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

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.

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

Pathogens ◽

10.3390/pathogens10010041 ◽

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.

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Phylogeny and morphology of genus Nephrocytium (Sphaeropleales, Chlorophyceae, Chlorophyta) from China

Phytotaxa ◽

10.11646/phytotaxa.319.1.4 ◽

2017 ◽

Vol 319 (1) ◽

pp. 84 ◽

Cited By ~ 2

Author(s):

XUDONG LIU ◽

HUAN ZHU ◽

BENWEN LIU ◽

GUOXIANG LIU ◽

ZHENGYU HU

Keyword(s):

Phylogenetic Analyses ◽

Light And Electron Microscopy ◽

Taxonomic Position ◽

Phylogenetic Position ◽

Phytoplankton Communities ◽

Close Phylogenetic Relationship ◽

The Family ◽

Close Relationship ◽

Molecular Phylogenetic

The genus Nephrocytium Nägeli is a common member of phytoplankton communities that has a distinctive morphology. Its taxonomic position is traditionally considered to be within the family Oocystaceae (Trebouxiophyceae). However, research on its ultrastructure is rare, and the phylogenetic position has not yet been determined. In this study, two strains of Nephrocytium, N. agardhianum Nägeli and N. limneticum (G.M.Smith) G.M.Smith, were identified and successfully cultured in the laboratory. Morphological inspection by light and electron microscopy and molecular phylogenetic analyses were performed to explore the taxonomic position. Ultrastructure implied a likely irregular network of dense and fine ribs on the surface of the daughter cell wall that resembled that of the genus Chromochloris Kol & Chodat (Chromochloridaceae). Phylogenetic analyses revealed that Nephrocytium formed an independent lineage in the order Sphaeropleales (Chlorophyceae) with high support values and a close phylogenetic relationship with Chromochloris. Based on combined morphological, ultrastructural and phylogenetic data, we propose a re-classification of Nephrocytium into Sphaeropleales, sharing a close relationship with Chromochloris.

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Phylogenetic analysis of SARS-CoV-2 data is difficult

Molecular Biology and Evolution ◽

10.1093/molbev/msaa314 ◽

2020 ◽

Author(s):

Benoit Morel ◽

Pierre Barbera ◽

Lucas Czech ◽

Ben Bettisworth ◽

Lukas Hübner ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Species Delimitation ◽

Phylogenetic Analyses ◽

Phylogenetic Inference ◽

Daily Basis ◽

Extreme Caution ◽

Data Analyses ◽

Phylogenetic Methods ◽

Degree Of Confidence

Abstract Numerous studies covering some aspects of SARS-CoV-2 data analyses are being published on a daily basis, including a regularly updated phylogeny on nextstrain.org. Here, we review the difficulties of inferring reliable phylogenies by example of a data snapshot comprising a quality-filtered subset of 8, 736 out of all 16, 453 virus sequences available on May 5, 2020 from gisaid.org. We find that it is difficult to infer a reliable phylogeny on these data due to the large number of sequences in conjunction with the low number of mutations. We further find that rooting the inferred phylogeny with some degree of confidence either via the bat and pangolin outgroups or by applying novel computational methods on the ingroup phylogeny does not appear to be credible. Finally, an automatic classification of the current sequences into sub-classes using the mPTP tool for molecular species delimitation is also, as might be expected, not possible, as the sequences are too closely related. We conclude that, although the application of phylogenetic methods to disentangle the evolution and spread of COVID-19 provides some insight, results of phylogenetic analyses, in particular those conducted under the default settings of current phylogenetic inference tools, as well as downstream analyses on the inferred phylogenies, should be considered and interpreted with extreme caution.

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A phylogenetic analysis and new delimitation of Crepidiastrum (Asteraceae, tribe Cichorieae)

Phytotaxa ◽

10.11646/phytotaxa.159.4.1 ◽

2014 ◽

Vol 159 (4) ◽

pp. 241 ◽

Cited By ~ 7

Author(s):

Yu-lan Peng ◽

Yu Zhang ◽

Xin-fen Gao ◽

Lin-jing Tong ◽

Liang Li ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Maximum Likelihood ◽

Chloroplast Dna ◽

Maximum Parsimony ◽

Phylogenetic Analyses ◽

Systematic Position ◽

Likelihood Inference ◽

Nuclear Its ◽

Chloroplast Dna Regions

The systematic position of Paraixeris humifusa (Asteraceae) is hard to define, because the circumscription of Paraixeris, Youngia and Crepidiastrum, three closely related genera in subtribe Crepidinae (Cichorieae), is not clear. This paper reports on the relationships between 30 species in subtribe Crepidinae, based on an analysis of nucleotides from one nuclear (ITS) and three chloroplast DNA regions ( trnL-F, rps16 and atpB-rbcL). The phylogenetic analyses used maximum parsimony with maximum likelihood inference. The monophyly of Crepidiastrum in the most recent generic classification of Shih & Kilian (2011) is explored. The results show that 12 species in Crepidiastrum constitute a monophyletic group, and that Paraixeris humifusa should be treated as Youngia humifusa.

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Two new asexual genera and six new asexual species in the family Microthyriaceae (Dothideomycetes, Ascomycota) from China

MycoKeys ◽

10.3897/mycokeys.85.70829 ◽

2021 ◽

Vol 85 ◽

pp. 1-30

Author(s):

Min Qiao ◽

Hua Zheng ◽

Ji-Shu Guo ◽

Rafael F. Castañeda-Ruiz ◽

Jian-Ping Xu ◽

...

Keyword(s):

New Taxa ◽

Dna Sequences ◽

Sequence Data ◽

Southern China ◽

Phylogenetic Analyses ◽

Large Subunit ◽

Aquatic Hyphomycetes ◽

Internal Transcribed Spacers ◽

The Family

The family Microthyriaceae is represented by relatively few mycelial cultures and DNA sequences; as a result, the taxonomy and classification of this group of organisms remain poorly understood. During the investigation of the diversity of aquatic hyphomycetes from southern China, several isolates were collected. These isolates were cultured and sequenced and a BLAST search of its LSU sequences against data in GenBank revealed that the closest related taxa are in the genus Microthyrium. Phylogenetic analyses, based on the combined sequence data from the internal transcribed spacers (ITS) and the large subunit (LSU), revealed that these isolates represent eight new taxa in Microthyriaceae, including two new genera, Antidactylariagen. nov. and Isthmomycesgen. nov. and six new species, Antidactylaria minifimbriatasp. nov., Isthmomyces oxysporussp. nov., I. dissimilissp. nov., I. macrosporussp. nov., Triscelophorus anisopterioideussp. nov. and T. sinensissp. nov. These new taxa are described, illustrated for their morphologies and compared with similar taxa. In addition, two new combinations are proposed in this family.

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Complete chloroplast genome sequences of Dioscorea: Characterization, genomic resources, and phylogenetic analyses

PeerJ ◽

10.7717/peerj.6032 ◽

2018 ◽

Vol 6 ◽

pp. e6032 ◽

Cited By ~ 12

Author(s):

Zhenyu Zhao ◽

Xin Wang ◽

Yi Yu ◽

Subo Yuan ◽

Dan Jiang ◽

...

Keyword(s):

Chloroplast Genome ◽

Phylogenetic Analyses ◽

Single Copy ◽

Genome Sequences ◽

Complete Chloroplast Genome ◽

Genomic Resources ◽

Chloroplast Genomes ◽

The Family ◽

Small Single Copy

Dioscorea L., the largest genus of the family Dioscoreaceae with over 600 species, is not only an important food but also a medicinal plant. The identification and classification of Dioscorea L. is a rather difficult task. In this study, we sequenced five Dioscorea chloroplast genomes, and analyzed with four other chloroplast genomes of Dioscorea species from GenBank. The Dioscorea chloroplast genomes displayed the typical quadripartite structure of angiosperms, which consisted of a pair of inverted repeats separated by a large single-copy region, and a small single-copy region. The location and distribution of repeat sequences and microsatellites were determined, and the rapidly evolving chloroplast genome regions (trnK-trnQ, trnS-trnG, trnC-petN, trnE-trnT, petG-trnW-trnP, ndhF, trnL-rpl32, and ycf1) were detected. Phylogenetic relationships of Dioscorea inferred from chloroplast genomes obtained high support even in shortest internodes. Thus, chloroplast genome sequences provide potential molecular markers and genomic resources for phylogeny and species identification.

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CHARACTER ASSESSMENT, GENUS LEVEL BOUNDARIES, AND PHYLOGENETIC ANALYSES OF THE FAMILY RHACOPHORIDAE:

Contemporary Herpetology ◽

10.17161/ch.vi1.11961 ◽

2000 ◽

pp. 1-31 ◽

Cited By ~ 9

Author(s):

Jeffery A. Wilkinson ◽

Robert C. Drewes

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Analyses ◽

Morphological Characters ◽

Current Status ◽

Phylogenetic Hypothesis ◽

Genus Level ◽

The Family ◽

Character Assessment

The first comprehensive phylogenetic analysis of the family Rhacophoridae was conducted by Liem (1970) scoring 81 species for 36 morphological characters. Channing (1989), in a reanalysis of Liem’s study, produced a phylogenetic hypothesis different from that of Liem. We compared the two studies and produced a third phylogenetic hypothesis based on the same characters. We also present the synapomorphic characters from Liem that define the major clades and each genus within the family. Finally, we summarize intergeneric relationships within the family as hypothesized by other studies, and the family’s current status as it relates to other ranoid families.

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Paedomorphosis, Aristotle's lantern, and the origin of the sand dollars (Echinodermata: Clypeasteroida)

Paleobiology ◽

10.1017/s0094837300009714 ◽

1990 ◽

Vol 16 (1) ◽

pp. 25-48 ◽

Cited By ~ 44

Author(s):

Rich Mooi

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Analyses ◽

Sister Group ◽

New Classification ◽

Crown Group ◽

New Information ◽

Sand Dollars ◽

Fossil Genus ◽

Tube Feet

Convincing hypotheses of the origin of major invertebrate groups are difficult to make in the absence of phylogenetic analyses. In spite of this, several scenarios exist for the origin of the unusual echinoid order Clypeasteroida. I expand upon the most probable of these models by performing a phylogenetic analysis on three clypeasteroid suborders, the enigmatic fossil genusTogocyamus, and the extinct Oligopygoida. This analysis shows that the oligopygoids are the sister group of the Clypeasteroida plusTogocyamus. The latter is here considered a plesion (extinct sister group) to the crown group Clypeasteroida. Within that order, the suborder Clypeasterina is the sister group to the Laganina plus Scutellina. A new classification of all these taxa is presented. The phylogeny is based on 47 characters and incorporates data on external appendages, Aristotle's lantern anatomy, and test structure of irregular echinoids, as well as new information on the morphology ofTogocyamus. The earliest clypeasteroids had a lantern similar to that of adult oligopygoids, which in turn inherited their lantern from a cassiduloid-like ancestor that retained the lantern into adulthood. This lantern is absent in adult cassiduloids. Subsequent changes, including modification of the lantern into a crushing mill, extreme flattening of the test, and proliferation of food-gathering tube feet have allowed clypeasteroids to become epifaunal inhabitants of environments characterized by fine, shifting substrates, a habitat previously inaccessible to most other irregular echinoids.

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Lindtneria asiae-orientalis sp. nov. (Stephanosporaceae, Basidiomycota) from China based on morphological and molecular characters

Phytotaxa ◽

10.11646/phytotaxa.260.3.8 ◽

2016 ◽

Vol 260 (3) ◽

pp. 283 ◽

Cited By ~ 1

Author(s):

SHI-LIANG LIU ◽

FANG WU ◽

SHUANG-HUI HE

Keyword(s):

Phylogenetic Analyses ◽

Distinct Species ◽

Northeastern China ◽

Heilongjiang Province ◽

Rdna Gene ◽

Orange Yellow ◽

The Family ◽

Molecular Characters

Lindtneria asiae-orientalis sp. nov. is described and illustrated from Heilongjiang Province, northeastern China. This fungus is characterized by buff-yellow to orange-yellow poroid hymenophores, septate generative hyphae with or without clamps, and relatively small ellipsoid to broadly ellipsoid basidiospores (5.8–7 × 4.7–5.2 µm). Phylogenetic analyses based on three rDNA gene regions (ITS, nLSU and tef1-α) support Lindtneria asiae-orientalis as a distinct species within the family Stephanosporaceae.

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

Zootaxa ◽

10.11646/zootaxa.4221.1.1 ◽

2017 ◽

Vol 4221 (1) ◽

pp. 1 ◽

Cited By ~ 7

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.

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