scholarly journals Extensive Phylogenetic Analysis of Piscine Orthoreovirus Genomic Sequences Shows the Robustness of Subgenotype Classification

Pathogens ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 41
Author(s):  
Marcos Godoy ◽  
Daniel A. Medina ◽  
Rudy Suarez ◽  
Sandro Valenzuela ◽  
Jaime Romero ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Variation ◽  
Sequence Analysis ◽  
Molecular Phylogeny ◽  
Phylogenetic Trees ◽  
Genomic Segment ◽  
Double Stranded Rna ◽  
The Family ◽  
Original Classification

Piscine orthoreovirus (PRV) belongs to the family Reoviridae and has been described mainly in association with salmonid infections. The genome of PRV consists of about 23,600 bp, with 10 segments of double-stranded RNA, classified as small (S1 to S4), medium (M1, M2 and M3) and large (L1, L2 and L3); these range approximately from 1000 bp (segment S4) to 4000 bp (segment L1). How the genetic variation among PRV strains affects the virulence for salmonids is still poorly understood. The aim of this study was to describe the molecular phylogeny of PRV based on an extensive sequence analysis of the S1 and M2 segments of PRV available in the GenBank database to date (May 2020). The analysis was extended to include new PRV sequences for S1 and M2 segments. In addition, subgenotype classifications were assigned to previously published unclassified sequences. It was concluded that the phylogenetic trees are consistent with the original classification using the PRV genomic segment S1, which differentiates PRV into two major genotypes, I and II, and each of these into two subgenotypes, designated as Ia and Ib, and IIa and IIb, respectively. Moreover, some clusters of country- and host-specific PRV subgenotypes were observed in the subset of sequences used. This work strengthens the subgenotype classification of PRV based on the S1 segment and can be used to enhance research on the virulence of PRV.

scholarly journals Overview and revision of the extant genera and subgenera of Trogidae (Coleoptera: Scarabaeoidea)

2016 ◽  
Vol 47 (1) ◽  
pp. 53-82 ◽  
Author(s):  
Werner P. Strümpher ◽  
Martin H. Villet ◽  
Catherine L. Sole ◽  
Clarke H. Scholtz
Keyword(s):  
Molecular Phylogeny ◽  
Endemic Species ◽  
Strong Support ◽  
Morphological Characters ◽  
New Combinations ◽  
Genus Level ◽  
Generic Rank ◽  
The Family ◽  
Taxonomic Changes

Extant genera and subgenera of the Trogidae (Coleoptera: Scarabaeoidea) are reviewed. Contemporary classifications of this family have been based exclusively on morphological characters. The first molecular phylogeny for the family recently provided strong support for the relationships between morphologically defined genera and subgenera. On the basis of morphological, molecular and biogeographical evidence, certain taxonomic changes to the genus-level classification of the family are now proposed. The family is confirmed as consisting of two subfamilies, Omorginae Nikolajev and Troginae MacLeay, the former with two genera,OmorgusErichson andPolynoncusBurmeister, and the latter with two genera,TroxFabricius andPhoberusMacLeaystat. rev.Phoberusis restored to generic rank to include all Afrotropical (including Madagascan endemic) species;Afromorgusis confirmed at subgeneric rank within the genusOmorgus; and the monotypic Madagascan genusMadagatroxsyn. n.is synonymised withPhoberus.The current synonymies ofPseudotroxRobinson (withTrox),ChesasBurmeister,LagopelusBurmeister andMegalotroxPreudhomme de Borre (all withOmorgus) are all accepted to avoid creating speculative synonyms before definitive phylogenetic evidence is available. New combinations resulting from restoringPhoberusto a monophyletic genus are listed in Appendix A.

scholarly journals Complete Genome Sequence of a Fusarium graminearum Double-Stranded RNA Virus in a Newly Proposed Family, Alternaviridae

2018 ◽  
Vol 6 (8) ◽  
Author(s):  
Hao He ◽  
Xiaoguang Chen ◽  
Pengfei Li ◽  
Dewen Qiu ◽  
Lihua Guo
Keyword(s):  
Phylogenetic Analysis ◽  
Fusarium Graminearum ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Rna Virus ◽  
Phytopathogenic Fungus ◽  
Double Stranded Rna ◽  
First Report ◽  
The Family

ABSTRACT We describe here a double-stranded RNA mycovirus, termed Fusarium graminearum alternavirus 1 (FgAV1/AH11), from the isolate AH11 of the phytopathogenic fungus F. graminearum . Phylogenetic analysis showed that FgAV1/AH11 belongs to a newly proposed family, Alternaviridae . This is the first report of a mycovirus in the family Alternaviridae that infects F. graminearum .

Morphological and molecular identification of some species of nematode of the family Protostrongylidae Leiper, 1926

2016 ◽  
Vol 3 (4) ◽  
pp. 454-461
Author(s):  
Салахутдинов ◽  
I. Salakhutdinov ◽  
Рузиев ◽  
B. Ruziev ◽  
Каримова ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Trees ◽  
Molecular Genetic ◽  
Digital Camera ◽  
Molecular Genetic Analysis ◽  
Nucleotide Sequences ◽  
Genetic Identification ◽  
Mountain Area ◽  
Phylogenetic Relations ◽  
The Family

Objective of research: conducting morphological and molecular-genetic identification and studying phylogenetic relations between protostrongylids. Materials and methods: helminthological material was collected from wild (Capra sibirica, C. falconeri, Ovis vignei and O. ammon) and domestic hollow horned ruminants (C. hircus and O. aries), and land mollusks of the family Xeropicta in the piedmont and mountain area of Uzbekisan. The morphology of protostrongylids was studied using the methods of Boev (1975) and Anderson (1978). To identify the nematode type we used temporary preparations treated with glycerol. The first-stage larvae were investigated by examination of fecal samples from animals taking into account the length, tail form and body size. To study the morphology of the third-stage protostrongylid larvae the feet of infected mollusks Xeropicta candaсharica were separated and placed into the artificial gastric juice where the cap was destroyed and the infected larvae were eliminated. After determination of species belonging of mature and larval nematodes the material was stored in separate test-tubes with distilled water under the low temperature (- 20 ºС) or in 70 % Ethanol for the molecular analysis. We used microscopes ML 2000 with a digital camera and Olympus CX3. DNA extraction, amplification and sequencing were performed with an automated sequencer. Phylogenetic analysis was conducted using the software Clustal X 2.0. Phylogenetic trees were created by the Neighbor–Joining method. Nucleotide sequences ITS-2 regions of species Protostrongylus rufescens (EU018485), P. shiozawai (AB478249), Ortostrongylus macrotis (EU018483), Cystocaulus ocreatus (EU018481) and Umingmakstrongylus pallikuukensis (AY648409) received from the NCBI GenBank were used in phylogenetic analysis. Results and discussion: Four species of adult protostrongylid nematodes: Protostrongylus rufescens, P. hobmaieri, Spiculocaulus leuckarti and Cystocaulus ocreatus were determined. DNA from four species of mature protostrongylids and larvae was amplified by using ITS-2 regions. Amplificate dimension of nematodes P. rufescens and P. hobmaieri was 380 base pairs (b.p.), S. leuckarti – 388, C. ocreatus – 399 b.p. According to the results of phylogenetic analysis and comparison of nucleotide sequences, five protostrongylid species were found in animals of the Caprinae subfamily: P. rufescens, P. hobmaieri, Protostrongylus sp., S. leuckarti and C. ocreatus. The morphological and molecular-genetic analysis of detected nematodes enables the precise identification.

scholarly journals Interaction of a Host Protein with Core Complexes of Bacteriophage Φ6 To Control Transcription

2010 ◽  
Vol 84 (9) ◽  
pp. 4821-4825 ◽  
Author(s):  
Xueying Qiao ◽  
Yang Sun ◽  
Jian Qiao ◽  
Leonard Mindich
Keyword(s):  
Green Fluorescent Protein ◽  
Rna Polymerase ◽  
Fluorescent Protein ◽  
Host Protein ◽  
Genomic Segment ◽  
Double Stranded Rna ◽  
Infection Period ◽  
The Family ◽  
Green Fluorescent ◽  
In Cells

ABSTRACT Bacteriophages of the family Cystoviridae have genomes consisting of three double-stranded RNA (dsRNA) segments, L, S, and M, packaged within a polyhedral capsid along with RNA polymerase. Transcription of genomic segment L is activated by the interaction of host protein YajQ with the capsid structure. Segment L codes for the proteins of the inner capsid, which are expressed early in infection. Green fluorescent protein (GFP) fusions with YajQ produce uniform fluorescence in uninfected cells and in cells infected with viruses not dependent on YajQ. Punctate fluorescence develops when cells are infected with YajQ-dependent viruses. It appears that the host protein binds to the infecting particles and remains with them during the entire infection period.

scholarly journals Molecular Phylogeny of Anabaena circinalis and Its Identification in Environmental Samples by PCR

2000 ◽  
Vol 66 (9) ◽  
pp. 4145-4148 ◽  
Author(s):  
Kim M. Fergusson ◽  
Christopher P. Saint
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Analysis ◽  
Molecular Phylogeny ◽  
Rna Polymerase ◽  
Environmental Samples ◽  
Mixed Population ◽  
Specific Pcr ◽  
Paralytic Shellfish ◽  
Morphological Differences ◽  
Anabaena Circinalis

ABSTRACT Although the cyanobacterium Anabaena circinalis occurs worldwide, Australian isolates are believed to exclusively possess the saxitoxin group neurotoxins (paralytic shellfish poisons). Identification of A. circinalis in a mixed population is complicated due to limited morphological differences betweenAnabaena species. Sequence analysis of the DNA-dependent RNA polymerase (rpoC1) gene from 24 Anabaenaisolates, including 12 designated A. circinalis, permitted a phylogenetic analysis to be performed. In addition, an A. circinalis-specific PCR was developed and tested successfully on environmental samples.

Phylogenetic relationships and a new classification of the family Cyclopteridae (Perciformes: Cottoidei)

Zootaxa ◽  
2017 ◽  
Vol 4221 (1) ◽  
pp. 1 ◽  
Author(s):  
KANAMI OKU ◽  
HISASHI IMAMURA ◽  
MAMORU YABE
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Cladistic Analysis ◽  
New Classification ◽  
The Family ◽  
Dorsal Process ◽  
Transformation Series

 Phylogenetic relationships of the family Cyclopteridae were reconstructed based on osteological and external characters.  The monophyly of the family was strongly supported by 47 commonly recognized synapomorphies, including six autapomorphies (plus one additional autapomorphy, presence of a dorsal process on the pelvis, recognized after the phylogenetic analysis) among the suborder Cottoidei.  As a result of the cladistic analysis, a single most parsimonious phylogeny was obtained, based on characters in 32 transformation series.  A new classification of Cyclopteridae based on reconstructed relationships, including three subfamilies [Liparopsinae, Cyclopterinae and Eumicrotreminae (newly established)] and four genera (Aptocyclus, Cyclopsis, Cyclopterus and Eumicrotremus), is proposed.    

scholarly journals Phylogenetic Analysis of the Species Theilovirus: Emerging Murine and Human Pathogens

2008 ◽  
Vol 82 (23) ◽  
pp. 11545-11554 ◽  
Author(s):  
Zhiguo Liang ◽  
A. S. Manoj Kumar ◽  
Morris S. Jones ◽  
Nick J. Knowles ◽  
Howard L. Lipton
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Analyses ◽  
Distinct Species ◽  
Encephalomyocarditis Virus ◽  
Gene Products ◽  
Human Pathogens ◽  
Central Nervous System Infections ◽  
The Family ◽  
Encephalomyelitis Virus

ABSTRACT The Cardiovirus genus of the family Picornaviridae includes two distinct species, Encephalomyocarditis virus and Theilovirus. We now report the complete nucleotide sequences of three Theiler's murine encephalomyelitis virus (TMEV) strains (TO Yale, TOB15, and Vie 415HTR) and of Vilyuisk human encephalomyelitis virus (VHEV). This information, together with the recently reported sequences of divergent theiloviruses (Theiler's-like rat virus [TRV] and Saffold viruses 1 and 2 [SAFV-1 and SAFV-2]), enables an updated phylogenetic analysis as well as a reexamination of several gene products important in the pathogenesis of this emerging group of viruses. In the light of the known neurotropism of TMEV and the new human SAFV-1 and SAFV-2, the resulting data suggest the existence of theiloviruses that cause human central nervous system infections. Our phylogenetic analyses point to the classification of presently known theiloviruses into five types: TMEV, VHEV, TRV, SAFV-1, and SAFV-2.

scholarly journals Nucleotide sequence, genome organization and phylogenetic analysis of pineapple mealybug wilt-associated virus-2

2001 ◽  
Vol 82 (1) ◽  
pp. 1-7 ◽  
Author(s):  
M. J. Melzer ◽  
A. V. Karasev ◽  
D. M. Sether ◽  
J. S. Hu
Keyword(s):  
Phylogenetic Analysis ◽  
Coat Protein ◽  
Genome Organization ◽  
Open Reading Frames ◽  
Double Stranded Rna ◽  
The Family ◽  
Mealybug Wilt ◽  
Pineapple Mealybug Wilt ◽  
Pineapple Mealybug ◽  
Reading Frames

The genome of pineapple mealybug wilt-associated closterovirus-2 (PMWaV-2) was cloned from double-stranded RNA isolated from diseased pineapple and its sequence determined. The 3′-terminal 14861 nt of the single-stranded RNA genome contains ten open reading frames (ORFs) which, from 5′ to 3′, potentially encode a >204 kDa polyprotein containing papain-like protease, methyltransferase and helicase domains (ORF1a), a 65 kDa RNA-dependent RNA polymerase (ORF1b), a 5 kDa hydrophobic protein (ORF2), a 59 kDa heat shock protein 70 homologue (ORF3), a 46 kDa protein (ORF4), a 34 kDa coat protein (ORF5), a 56 kDa diverged coat protein (ORF6), a 20 kDa protein (ORF7), a 22 kDa protein (ORF8) and a 6 kDa protein (ORF9). A 132 nt untranslated region was present at the 3′ terminus of the genome. This genome organization is typical of the monopartite closteroviruses, including the putative +1 ribosomal frameshift allowing expression of ORF1b. Phylogenetic analysis revealed that within the family Closteroviridae the mealybug-transmitted PMWaV-2 is more closely related to other mealybug-transmitted members than to those which are transmitted by aphids or whiteflies. Within this group, PMWaV-2 shares the greatest sequence identity with grapevine leafroll-associated virus-3, another mealybug-transmitted closterovirus.

scholarly journals Lysinibacter cavernae gen. nov., sp. nov., a new member of the family Microbacteriaceae isolated from a karst cave

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3305-3312 ◽  
Author(s):  
Li Tuo ◽  
Lin Guo ◽  
Shao-Wei Liu ◽  
Jia-Meng Liu ◽  
Yu-Qin Zhang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Rrna Gene ◽  
Karst Cave ◽  
The Family ◽  
Pr China ◽  
The Media ◽  
Diamino Acid

A Gram-stain-positive, aerobic, straight or slightly bent rod-shaped, non-motile, non-spore-forming bacterium, designated strain CC5-806T, was isolated from a soil sample collected from a wild karst cave in the Wulong region, Chongqing, PR China and examined using a polyphasic approach to clarify its taxonomic position. This bacterium did not produce substrate mycelium or aerial hyphae, and no diffusible pigments were observed on the media tested. Strain CC5-806T grew optimally without NaCl at 20 °C and at pH 7.0. Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that strain CC5-806T belonged to the family Microbacteriaceae and showed the highest levels of 16S rRNA gene sequence similarities with Frigoribacterium endophyticum EGI 6500707T (97.56 %), Frigoribacterium faeni 801T (97.53 %) and Glaciihabitans tibetensis MP203T (97.42 %). Phylogenetic trees revealed that strain CC5-806T did not show a clear affiliation to any genus within the family Microbacteriaceae. The DNA G+C content of strain CC5-806T was 62.6 mol%. The cell-wall peptidoglycan contained l-lysine as a diagnostic diamino acid. The predominant menaquinones were MK-11, MK-10 and MK-9. Phosphatidylglycerol, diphosphatidylglycerol, an unidentified glycolipid, four unidentified phospholipids and other polar lipids were detected in the polar lipid extracts. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and iso-C14 : 0. On the basis of the phylogenetic analysis, and phenotypic and chemotaxonomic characteristics, strain CC5-806T was distinguishable from phylogenetically related genera in the family Microbacteriaceae. It represents a novel species of a novel genus, for which the name Lysinibacter cavernae gen. nov., sp. nov. is proposed. The type strain is CC5-806T ( = DSM 27960T = CGMCC 1.14983T).

scholarly journals New Data Define the Molecular Phylogeny and Taxonomy of Four Freshwater Suctorian Ciliates With Redefinition of Two Families Heliophryidae and Cyclophryidae (Ciliophora, Phyllopharyngea, Suctoria)

2021 ◽  
Vol 12 ◽  
Author(s):  
Mingzhen Ma ◽  
Yuqing Li ◽  
Qingxiang Yuan ◽  
Xuetong Zhao ◽  
Khaled A. S. Al-Rasheid ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Phylogeny ◽  
Phylogenetic Analyses ◽  
Ssu Rdna ◽  
Freshwater Lake ◽  
The Other ◽  
Sufficient Evidence ◽  
Rdna Sequences ◽  
The Family ◽  
Molecular Phylogenetic

Four suctorian ciliates, Cyclophrya magna Gönnert, 1935, Peridiscophrya florea (Kormos & Kormos, 1958) Dovgal, 2002, Heliophrya rotunda (Hentschel, 1916) Matthes, 1954 and Dendrosoma radians Ehrenberg, 1838, were collected from a freshwater lake in Ningbo, China. The morphological redescription and molecular phylogenetic analyses of these ciliates were investigated. Phylogenetic analyses inferred from SSU rDNA sequences show that all three suctorian orders, Endogenida, Evaginogenida, and Exogenida, are monophyletic and that the latter two clusters as sister clades. The newly sequenced P. florea forms sister branches with C. magna, while sequences of D. radians group with those from H. rotunda within Endogenida. The family Heliophryidae, which is comprised of only two genera, Heliophrya and Cyclophrya, was previously assigned to Evaginogenida. There is now sufficient evidence, however, that the type genus Heliophrya reproduces by endogenous budding, which corresponds to the definitive feature of Endogenida. In line with this and with the support of molecular phylogenetic analyses, we therefore transfer the family Heliophryidae with the type genus Heliophrya to Endogenida. The other genus, Cyclophrya, still remains in Evaginogenida because of its evaginative budding. Therefore, combined with morphological and phylogenetic analysis, Cyclophyidae are reactivated, and it belongs to Evaginogenida.

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