scholarly journals Enhanced genome annotation strategy provides novel insights on the phylogeny of Flaviviridae

2019 ◽  
Author(s):  
Adriano de Bernardi Schneider ◽  
Denis Jacob Machado ◽  
Daniel Janies
Keyword(s):  
Phylogenetic Relationship ◽  
Soybean Cyst Nematode ◽  
Phylogenetic Analyses ◽  
Optimality Criteria ◽  
Entire Family ◽  
Close Phylogenetic Relationship ◽  
The Family ◽  
Relationship Of ◽  
Reference Genomes ◽  
Annotation Strategy

The ongoing and severe public health threat of viruses of the family Flaviviridae, including dengue, hepatitis C, West Nile, yellow fever, and zika, demand a greater understanding of how these viruses evolve, emerge and spread in order to respond. Central to this understanding is an updated phylogeny of the entire family. Unfortunately, most cladograms of Flaviviridae focus on specific lineages, ignore outgroups, and rely on midpoint rooting, hampering their ability to test ingroup monophyly and estimate ingroup relationships. This problem is partly due to the lack of fully annotated genomes of Flaviviridae, which has genera with slightly different gene content, hindering genome analysis without partitioning. To tackle these problems, we developed an annotation pipeline for Flaviviridae that uses a combination of ab initio and homology-based strategies. The pipeline recovered 100% of the genes in reference genomes and annotated over 97% of the expected genes in the remaining non curated sequences. We further demonstrate that the combined analysis of genomes of all genera of Flaviviridae (Flavivirus, Hepacivirus, Pegivirus, and Pestivirus), as made possible by our annotation strategy, enhances the phylogenetic analyses of these viruses for all optimality criteria that we tested (parsimony, maximum likelihood, and posterior probability). The final tree sheds light on the phylogenetic relationship of viruses that are divergent from most Flaviviridae and should be reclassified, especially the soybean cyst nematode virus 5 (SbCNV-5) and the Tamana bat virus. We also corroborate the close phylogenetic relationship of dengue and zika viruses with an unprecedented degree of support.

scholarly journals Additions to Occultibambusaceae (Pleosporales, Dothideomycetes): Unrevealing Palmicolous Fungi in China

Diversity ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 516
Author(s):  
Xian-Dong Yu ◽  
Sheng-Nan Zhang ◽  
Ratchadawan Cheewangkoon ◽  
Jian-Kui Liu
Keyword(s):  
New Species ◽  
Phylogenetic Relationship ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Ecological Significance ◽  
Generic Type ◽  
The Family ◽  
Distinct Lineage ◽  
Relationship Of ◽  
A New Species

During a survey of microfungi associated with palms from karst formations, three novel ascomycetes were found from decaying petioles of Trachycarpus fortunei (Arecaceae) in Guizhou, China. Multi-gene phylogenetic analyses based on a combined SSU, ITS, LSU, RPB2 and TEF1α sequence data showed that these collections were affiliated to Brunneofusispora and Neooccultibambusa in the family Occultibambusaceae. A new species Brunneofusispora inclinatiostiola is introduced. It is phylogenetically close to B. clematidis but represents a distinct lineage. Morphologically, it differs from the latter in having immersed ascomata with eccentric, periphysate ostiole and smaller ascospores. Morpho-phylogenetic evidence also revealed two new Neooccultibambusa species, N. kaiyangensis and N. trachycarpi. Together with the generic type N. chiangraiensis, they formed a distinct lineage within the genus Neooccultibambusa. Three novel palmicolous fungi of Occultibambusaceae are described, illustrated and notes on their identification are provided. The ecological significance of the new taxa and the phylogenetic relationship of genera in Occultibambusaceae is discussed.

scholarly journals Lemnaceae and Orontiaceae Are Phylogenetically and Morphologically Distinct from Araceae

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2639
Author(s):  
Nicholas P. Tippery ◽  
Donald H. Les ◽  
Klaus J. Appenroth ◽  
Kandregula Sowjanya Sree ◽  
Daniel J. Crawford ◽  
...  
Keyword(s):  
Phylogenetic Relationship ◽  
Molecular Evidence ◽  
Family Status ◽  
Close Phylogenetic Relationship ◽  
The Family ◽  
Relationship Of

Duckweeds comprise a distinctive clade of pleustophytic monocots that traditionally has been classified as the family Lemnaceae. However, molecular evidence has called into question their phylogenetic independence, with some authors asserting instead that duckweeds should be reclassified as subfamily Lemnoideae of an expanded family Araceae. Although a close phylogenetic relationship of duckweeds with traditional Araceae has been supported by multiple studies, the taxonomic disposition of duckweeds must be evaluated more critically to promote nomenclatural stability and utility. Subsuming duckweeds as a morphologically incongruent lineage of Araceae effectively eliminates the family category of Lemnaceae that has been widely used for many years. Instead, we suggest that Araceae subfamily Orontioideae should be restored to family status as Orontiaceae, which thereby would enable the recognition of three morphologically and phylogenetically distinct lineages: Araceae, Lemnaceae, and Orontiaceae.

Morphological re-description and phylogenetic relationship of five myxosporean species of the family Myxobolidae infecting Nile tilapia

2017 ◽  
Vol 124 (3) ◽  
pp. 201-214 ◽  
Author(s):  
R Abdel-Gaber ◽  
F Abdel-Ghaffar ◽  
S Maher ◽  
AM El-Mallah ◽  
S Al Quraishy ◽  
...  
Keyword(s):  
Phylogenetic Relationship ◽  
Nile Tilapia ◽  
The Family ◽  
Relationship Of ◽  
Myxosporean Species

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

Phytotaxa ◽  
2017 ◽  
Vol 319 (1) ◽  
pp. 84 ◽  
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.

Evolutionary relationships ofHyphodiscus hymeniophilus(anamorphCatenulifera rhodogena) inferred from β-tubulin and nuclear ribosomal DNA sequences

2006 ◽  
Vol 84 (2) ◽  
pp. 243-253 ◽  
Author(s):  
Wendy A. Untereiner ◽  
Françoise A. Naveau ◽  
Jason Bachewich ◽  
Andrea Angus
Keyword(s):  
Phylogenetic Relationship ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Its Sequences ◽  
Nuclear Ribosomal Dna ◽  
Phialocephala Fortinii ◽  
Piptoporus Betulinus ◽  
Close Phylogenetic Relationship ◽  
Relationship Of ◽  
Β Tubulin

During an investigation of lignicolous ascomycetes from Luxembourg, we isolated a Phialophora -like species that produced striking red colonies. To confirm the identity of this fungus as Catenulifera rhodogena , we compared it with isolates of Catenulifera rhodogena and Hyphodiscus hymeniophilus on a variety of media. Portions of the β-tubulin gene and the nuclear ribosomal DNA cistron (internal transcribed spacers (ITS) and large subunit (LSU)) were sequenced to examine the relationship of isolates of Catenulifera rhodogena and Hyphodiscus hymeniophilus from different substrates and to test the hypothesis that Cadophora and Catenulifera are congeneric. The phylogenetic position of Catenulifera within the Ascomycota was investigated based on the analysis of the small-subunit (SSU) rDNA sequences. The isolates examined were indistinguishable micromorphologically and closely related phylogenetically. Three strains of Catenulifera rhodogena from bark or wood and one strain from Piptoporus betulinus formed a strongly supported clade in analyses of β-tubulin and ITS sequences. This clade did not encompass the ex-type isolates of Cistella rubescens and Scopulariopsis rhodogena or a second isolate of Catenulifera rhodogena from Piptoporus betulinus. Analysis of partial LSU sequences confirmed the close phylogenetic relationship of Catenulifera rhodogena and Hyphodiscus hymeniophilus but provided no evidence that the isolates could be grouped by substrate or that Catenulifera is synonymous with Cadophora. The position of Catenulifera within the Helotiales was not resolved based on the comparison of LSU and SSU sequences, but the isolate for which we obtained complete SSU sequence grouped with the root endophyte Phialocephala fortinii. Comparison of ITS sequences confirmed the close phylogenetic relationship of Hyphodiscus to members of the Dermateaceae and Hyaloscyphaceae.

The close phylogenetic relationship of Nitrobacter and Rhodopseudomonas palustris

1982 ◽  
Vol 131 (3) ◽  
pp. 287-290 ◽  
Author(s):  
Elke Seewaldt ◽  
Karl-Heinz Schleifer ◽  
Eberhard Bock ◽  
Erko Stackebrandt
Keyword(s):  
Phylogenetic Relationship ◽  
Rhodopseudomonas Palustris ◽  
Close Phylogenetic Relationship ◽  
Relationship Of

scholarly journals Latrocimicinae completes the phylogeny of Cimicidae: meeting old morphologic data rather than modern host phylogeny

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Sándor Hornok ◽  
Tamara Szentiványi ◽  
Nóra Takács ◽  
Áron Botond Kovács ◽  
Olivier Glaizot ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Evolutionary Relationships ◽  
Bed Bugs ◽  
Relevant Study ◽  
Phylogenetic Methods ◽  
Close Phylogenetic Relationship ◽  
The Family ◽  
Host Phylogeny ◽  
Medical Importance ◽  
Morphologic Data

AbstractThe family Cimicidae includes obligate hematophagous ectoparasites (bed bugs and their relatives) with high veterinary/medical importance. The evolutionary relationships of Cimicidae and their hosts have recently been reported in a phylogenetic context, but in the relevant study, one of the six subfamilies, the bat-specific Latrocimicinae, was not represented. In this study the only known species of Latrocimicinae, i.e., Latrocimex spectans, was analyzed with molecular and phylogenetic methods based on four (two nuclear and two mitochondrial) genetic markers. The completed subfamily-level phylogeny of Cimicidae showed that Latrocimicinae is most closely related to Haematosiphoninae (ectoparasites of birds and humans), with which it shares systematically important morphologic characters, but not hosts. Moreover, in the phylogenetic analyses, cimicid bugs that are known to infest phylogenetically distant bat hosts clustered together (e.g., Leptocimex and Stricticimex within Cacodminae), while cimicid subfamilies (Latrocimicinae, Primicimicinae) that are known to infest bat hosts from closely related superfamilies clustered distantly. In conclusion, adding Latrocimicinae significantly contributed to the resolution of the phylogeny of Cimicidae. The close phylogenetic relationship between Latrocimicinae and Haematosiphoninae is consistent with long-known morphologic data. At the same time, phylogenetic relationships of genera within subfamilies are inconsistent with the phylogeny of relevant hosts. Graphical abstract

Redescription of the genus Curiades Pascoe 1880 (Coleoptera: Curculionidae: Entiminae: Naupactini), a potential mimic of Mutillidae from Brazil

Zootaxa ◽  
2012 ◽  
Vol 3570 (1) ◽  
pp. 82 ◽  
Author(s):  
M. GUADALUPE DEL RÍO ◽  
ANALIA A. LANTERI
Keyword(s):  
Phylogenetic Relationship ◽  
Type Species ◽  
Morphological Characters ◽  
Color Pattern ◽  
Monotypic Genus ◽  
Present Contribution ◽  
Diagnostic Features ◽  
Line Drawings ◽  
Close Phylogenetic Relationship ◽  
Relationship Of

The monotypic genus Curiades Pascoe 1880 (Curculionidae: Entiminae: Naupactini) is redescribed based on the type species C. boisduvali (Boheman 1840), endemic to Río de Janeiro, Brazil. Curiades boisduvali shows a characteristic color pattern and vestiture composed of long erect setae that resembles species of Dasymutilla Ashmead 1899, a genus of Mutillidae (Hymenoptera) whose wingless females have aposematic colors and painful stings. The similarities between the wasp (model) and the weevil (mimic) suggest a case of Batesian mimicry. The morphological characters of the rostrum and antennae justify a close phylogenetic relationship of Curiades and Platyomus Sahlberg 1823, even though based on its hairy vestiture the former is superficially more similar to Trichaptus Pascoe 1880, another Brazilian naupactine mimic of mutillid wasps. The present contribution includes a redescription of Curiades and its only known species, accompanied by habitus photographs, line drawings of genitalia and other diagnostic features.

Nerve cells of Xenoturbella bocki (phylum uncertain) and Harrimania kupfferi (Enteropneusta) are positively immunoreactive to antibodies raised against echinoderm neuropeptides

2005 ◽  
Vol 85 (6) ◽  
pp. 1519-1524 ◽  
Author(s):  
Thomas Stach ◽  
Samuel Dupont ◽  
Olle Israelson ◽  
Geraldine Fauville ◽  
Hiroaki Nakano ◽  
...  
Keyword(s):  
Phylogenetic Relationship ◽  
Dna Sequence ◽  
Sequence Data ◽  
Nerve Cells ◽  
Phylogenetic Position ◽  
Dna Sequence Data ◽  
Close Phylogenetic Relationship ◽  
Positive Immunoreactivity ◽  
Phylogenetic Hypotheses ◽  
Relationship Of

The phylogenetic position of Xenoturbella spp. has been uncertain since their discovery in 1949. It has been recently suggested that they could be related to Ambulacraria within Deuterostomia. Ambulacraria is a taxon that has been suggested to consist of Hemichordata and Echinodermata. The hypothesis that X. bocki was related to Ambulacraria as well as the hypothesis of a monophyletic Ambulacraria is primarily based on the analysis of DNA sequence data. We tested both phylogenetic hypotheses using antibodies raised against SALMFamide 1 and 2 (S1, S2), neuropeptides isolated from echinoderms, on X. bocki and the enteropneust Harrimania kupfferi. Both species showed distinct positive immunoreactivity against S1 and S2. This finding supports the Ambulacraria-hypothesis and suggests a close phylogenetic relationship of X. bocki to Ambulacraria. In particular, the presence of immunoreactivity against S2 can be interpreted as a synapomorphy of Enteropneusta, Echinodermata, and Xenoturbella spp.

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