Phylogenetic analysis and revision of subfamily classification of Belostomatidae genera (Insecta: Heteroptera: Nepomorpha)

2017 ◽  
Vol 182 (2) ◽  
pp. 319-359 ◽  
Author(s):  
JosÉ Ricardo I Ribeiro ◽  
Shin-Ya Ohba ◽  
Dominique Pluot-Sigwalt ◽  
Fabiano Stefanello ◽  
Wenjun Bu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Subfamily Classification

scholarly journals Detection of Rhodococcus fascians, the Causative Agent of Lily Fasciation in South Korea

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 241
Author(s):  
Joon Moh Park ◽  
Jachoon Koo ◽  
Se Won Kang ◽  
Sung Hee Jo ◽  
Jeong Mee Park
Keyword(s):  
Phylogenetic Analysis ◽  
South Korea ◽  
Nicotiana Benthamiana ◽  
Economic Value ◽  
Virulence Gene ◽  
Economic Losses ◽  
Herbaceous Perennials ◽  
Rhodococcus Fascians ◽  
Different Strains

Rhodococcus fascians is an important pathogen that infects various herbaceous perennials and reduces their economic value. In this study, we examined R. fascians isolates carrying a virulence gene from symptomatic lily plants grown in South Korea. Phylogenetic analysis using the nucleotide sequences of 16S rRNA, vicA, and fasD led to the classification of the isolates into four different strains of R. fascians. Inoculation of Nicotiana benthamiana with these isolates slowed root growth and resulted in symptoms of leafy gall. These findings elucidate the diversification of domestic pathogenic R. fascians and may lead to an accurate causal diagnosis to help reduce economic losses in the bulb market.

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.

Cladistic analysis of the Zethus (Zethoides) (Hymenoptera, Vespidae, Eumeninae) species groups with insights on the current subgeneric classification of Zethus Fabricius, 1804

2018 ◽  
Vol 49 (2) ◽  
pp. 103-129 ◽  
Author(s):  
Rogério Botion Lopes ◽  
Fernando Barbosa Noll
Keyword(s):  
Phylogenetic Analysis ◽  
Cladistic Analysis ◽  
Species Groups

Zethus is the largest genus in Eumeninae, with over 250 species. Currently, it is divided in four subgenera: Z. (Zethus), Z. (Zethusculus), Z. (Zethoides) and Z. (Madecazethus). Z. (Zethoides), with 42 species, is subdivided in eight species groups, each considered a phylogenetic unit, that were created without any phylogenetic analysis. Eighteen species of Z. (Zethoides) corresponding to different groups were examined, altogether with terminals from distinct lineages of Zethus, Zethini and Eumenini, to perform a cladistics analysis to verify the proposed divisions. Zethus (Zethoides) and all of its species groups, except for the Z. biglumis group, were monophyletic. Zethus s.s. was paraphyletic in relation to Z. (Madecazethus), Z. (Zethoides) and Ctenochilus. Z. (Zethusculus) was also retrieved paraphyletic. Despite the subgeneric incongruences, the outgroups were too poorly represented to carry a taxonomic modification. Thus, the only alteration was the inclusion of the Z. clypearis group in the Z. biglumis group.

A revised infrageneric classification of Bellevalia Lapeyr. (Asparagaceae: Scilloideae) based on molecular analysis

Phytotaxa ◽  
2021 ◽  
Vol 525 (1) ◽  
pp. 70-84
Author(s):  
AZARNOOSH JAFARI ◽  
JAMIL VAEZI ◽  
MOHAMMAD MAHDI FORGHANIFARD ◽  
FÉLIX FOREST ◽  
JOHN C. MANNING
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Analysis ◽  
Trnl Intron ◽  
Leaf Margin ◽  
Infrageneric Classification ◽  
Flower Shape ◽  
Representative Species

Within the genus Bellevalia (Asparagaceae: Scilloideae: Hyacintheae), flower shape and colour, the ratio of leaf to scape length, and the orientation of the pedicels were traditionally used to delimit sections, subsections and species. We conducted a phylogenetic analysis of representative species from sections Bellevalia, Conicae, Nutantes and Oxydontae, representing four out of the six sections that are currently recognised, using the four chloroplast regions rbcL, matK, trnL intron, and trnL-F spacer. Our results indicate that the sections are not monophyletic as currently circumscribed. Our analyses retrieve two major, well-supported clades. The first clade (sect. Conicae) includes only species with ciliate leaves and green-veined perianth lobes, and the second clade (sect. Bellevalia) includes the species lacking these characteristics. Within the second clade, the species with yellow anthers are separated from those with violet anthers. Our molecular analysis does not support the traditional subdivisions of the genus but establishes the value of cilia on the leaf margin, green veins in the perianths lobes, and the colour of the anthers as indicators of relationships among the species. We recommend that the current four sections and six subsections of Bellevalia be reduced to two sections without subsections and we provide an updated and corrected nomenclature for these sections and subsections, designating lectotypes where necessary.

An Umbra-related Virus Found in Vasconcellea X Heilbornii (Caricaceae)

2021 ◽  
Author(s):  
Juan F Cornejo-Franco ◽  
Francisco Flores ◽  
Dimitre Mollov ◽  
diego fernando quito-avila
Keyword(s):  
Phylogenetic Analysis ◽  
New Genus ◽  
Complete Sequence ◽  
Open Reading Frames ◽  
Rna Dependent Rna Polymerase ◽  
Sequence Comparisons ◽  
Genomic Features ◽  
Overlapping Open Reading Frames ◽  
Reading Frames

Abstract The complete sequence of a new viral RNA from babaco (Vasconcellea x heilbornii) was determined. The genome consisted of 4,584 nucleotides organized in two non-overlapping open reading frames (ORFs 1 and 2), a 9-nt-long noncoding region (NCR) at the 5’ terminus and a 1,843 -nt-long NCR at the 3’ terminus. Sequence comparisons of ORF 2 revealed homology to the RNA-dependent-RNA-polymerase (RdRp) of several umbra- and umbra-related viruses. Phylogenetic analysis of the RdRp placed the new virus in a well-supported and cohesive clade that includes umbra-like viruses reported from papaya, citrus, opuntia, maize and sugarcane hosts. This clade shares a most recent ancestor with the umbraviruses but has different genomic features. The creation of a new genus, within the Tombusviridae, is proposed for the classification of these novel viruses.

scholarly journals A new subfamily classification of the palm family (Arecaceae): evidence from plastid DNA phylogeny

2006 ◽  
Vol 151 (1) ◽  
pp. 15-38 ◽  
Author(s):  
CONNY B. ASMUSSEN ◽  
JOHN DRANSFIELD ◽  
VINNIE DEICKMANN ◽  
ANDERS S. BARFOD ◽  
JEAN-CHRISTOPHE PINTAUD ◽  
...  
Keyword(s):  
Plastid Dna ◽  
Dna Phylogeny ◽  
Subfamily Classification

scholarly journals Phylogenetic analysis of SARS-CoV-2 data is difficult

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.

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

Phytotaxa ◽  
2014 ◽  
Vol 159 (4) ◽  
pp. 241 ◽  
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.

A new fossil species of the Australian endemic genus Peradenia Naumann & Masner (Hymenoptera: Proctotrupoidea, Peradeniidae) from Baltic Amber

2001 ◽  
Vol 32 (2) ◽  
pp. 191-194 ◽  
Author(s):  
Jens-Wilhelm Janzen ◽  
Norman F. Johnson ◽  
Luciana Musetti
Keyword(s):  
Baltic Amber ◽  
Australian Capital Territory ◽  
Fossil Species ◽  
Southeastern Australia ◽  
Extant Species ◽  
The Family ◽  
The Status ◽  
Subfamily Classification ◽  
A New Species

AbstractThe family Peradeniidae (Hymenoptera: Proctotrupoidea) is represented by two rare extant species from southeastern Australia (Australian Capital Territory, Victoria, Tasmania). A new species, Peradenia galerita sp. n., is described from Eocene Baltic amber. The fossil species is very similar to the living Perndenia, but has the short metasomatic petiole typical of most Proctotrupoidea. The subfamily classification of Heloridae proposed by Rasnitsyn and the status of Peradeniidae are briefly reviewed. The subfamily Mesohelorinae Rasnitsyn, 1990 is a junior synonym of Protohelorinae Rasnitsyn, 1980 (syn. n.).

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