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Phylogenetic Analysis - Science method

Exchange knowledge in the field of molecular systematics, phylogenetic reconstruction and their application to systematics, biogeography and evolutionary studies
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Publications related to Phylogenetic Analysis (10,000)
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Article
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Hypervirulent Klebsiella pneumoniae (hvKp) can cause serious infections and has been increasingly reported clinically. However, we still lack the knowledge to what degree hvKp colonize the community. In this study, we investigated colonization of hvKp in healthy human gut and the relationship between gut hvKp and clinically important invasive strai...
Article
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Gastrochilus wolongensis (Orchidaceae), a new orchid species from Sichuan Province, Southwest China, is described and illustrated. It morphologically resembles G. sinensis, but differs markedly from the latter in having black-purple stripes (vs. purplish-red spots) on the adaxial side of the petals and sepals, a reniform epichile densely covered wi...
Article
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Background: Some strains of Streptococcus mitis exhibit β-hemolysis due to the β-hemolytic activity of cholesterol-dependent cytolysin (CDC). Recently, a gene encoding an atypical lectinolysin-related CDC was found in S. mitis strain Nm-76. However, the product of this gene remains uncharacterized. We aimed to characterize this atypical CDC and it...
Article
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Objective A single study conducted about three decades ago on hepatitis D virus (HDV) infection among Baka pygmies in Cameroon reported a very high anti-HDV antibodies prevalence of 46%, but HDV genetic diversity has not been studied in this population. The genetic diversity of strains from endemic ancient populations may help to understand the ori...
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Notch signalling pathway plays a key role in metazoan biology by contributing to resolution of binary decisions in the life cycle of cells during development. Outcomes such as proliferation/differentiation dichotomy are resolved by transcriptional remodelling that follows a switch from Notch on to Notch off state, characterised by dissociation of N...
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In August 2021, jimson weed (Datura stramonium) plants growing as weeds in potato fields in Bolu province, Turkey, exhibited leaf spots with dark concentric rings. Sunken and lens-shaped lesions with a light center were also frequently observed on petioles, branches, and stems. Based on morphological characteristics and phylogenetic analysis of the...
Article
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Background Several SARS-CoV-2 variants with increased transmissibility and/or potential immune escape have emerged and rapidly spread worldwide. Ongoing surveillance analyses are performed worldwide to designate new variants of concern (VOC) of coronavirus. Main text This report identifies the first Egyptian patient with a confirmed SARS-CoV-2 omi...
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Background CesA and Cs l gene families, which belong to the cellulose synthase gene superfamily, plays an important role in the biosynthesis of the plant cell wall. Although researchers have investigated this gene superfamily in several model plants, to date, no comprehensive analysis has been conducted in the common bean. Results In this study, w...
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Background Dengue virus (DENV) is a member of insect vector-borne viruses, and it causes dengue fever. Southeast Asia is the epi-center of dengue fever in the world. The characterization of the virus is essential to identify the transmission and evolution of DENV. Objectives In 2017, there was an outbreak of Dengue virus type 1 (DENV1) in northern...
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Tachinidae are one of the most diverse clades of Diptera. All tachinids are parasitoids of insects and other arthropods, and thus are considered an important source of biological pest control. Antennae are the most important olfactory organs of Tachinidae playing key roles in their lives, especially in locating hosts, and details of antennal ultras...
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Two new umbravirus-like associated RNAs (ulaRNAs) were found, respectively, in maize and Johnsongrass samples from Ecuador. The complete sequences consist of 3,053 and 3,025 nucleotides, respectively, and contain four open reading frames (ORFs). Their genome sequences were 58% identical to each other and 28 to 60% identical to the most closely rela...
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Iridoviruses are emerging pathogens that are widespread in diverse environments and hosts. Numerous members of the family Iridoviridae are known to cause severe disease in freshwater and marine organisms. Here, we report the complete genome sequence and phylogenetic analysis of iridovirus strain LPIV-ZS-2021, isolated from a small yellow croaker (L...
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We conducted nucleotide and amino acid sequence alignment and phylogenetic analysis of porcine circovirus ORF2 (Cap protein) from 17 PCV2-positive clinical samples from nine different northern Vietnamese provinces (Mar 2018–Nov 2020), four local vaccines, and 77 reference strains. We identified one PCV2a (1/17 = 5.9%), five PCV2b (5/17 = 29.9%), an...
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Two double stranded RNAs (dsRNAs) that likely represent the genome of an alphapartitivirus, tentatively named "impatiens cryptic virus 1" (ICV1), were recovered from Impatiens balsamina L. RNA1 (2008 bp) codes for the RNA-dependent RNA polymerase (RdRp) of ICV1, which shares <83% amino acid sequence identity with the RdRps of other alphapartitiviru...
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Microbial communities inhabiting caves in quartz-rich rocks are still underexplored, despite their possible role in the silica cycle. The world's longest orthoquartzite cave, Imawarì Yeuta, represents a perfect arena for the investigation of the interactions between microorganisms and silica in non-thermal environments due to the presence of extrao...
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Research on niche specialization in the microbial communities of ammonia oxidizers is important for assessing the consequences of vegetation shift on nitrogen (N) cycling. In this study, soils were sampled from three tree stands (needleleaf, mixed, and evergreen broadleaf) from the Hannam experimental forest in South Korea in spring (May 2019), sum...
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From 2016 to 2019, the largest outbreak caused by the Yellow Fever virus (YFV) in the 21 st century in the Americas occurred in southeastern Brazil. A sylvatic cycle of transmission was reported near densely populated areas, such as the large metropolitan area of the city of São Paulo. Here, we describe the origin, spread, and movement of the YFV t...
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Phytophthora sojae is a destructive soybean pathogen that orchestrates various secreted proteins (effectors) to modulate plant immunity and facilitate infection. Although a number of effectors have been identified and functionally studied in P. sojae, the way these molecules are regulated is marginally known. In this study, we performed a weighted...
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Tobacco (Nicotiana tabacum L.), which creates jobs for 33 million people and contributes two trillion dollars’ tax annually, is one of the most important economic plants globally. However, tobacco is seriously threatened by numerous diseases during production. Previously, the field survey of tobacco diseases was conducted in the Guizhou and Guangxi...
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Coral transcriptomic data largely rely on short-read sequencing, which severely limits the understanding of coral molecular mechanisms and leaves many important biological questions unresolved. Here, we sequence the full-length transcriptomes of four common and frequently dominant reef-building corals using the PacBio Sequel II platform. We obtain...
Article
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Fourteen Rhizoctonia isolates obtained from coriander plants with symptoms of damping-off and web blight were collected in vegetable production areas between the years 2015 and 2017 in five geographical regions of Brazil. Identification was performed using phylogenetic analysis of the internal transcribed spacer region of ribosomal DNA, evaluation...
Article
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Background Bupleurum chinense(B. chinense) is a plant that is widely distributed globally and has strong pharmacological effects. Though the chloroplast(cp) genome of B. chinense has been studied, no reports regarding the mitochondrial(mt) genome of B. chinense have been published yet. Results The mt genome of B.chinense was assembled and function...
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Chaetosphaeriaceae is one of the largest families in Sordariomycetes with its members commonly found on decaying leaf, fruit, branch, bark and wood in both terrestrial and submerged environment in nature. This paper reports our research result of diversity, taxonomy and phylogeny of anamorphic Chaetosphaeriaceae in China, which is based on a system...
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Background – Waltheria marielleae is a new species of Malvaceae endemic to north-eastern Brazil that occurs only in the states of Pernambuco and Alagoas, in areas of Atlantic Forest and Caatinga. It is characterized by cinereous leaves, axillary and sessile to subsessile inflorescences, pallid yellow corollas with apically eciliate petals and fan-p...
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The rapid spread of SARS-CoV-2 variants in the global population is indicative of the development of selective advantages in emerging virus strains. Here, we performed a case-control investigation of the clinical and demographic characteristics, clinical history, and virological markers to predict disease progression in hospitalized adults for COVI...
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Despite extensive vaccination and booster programs, SARS-CoV-2 outbreaks in long-term care facilities (LTCF) continue to occur. We retrospectively describe a SARS-CoV-2 outbreak amongst a partially vaccinated LTCF population in The Netherlands which occurred in March 2021. The facility comprised three floors functioning as separate wards. Nasophary...
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Poster session 3, September 23, 2022, 12:30 PM - 1:30 PM Objectives Method: Part 1—Epidemiological pattern, phenotypic Identification, and anti-fungal susceptibility pattern by broth microdilution method Part 2-Molecular Identification, Sangers Sequencing, Phylogenetic Analysis and Dendogram Molecular Identification Results Figure 1 Epidemiologica...
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Avian haemosporidian parasites have received considerable attention in ecology and evolution as a result of their wide distribution and ease of detection. However, conventional PCR-based detection methods may sometimes underestimate haemosporidian mixed infections, which are frequent in natural populations. This underestimation is due to difference...
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The genera Monostroma and Gayralia belong to the order of monostromatic green algae; however, their taxonomic delimitation remains controversial at the genus level. This study attempts to address this issue through the combined analysis of the morphology and nuclear-encoded Internal Transcribed Spacer region sequences of monostromatic green algal s...
Article
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Lycoris insularis S.Y.Zhang & J.W.Shao, a new fertile diploid species from coastal provinces in eastern China is described. This new species is most similar to L. sprengeri in morphology and has been misidentified as the latter for a long time. However, it can be distinguished from the latter by the relatively longer perianth tube (1.5‒2.5 cm vs. l...
Article
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The bile resistance of intestinal bacteria is among the key factors responsible for their successful colonization of and survival in the mammalian gastrointestinal tract. In this study, we demonstrated that lactate-producing Atopobiaceae bacteria (Leptogranulimonas caecicola TOC12T and Granulimonas faecalis OPF53T) isolated from mouse intestine sho...
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During faunal studies of psammophilic ciliates along the coast of Qingdao, China, several marine karyorelictean species were isolated. Among them, four species within the genus Remanella were investigated, including two species new to science: i.e., R. rugosa, Remanella elongata sp. nov., Remanella aposinica sp. nov., and R. unicorpusculata. Remane...
Preprint
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The data provided here is related to the article "Resolving the Deep Phylogeny: Implications for Early Adaptive Radiation, Cryptic, and Present-day Ecological Diversity of Papuan Microhylid Frogs" [1]. The dataset is based on 233 tissue samples of the subfamily Asteroprhyinae, with representatives from all recognized genera, in addition to three ou...
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blaIMP and blaVIM are the most detected plasmid-encoded carbapenemase genes in Pseudomonas aeruginosa. Previous studies have reported plasmid sequences carrying blaIMP variants, except blaIMP-56. In this study, we aimed to characterize a plasmid carrying blaIMP-56 in a P. aeruginosa strain isolated from a Mexican hospital. The whole genome of P. ae...
Article
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Oedogoniales comprises the three genera Oedogonium, Oedocladium, and Bulbochaete, which include more than 600 described species. The classification of Oedogoniaceae is currently based on morphology, and the complicated morphological characteristics make species identification difficult, with the limited molecular data also restricting the phylogene...
Article
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Natural killer (NK) cells belong to the innate immune system. The germline‐encoded natural killer cell receptors represent activating and inhibitory receptors regulating multiple NK cell activities. The natural cytotoxicity receptors (NCRs) are activating natural cytotoxicity triggering receptors 1, 2 and 3 (NKp46, NKp44, and NKp30), encoded by the...
Article
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Microcystis aeruginosa is a major harmful cyanobacterium causing water bloom worldwide. Cyanophage has been proposed as a promising tool for cyanobacterial bloom. In this study, M. aeruginosa FACHB-1326 was used as an indicator host to isolate cyanophage from Lake Taihu. The isolated Microcystis cyanophage Mae-Yong1326-1 has an elliptical head of a...
Article
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Haloclavidae Verrill, 1899 is a family of burrowing sea anemones grouped within the superfamily Actinioidea (Rafinesque, 1815). Currently, it includes 30 species in 10 genera. Characters given for this family in descriptions of its taxa have not been consistent, with numerous exceptions to the expectations of the familial diagnosis. Previous phylog...
Preprint
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Monkeypox has spread unprecedentedly to nearly 100 countries and infected more than 51,000 people since 1 May 2022. This large-scale outbreak constituted a public health emergency of international concern (PHEIC), as declared by the World Health Organization. To better recognize and control this outbreak, we explore here through phylogenetic analys...
Article
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New developments in sequencing technology and nucleotide analysis have allowed us to make great advances in reconstructing anuran phylogeny. As a clade of representative amphibians that have radiated from aquatic to arboreal habitats, our understanding of the systematic status and molecular biology of rhacophorid tree frogs is still limited. We det...
Article
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Histone modifications (HMs) play important roles in the regulation of gene expression in every domain of life. Tea (Camellia assamica), which is a woody perennial plant, is exposed to various stresses during its different developmental stages and HMs are expected to play crucial roles in its adaptation under different stress conditions. Characteriz...
Article
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Opportunistic pathogens such as Pseudomonas aeruginosa adapt their genomes rapidly during chronic infections. Understanding their epigenetic regulation may provide biomarkers for diagnosis and reveal novel regulatory mechanisms. We performed single-molecule real-time sequencing (SMRT-seq) to characterize the methylome of a chronically adapted P. ae...
Article
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Complete mitochondrial genome and phylogenetic analysis of Devario kakhienensis, endemic minnow from southwest China, for the first time was presented. It was determined to be a 16,777 bp long circular molecule and the genome organization was consistent with that of Danioninae species published previously. Based on PCGs, the maximum likelihood phyl...
Article
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The Pygmy corydoras Corydoras pygmaeus Knaack, 1966, is the smallest member of the genus Corydoras, belonging to the family Callichthyidae and order Siluriformes. The complete mitochondrial genome of C. pygmaeus was sequenced and assembled using next-generation sequencing technology, and phylogenetically compared with those of other species of this...
Article
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SMXL6,7,8 are important target proteins in strigolactone (SL) signal pathway, which negatively regulate the reception and response of SL signal, and play an important role in regulating plant branching. However, there is a relative lack of research on soybean SMXL gene family. In this study, 31 soybean SMXL genes were identified by phylogenetic ana...
Article
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Potentilla anserina L. is an important traditional Chinese medicinal herb and edible plant with a long usage history. As an indispensable sustainable resource, it has various pharmacological functions and active ingredients. Here, we report its complete chloroplast (cp) genome for the first time. The complete chloroplast genome of Potentilla anseri...
Article
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In this study, we sequenced the complete mitochondrial genome of Agriotes fuscicollis Miwa, 1928 (Coleoptera: Elateridae). The results showed that the length of complete mitochondrial genome was 15,866 bp with 26.8% GC content, containing 39.6% A, 33.5% T, 16.8% C, 10% G. There were 13 protein-coding genes (PCGs), 22 transfer RNA genes, and 2 ribos...
Article
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The complete mitochondrial genome of Pseudemys concinna in Korea was sequenced and characterized. The mitochondrial genome is constituted of 37 genes (13 protein-coding genes, 22 transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes) and a noncoding region. Phylogenetic analysis based on the complete mitochondrial genome showed that P. conc...
Article
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African Shovel-snout snakes ( Prosymna Gray, 1849) are small, semi-fossorial snakes with a unique compressed and beak-like snout. Prosymna occur mainly in the savanna of sub-Saharan Africa. Of the 16 currently recognised species, four occur in Angola: Prosymna ambigua Bocage, 1873, P. angolensis Boulenger, 1915, P. frontalis (Peters, 1867), and P....
Poster
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Hepatitis E virus (HEV) is responsible for acute entero-transmissible hepatitis in humans. In Italy, an increase in autochthonous cases of HEV has recently been documented, and several cases have been epidemiologically linked to the consumption of raw or undercooked wild boar and pork liver or meat. Strains circulating in pigs and humans have a hig...
Article
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Homalocladium platycladum is a fascinating ornamental plant that has long been used in Chinese medicine. Here, we characterize the complete chloroplast genome sequence of this plant (GenBank: NC_062330). This circular genome has a total length of 163,202 bp containing a large single-copy region (87,820bp), a small single-copy region (13,538bp), and...
Article
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Both Impatiens macrovexilla and I. macrovexilla var. yaoshanensis have potential to be exploited as ornamental plants, despite some of their morphological differences. In the present study, the complete chloroplast genome sequences of the two taxa are reported for the first time, which could facilitate their infraspecies classification, and analyse...
Article
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Salix wilhelmsiana M.B. Bieberstein 1819 is a perennial woody plant with high economic and ecological value. In this study, we annotated the chloroplast (cp) genome of Salix wilhelmsiana M.B. The results showed that the length of the complete cp genome is 155,577 bp, which is typically composed of two single-copy regions (large single-copy (LSC) of...
Article
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Vincetoxicum junzifengense B.J. Ye and S.P. Chen 2022 is a newly described species which belongs to the genus Vincetoxicum in the family Apocynaceae. The complete plastid genome of Vincetoxicum junzifengense B.J. Ye and S.P. Chen 2022 was determined and analyzed in this study. The total chloroplast genome was 159,666 bp in length, consisting of a l...
Article
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Persicaria maackiana (Regel) Nakai ex T. Mori (1922), a species of the Polygonaceae family, is an annual plant widely distributed in Northeast Asia. We aimed to sequence the complete chloroplast genome of P. maackiana using Illumina HiSeq paired-end sequencing. The chloroplast genome was determined to be 160,635 bp. The complete chloroplast genome...