species Planococcus ficus and Pseudococcus longispinus. We report that two GLRaVs (-4 and -9), for which no vector transmission evidence was available, are mealybug-borne. The analyses performed indicated no evidence of mealybug–GLRaV specificity; for example, different vector species transmitted GLRaV-3 and one vector species, Planococcus ficus, transmitted five GLRaVs. Based on available data, there is no compelling evidence of vector–virus specificity in the mealybug transmission of GLRaVs. However, more studies aimed at increasing the number of mealybug species tested as vectors of different GLRaVs are necessary. This is especially important given the increasing importance of grapevine leafroll disease spread by mealybugs in vineyards worldwide.

scholarly journals Identification and characterization of Fep15, a new selenocysteine-containing member of the Sep15 protein family

2006 ◽  
Vol 394 (3) ◽  
pp. 575-579 ◽  
Author(s):  
Sergey V. Novoselov ◽  
Deame Hua ◽  
Alexey V. Lobanov ◽  
Vadim N. Gladyshev
Keyword(s):  
Mammalian Cells ◽  
Insertion Sequence ◽  
Phylogenetic Analyses ◽  
Dependent Manner ◽  
Putative Active Site ◽  
A Genome ◽  
Sequence Elements ◽  
Identification And Characterization ◽  
Insertion Sequence Elements

Sec (selenocysteine) is a rare amino acid in proteins. It is co-translationally inserted into proteins at UGA codons with the help of SECIS (Sec insertion sequence) elements. A full set of selenoproteins within a genome, known as the selenoproteome, is highly variable in different organisms. However, most of the known eukaryotic selenoproteins are represented in the mammalian selenoproteome. In addition, many of these selenoproteins have cysteine orthologues. Here, we describe a new selenoprotein, designated Fep15, which is distantly related to members of the 15 kDa selenoprotein (Sep15) family. Fep15 is absent in mammals, can be detected only in fish and is present in these organisms only in the selenoprotein form. In contrast with other members of the Sep15 family, which contain a putative active site composed of Sec and cysteine, Fep15 has only Sec. When transiently expressed in mammalian cells, Fep15 incorporated Sec in an SECIS- and SBP2 (SECIS-binding protein 2)-dependent manner and was targeted to the endoplasmic reticulum by its N-terminal signal peptide. Phylogenetic analyses of Sep15 family members suggest that Fep15 evolved by gene duplication.

Identification and genetic characterization of avian-origin H3N2 canine influenza viruses isolated from the Liaoning province of China in 2012

Virus Genes ◽  
2014 ◽  
Vol 49 (2) ◽  
pp. 342-347 ◽  
Author(s):  
Xinyan Yang ◽  
Chunguo Liu ◽  
Fei Liu ◽  
Dafei Liu ◽  
Yan Chen ◽  
...  
Keyword(s):  
Genetic Characterization ◽  
Influenza Viruses ◽  
Liaoning Province ◽  
Avian Origin ◽  
Canine Influenza

scholarly journals Genome-wide identification and characterization of COMT gene family during the development of blueberry fruit

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yushan Liu ◽  
Yizhou Wang ◽  
Jiabo Pei ◽  
Yadong Li ◽  
Haiyue Sun
Keyword(s):  
Gene Family ◽  
Fruit Development ◽  
Lignin Content ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Vaccinium Corymbosum ◽  
Land Plant ◽  
Phylogenetic Structure ◽  
Genome Wide

Abstract Background Caffeic acid O-methyltransferases (COMTs) play an important role in the diversification of natural products, especially in the phenylalanine metabolic pathway of plant. The content of COMT genes in blueberry and relationship between their expression patterns and the lignin content during fruit development have not clearly investigated by now. Results Ninety-two VcCOMTs were identified in Vaccinium corymbosum. According to phylogenetic analyses, the 92 VcCOMTs were divided into 2 groups. The gene structure and conserved motifs within groups were similar which supported the reliability of the phylogenetic structure groupings. Dispersed duplication (DSD) and whole-genome duplication (WGD) were determined to be the major forces in VcCOMTs evolution. The results showed that the results of qRT-PCR and lignin content for 22 VcCOMTs, VcCOMT40 and VcCOMT92 were related to lignin content at different stages of fruit development of blueberry. Conclusion We identified COMT gene family in blueberry, and performed comparative analyses of the phylogenetic relationships in the 15 species of land plant, and gene duplication patterns of COMT genes in 5 of the 15 species. We found 2 VcCOMTs were highly expressed and their relative contents were similar to the variation trend of lignin content during the development of blueberry fruit. These results provide a clue for further study on the roles of VcCOMTs in the development of blueberry fruit and could promisingly be foundations for breeding blueberry clutivals with higher fruit firmness and longer shelf life.

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