Phylogenetic Analysis - Science method

P ASTEURELLA multocida infection has serious complications for both human and animal health. In bovines, it is the predominant cause of fatal pneumonia, with a mortality rate up to 100%, especially in severe undiagnosed cases. Therefore, this study was conducted for molecular identification and characterization of P. multocida in nasal swabs and pn...

Background At the end of 2021, an epidemic of reproductive abnormalities in cows occurred in Jilin Province, China, posing an urgent need for a rapid diagnosis. Results To identify the cause of the disease, a total of 172 samples were collected from 21 dead calves and 45 aborting or pregnant cows in 10 farms across the province. Routine PCR or RT-...

Background Lassa fever (LF) is a viral hemorrhagic illness endemic in Nigeria and other West African countries. In recent years, the number of reported cases of LF in Nigeria has increased. In this study, we discussed the epidemiology of LF, the phylogenomics of the LF virus, issues associated with the increased cases of LF, and recommendations for...

Getah virus (GETV), belonging to the genus Alphavirus within the family Togaviridae, is a mosquito-borne virus that causes fever, rash, and edema in horses and fatalities and pregnancy disorders in pigs. It has caused occasional outbreaks in horse populations in Japan, China, and India, and endemic areas are gradually expanding, particularly in Asi...

The emergence of SARS-CoV-2 variants has heightened concerns about vaccine efficacy, posing challenges in controlling the spread of COVID-19. As part of the COVID-19 Vaccine Effectiveness and Variants (COVVAR) study in Uganda, this study aimed to genotype and characterize SARS-CoV-2 variants in patients with COVID-19-like symptoms who tested positi...

Background During prolonged FDC therapy, the emergence of FDC non-susceptibility in CRAB has been reported. Here, we report a transmission cluster of FDC-non-susceptible CRAB in four patients, all naïve to FDC treatment, characterized by a premature stop codon and amino acid deletion in the PirA protein. Methods CRAB strains obtained from patients...

The family Boletaceae primarily consists of ectomycorrhizal fungi, which are essential for maintaining the health of forest ecosystems. These fungi form symbiotic relationships with trees, facilitating nutrient exchange and en?hancing plant growth. In the present study, specimens of Caloboletus guan?yui were collected from the Mizoram University ca...

During a survey of microfungi associated with coffee trees in Jinghong City, Yunnan Province, China, decaying twigs of Arabica coffee with black fungi fruiting bodies were collected, and an interesting fungus was subsequently isolated and identified. Maximum likelihood and Bayesian analyses of combined ITS, LSU, SSU, rpb2, and tef1-α genes showed t...

Peach (Prunus persica L.) is a globally significant fruit valued for its high edible and ornamental qualities. Peach leaf spot disease has become increasingly prevalent in recent years, negatively affecting fruit quality and esthetic appeal. During the summer of 2024, symptoms of leaf spots were observed on peach trees in an orchard in Bazhong City...

The tapeworm Ligula intestinalis (Linnaeus, 1758) is a broadly distributed parasite with high epidemiological significance. Its first intermediate hosts are crustaceans, its second intermediate hosts are fish, while the definitive hosts are various fish-eating birds and, as recently shown, ringed seals. The stages of Ligula intestinalis in fish are...

Background The global poultry industry has been experiencing increasing condemnation at slaughterhouses since 2011, due to the emergence of avian reovirus (ARV) variant strains. Recently seven ARV genogroup clusters were identified based on the σC sequence of the S1 segment that was used as a genetic marker to characterize and classify ARV. Result...

†Cryptovaranoides microlanius from the latest Triassic of England was described in 2022 as a crown-clade squamate, of importance as the oldest such modern-type lizard, extending their temporal range downward by 35 Myr. This view was challenged in 2023, and †Cryptovaranoides was reinterpreted as an archosauromorph. These decisions matter because the...

The genus Maculabatis is a group of batoid rays from the Dasyatidae family, consisting of two main complexes: the gerrardi (spotted species) and the pastinacoides (plain species). This study investigated the diversity within the Maculabatis gerrardi complex, revealing the presence of two distinct geographical lineages, with a potential new species...

Southwest China is extremely rich in fungal resources, and a large number of new taxa have been discovered in recent years. In the present study, we examined 26 specimens of the genera Hydnum and Lentaria sensu lato, most of which were obtained in Yunnan Province. Through ITS-nrLSU-tef1 phylogenetic analysis, combined with morphological studies and...

The MEI2 homologs from organisms belonging to various eukaryotic groups with a specific focus on dinoflagellates were studied. The diversity of these homologs revealed in different dinoflagellate species was analyzed. The results of phylogenetic analysis allowed to identify at least six groups of MEI2-like proteins. The features of the amino acid c...

Objective Oncomelania hupensis robertsoni is the only intermediate host of Schistosoma japonicum in hilly regions of south-west China, which plays a key role during the transmission of Schistosomiasis. This study aimed to sequence the complete mitochondrial genome of Oncomelania hupensis robertsoni and analyze genetic differentiation of Oncomelania...

Pyranose oxidase (POx) is an FAD-dependent oxidoreductase and belongs to the glucose–methanol–choline (GMC) superfamily of oxidoreductases. As recently reported, POxs and FAD-dependent C‑glycoside oxidases (CGOxs) share the same sequence space, and phylogenetic analysis of actinobacterial sequences belonging to this shared sequence space showed tha...

Genomic and chemical analysis has revealed that numerous species of filamentous cyanobacteria harbor complex secondary metabolisms tailored to their particular ecological niche. The metabolomic analysis of strains and environmental samples from benthic cyanobacterial mats (BCMs) from coral reefs has the potential to expand the library of marine cya...

Osteobrama peninsularis has been reported in southern Indian drainages, particularly in the Krishna River drainage. This study provides new findings of O. peninsularis in two distant locations: the Kangsabati River (Suvarnarekha River drainage) in West Bengal and Wyra Lake (Godavari River drainage) in Telangana. This marks the first record of O. pe...

OBJECTIVE This study investigates the molecular epidemiology of orf virus (ORFV) in the Fujian province in 2024, with the goal of gaining insights that can enhance disease prevention and control strategies. METHODS This experimental study was conducted from January 2024 through March 2024. The samples, showing suspected orf lesions, tested positiv...

Hepatitis B virus infection is a major global health problem, particularly in HIV-infected patients and increases the risk of liver damage. The purpose of this study was to assess the HBV prevalence and genotypes among HIV-infected patients in Brazzaville, Republic of the Congo. This cross-sectional study was conducted among HIV-positive patients a...

Understanding the origin of eukaryotic cells is one of the most difficult problems in all of biology. A key challenge relevant to the question of eukaryogenesis is reconstructing the gene repertoire of the last eukaryotic common ancestor (LECA). As data sets grow, sketching an accurate genomics-informed picture of early eukaryotic cellular complexi...

The molecular clock hypothesis assumes that mutations accumulate on an organism’s genome at a constant rate over time, but this assumption does not always hold true. While modelling approaches exist to accommodate deviations from a strict molecular clock, assumptions about rate variation may not fully represent the underlying evolutionary processes...

Lagoviruses are viruses of the Caliciviridae family affecting lagomorphs. Both pathogenic and non-pathogenic lagoviruses affect the European rabbit (Oryctolagus cuniculus), and they are phylogenetically distinguished. Rabbit Hemorrhagic Disease Virus (RHDV/GI.1) and Rabbit Hemorrhagic Disease Virus-2 (RHDV-2/GI.2) belong to the first group, while i...

Jingchuvirales (negative-sense RNA viruses) were initially discovered in invertebrates, with both exogenous and endogenous jingchuviruses subsequently identified in fish, reptiles and mammals. To date, jingchuviruses have only been described metagenomically. By screening primary tumor tissues and tumor cell lines from the endangered Tasmanian devil...

The genus Hydnoporia (Hymenochaetales, Hymenochaetaceae) was first described by Murrill in 1907. However, species of Hydnoporia were subsequently reclassified into the genera Hymenochaete, Hymenochaetopsis, and Pseudochaete due to overlapping morphological characteristics, leading to multiple synonyms and confusion among researchers. Recent phyloge...

Rotaviruses are well-recognized pathogens responsible for diarrhea in humans and various animal species, with Rotavirus A the most often detected and most thoroughly described. Rotaviral disease is an important concern in pathology of pigeons as well, as pigeon rotavirus A was proven to play a major role in young pigeon disease (YPD). However, rota...

The ABC1K (activity of bc1 complex kinase) atypical protein kinase family regulates diverse physiological functions in plants, including the development, growth, and response of plants to various stress stimuli. However, to date, only a few members of the alfalfa ( Medicago sativa ) ABC1K gene family have been identified, which severely limits the...

In order to enrich our taxonomic and systematic comprehension of Ovulidae within the evolutionary framework of Littorinimorpha. we present a comprehensive analysis of the mitochondrial genome (mitogenome) sequence of Volva habei using next-generation sequencing technology (GenBank accession number OR492307). The mitogenome spans a total length of 1...

A new species of Flabelligena Gillet, 2001 (Annelida: Acrocirridae) was described from deep-sea sediment collected off Minamidaito Island and on Kita-Koho Seamount, 644–774 m depth. The new species can be discriminated from other known Flabelligena species by having three pairs of branchiae, 1–2 noto/neurochaetae, and ventral genital papillae on ch...

Southern Brazil is home to a large biodiversity of elasmobranchs from the Brazilian coast. Several genera and species of small sharks of the Triakidae family live in this marine environment. Studies on these shark species are scarce, with few genetic data and little information on animal population structures. The present study aimed to sequence th...

Gray blight is a serious threat to the tea [Camellia sinensis (L.) O. Kuntze] production in major tea cultivating countries including India. The disease is caused by Pestalotiopsis-like species. In this study, five isolates of Pseudopestalotiopsis species isolated from symptomatic tea leaf samples in North Bengal, India were investigated. Based on...

Porcine stool-associated RNA virus (Posavirus) is an unclassified virus with sequence similarity to viruses in the order of Picornaviridae. In China, lineage 1 Posavirus (Posavirus 1) has been circulating in the field since its initial emergence in 2014 however no other lineages have been reported. To investigate the genetic diversity of Posavirus...

Auxins play significant roles in plant growth and development. The transporter inhibitor response1/auxin signaling F-box ( TIR1/AFB ) gene family encodes the auxin receptor proteins and plays an essential role in the auxin signaling pathway. Here we identified and characterized the TIR1/AFB family in Carya cathayensis (Cc) plants (named as CcTIR1/A...

The Ziziphus tree species offer valuable socio-economic and ecological benefits but experience significant damage from insect pests. In Ethiopia, there is limited knowledge of the insects attacking Ziziphus fruits, and a study aimed to identify these pests, assess their impact and understand how different land use types (LUTs) affect them was condu...

Starch degradation, a crucial source for soluble sugar, significantly influences fruit flavor development during ripening. Key enzymes in this process include α-amylases (AMYs) and β-amylases (BAMs). In this study, we identified 5 PpAMYs and 9 PpBAMs in peach and categorized them into three and four groups, respectively, based on the gene structure...

Background Based on unique morphological features and phylogenetic analysis of combined LSU and ITS sequences, Paramirandina guttulata is established as the third species in Paramirandina, along with P. aquatica and P. cymbiformis. All three species of Paramirandina were reported from freshwater habitats in China. New information Paramirandina gut...

Helitrons are rolling-circle transposons that amplify through rolling-circle replication mechanism. Since Helitrons were relatively recently identified, their impact on genome evolution is still not fully understood. Here, we describe that a single Helitron subfamily specifically accumulates in the subtelomeric regions of Hydractinia symbiolongicar...

The species of the antlion tribe Myrmeleontini from Taiwan are revised. In total, nine species from two genera Baliga (2 spp.) and Myrmeleon (7 spp.) are redescribed and an identification key is provided. One new combination, B. brunneipennis (Esben-Petersen, 1913) comb. nov., and one new synonymy, M. alticolus Miller & Stange, 1999 syn. nov. = B....

Premise of the study With over 3100 species, Astragalus (Fabaceae) has long fascinated botanists as the largest genus of flowering plants. With an origin in the Middle Miocene, Astragalus has one of the highest diversification rates known in flowering plants. Comprehensive taxonomic treatments exist, and the genus is currently subdivided into 136 s...

Centre d'étude et de conservation des ressources végétales (CECRV) 411, route du Hayet, F40180 Heugas cecrvbayonne@orange.fr Résumé : L'angélique des estuaires, considérée comme endémique de l'ouest de la France, vit très souvent en sympatrie avec l'angélique des bois. Nombreux sont les individus de phénotype intermédiaire qu'il est très difficile...

Acute Oak Decline (AOD), a bacterial disease previously known in Northern and Central Europe, has recently been reported in Salento (a Mediterranean coastal region of Southern Italy), where holm oak trees exhibiting AOD-like symptoms have tested positive for infection with AOD-related bacteria such as Brenneria goodwinii and Gibbsiella quercinecans...

Pathogen sequencing during the COVID-19 pandemic has generated more whole genome sequencing data than for any other epidemic, allowing epidemiologists to monitor the transmission and evolution of SARS-CoV-2. However, large parts of the world are heavily underrepresented in sequencing efforts, including the Caribbean islands. We performed genome seq...

Kockovaella, in the family Cuniculitremaceae of the order Tremellales, is a globally distributed genus of blastoconidia-forming fungi. Currently, 23 species have been described and accepted as members of the genus. In this study, five yeast strains were isolated from plant leaf surfaces collected in the Fujian and Guizhou Provinces of China and ide...

Oligochaetes play a significant role in aquatic ecosystems, and studying their development can contribute to a deeper understanding of the evolutionary features of embryonic development in the phylum Annelida. In this paper, we initially explored a littoral oligochaete species from the White Sea, which is abundant in the vicinity of the White Sea B...

Species in the beetle family Histeridae exhibit numerous defensive adaptations, from a generally compact and spheroid body shape to retractable tarsi, legs, heads, and antennae. Modes of antennal concealment are particularly variable, underscoring the importance of protecting these essential sensory structures. Understanding the evolution of these...

F. khargensis is a yeast and was first described in 2014 from environmental samples. F. khargensis belongs to the genus Fereydounia that grows as a yeast, was first identified in East Asia. The basidiomycetous yeast Fereydounia khargensis is recorded for the first time from living plants and in East Asia. Phylogenetic analysis indicates a relations...

Background: Zingiber Mill., a morphologically diverse herbaceous perennial genus of Zingiberaceae, is distributed mainly in tropical to warm-temperate Asia. In China, species of Zingiber have crucial medicinal, edible, and horticultural values; however, their phylogenetic relationships remain unclear. Methods: To address this issue, the complete pl...

Lobster phyllosoma larvae collected during surveys over the continental shelf of eastern South Africa (southwestern Indian Ocean) were analysed to determine the role of the KwaZulu-Natal (KZN) Bight as a pelagic nursery area. Surface waters in the shallow bight and further offshore, between the 20- and 1,000-m depth contours, were sampled with plan...

Background Lachninae (Insecta: Aphididae) represent a fascinating group of aphids that are traditionally divided into five tribes. Among these, members of the tribe Tuberolachnini exhibit remarkable morphological and biological diversity. One genus of this group, Miyalachnus, known from Japan, is characterized by unique features. Our study aimed to...

The genus Isonychia Eaton, 1871 is widely distributed across the Holarctic and Oriental regions. However, no representatives of this genus have been reported from southwestern China, a region known for its high biodiversity. Here, we described and illustrated Isonychia latiassp. nov., a new species recently collected from Guizhou Province, southwes...

Microalgae are known for their efficient removal of hexavalent chromium (Cr(VI)) through biosorption and bioaccumulation, yet the subsequent release of Cr(VI) upon cell death remains a challenge. The reduction of Cr(VI) to the less toxic trivalent chromium [Cr(III)] is another critical remediation strategy that mitigates the risk of Cr(VI) re-relea...

Ichthyobodo necator is a damaging and economically important protozoan parasite; however, its clinical patterns and incidence, correlated to environmental factors, are still poorly understood. This study provides the first report of Ichthyobodo necator infestation among Dicentrarchus labrax. We recorded significant mortalities in the cultured D. la...

The genus Vitis, known for its economically important fruit—grape—is divided into three geographical groups, American, East Asian, and Eurasian, along with a hybrid group. However, previous studies on grape phylogeny using chloroplast genomes have been hindered by limited sample sizes and inconsistent methodologies, resulting in inaccuracies. In th...

Introduction. As a result of routine testing of HIV-1 drug resistance (DR), a significant amount of viral nucleotide sequences and epidemiological data of HIV-infected individuals have been collected. Combined with the increasing use of bioinformatics methods in practice, it has become possible to study the features of HIV-1 resistant variants spre...

We describe two new caecilian species of the genus Caecilia (Gymnophiona: Caeciliidae) from the wet tropical Chocó Forest, northwestern Ecuador. We applied an integrative taxonomic approach, taking into consideration external morphology, os-teology from intensive ct-scanning, and molecular phylogenetic analyses. The two new species were compared to...

DNA barcoding, a robust tool for species identification, holds significant promise for enhancing authenticity and quality control in herbal and Ayurvedic medicines. The traditional methods, often time-consuming and impractical for industrial-scale applications, are complemented by DNA barcoding, which offers efficient and reliable plant species ide...

A novel genus, Paradingleyomyces was introduced to accommodate Pa. lepidopterorumsp. nov., based on a multigene phylogenetic analysis and its distinct morphological characteristics. Maximum likelihood (ML) and Bayesian inference analyses (BI) of ITS, SSU, LSU, tef-1α, rpb1, and rpb2 sequence data shown that Pa. lepidopterorum formed an independent...

To date, seven novel parvoviruses have been identified in pigs and designated as porcine parvovirus 2–7 (PPV2–7). The presence of these emerging viruses has been reported in several countries around the world, although their pathogenic role and clinical and economical relevance are largely unknown. Here, we report the estimated prevalence and genet...

Leontopodium nyingchiense, a new species of Asteraceae from the Xizang (Tibet) Autonomous Region of China, is described and illustrated here. Morphologically, it is most similar to L. lingianum but can be distinguished by the combination of monoecious and dioecious individuals, involucral bracts arranged in 3–5 series (with outer series herbaceous...

Objective: Phylogeny as a science that study the evolutionary relationships between species and populations of organisms, as well as their evolutionary history, diversity and patterns of population changes, by integrating genomic data, has become a strong approach in the study of the systematic of species named phylogenomics. The aim of the present...