Phylogenetic Analysis - Science method

The evolutionary origins of modern amphibians (Lissamphibia) represent one of the most persistent controversies in vertebrate palaeontology. This study examines the competing hypotheses regarding lissamphibian ancestry, specifically whether they evolved from temnospondyl amphibians, lepospondyl amphibians, or whether different lissamphibian groups...

This study reports and characterizes the complete mitogenome of Theloderma albopunctatum. The mitogenome was 15,780 bp in length and contained 13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes, with 29.35% A, 25.17% T, 14.24% G, and 31.24% C. The original data were assembled and annotated, and the complete mitochondrial ge...

In this study, we identified a novel mitovirus, designated as "Pleurotus pulmonarius duamitovirus 1" (PpDMV1), from the edible fungus Pleurotus pulmonarius. Genome sequencing revealed a 2,622-nucleotide (nt) genome containing a single 2,001-nt open reading frame (ORF) encoding an RNA-dependent RNA polymerase (RdRp). Full-length genome sequence comp...

The present study determined the complete chloroplast genome of Allophylus viridis, an important medicinal plant. The chloroplast genome of this species was 169,213 bp in length, consisting of a pair of inverted repeats of 32,829 bp separated by the large single copy of 85,297 bp and small single copy of 18,258 bp regions. 134 genes were determined...

Background The cytochrome P450 superfamily comprises a large group of enzymes crucial for the biosynthesis and metabolism of diverse endogenous and exogenous secondary metabolites in plants. Chrysanthemum, an ornamental genus with considerable medicinal value, is one of the most economically important floricultural crops in the world. The character...

Continued outbreaks of porcine epidemic diarrhea are causing serious economic losses to the swine industry in China. To monitor the prevalence, genetic mutations, and pathogenicity of porcine epidemic diarrhea virus (PEDV), 172 samples were collected from eight cities in Sichuan Province from 2020 to 2022. RT-PCR analysis revealed that 25.0% (43/17...

A toxic epibenthic dinoflagellate Coolia malayensis is reported for the first time in Cancabato Bay, Tacloban City, the Philippines. Typically found in tropical and subtropical waters, this genus is observed to often coexist with other ciguatoxigenic dinoflagellates. Two strains of C. malayensis were established into clonal cultures, both producing...

Introducción. El cacao es un cultivo perenne de importancia en el sureste de México, donde la chinche negra del cacao (Antiteuchus tripterus Fabricius) se ha reportado como plaga. El control del insecto mediante hongos entomopatógenos constituye una alternativa sustentable. Objetivo. Caracterizar y seleccionar aislamientos nativos de Metarhizium br...

In this work, we performed the genetic characterization of a new variant of orthohantavirus associated with a fatal case of hantavirus pulmonary syndrome, outside the known endemic region, in northwestern Argentina. We first confirmed an orthohantavirus infection by ELISA, testing for the detection of IgM and IgG antibodies. Then, we extracted RNA...

Foshou yam (Dioscorea esculenta) is a tuber food crop in China. It is a rare species of the yam family and known for its high nutritional value. From 2019 to 2021, tuber rot was observed in Foshou yam in Wuxue, Hubei Province, China. Fungal strains were isolated from diseased tubers, and ten representative strains were identified based on microscop...

Purpose To describe a new species of Oochoristica Lühe, 1898, an anoplocephalid cestode included in Linstowiinae (Cyclophyllidea), parasitizing Sceloporus ochoterenae Smith in Zoyatepec, Guerrero, Mexico. Methods All specimens were fixed with 4% hot formalin. A morphologic study was made using stained material under light microscopy. Some specimen...

Sorbus monbeigii (Cardot) N.P.Balakr. is a woody tree of the Rosaceae family. Interspecific hybridization is prevalent in Sorbus, and the limited molecular data suggest that the taxonomic status requires further study. Therefore, we assembled and annotated the complete chloroplast genome of S. monbeigii. The chloroplast genome of S. monbeigii is 16...

For the first time, Bethylus Latreille, the type genus of Bethylidae (Hymenoptera, Chrysidoidea, Bethylinae), is reported from the Korean Peninsula based on the discovery of a new species, Bethylus colligatus sp. nov. , which was collected in Gangwon Province near the Demilitarized Zone. This new species is described and illustrated. A phylogenetic...

Turdus atrogularis is a species with a controversial taxonomic status. In this study, the first complete mitochondrial genome of T. atrogularis was sequenced and characterized. The mitochondrial genome (mitogenome) is 16,757 bp in length, with a higher AT content than GC content. The mitogenome consists of 13 protein-coding genes, 22 tRNA genes, 2...

Background Gray mold caused by Botrytis cinerea is a major threat to the production of strawberry. An increasing number of studies have reported that wall-associated kinase/wall-associated kinase-like (WAK/WAKL) played an important role in the recognition of oligogalacturonic acids (OGs) and the induction of plant defense, but there have been no sy...

To understand the genetic variation trend of the S gene of porcine epidemic diarrhea virus (PEDV) epidemic strains in various regions of Zhejiang Province, this study collected pig diarrhea samples from different pig farms in Zhejiang Province from 2019 to 2024. The positive samples were identified by fluorescence quantitative RT-PCR, and the S gen...

Spatial phylogenetic approaches enhance biodiversity analyses by incorporating information about species' evolutionary similarity. However, existing software packages for analysing spatial phylogenetic diversity (PD) patterns only provide full support for binary (presence–absence) community data. A major gap exists in support for occurrence probabi...

In this study, DNA barcode analysis and phylogenetic position of endemic species Lysimachia savranii were determined using nrDNA ITS and cpDNA rbcL sequences. Green leaves of endemic L. savranii were brought to the laboratory and genomic DNA was isolated. ITS (ITS5A and ITS4) and rbcL (rbcLaF and rbcLaR) primers were used to perform the PCR amplifi...

Cordyceps sensu lato species are highly important for medicinal purposes and functional food nutrients. Two new species belonging to Cordyceps sensu lato are introduced, i.e., Papiliomyces sinensis and Paraisaria pseudoarcta . To comprehensively describe the significance of these two species, morphological data were supplemented with phylogenetic a...

This study aimed to characterize the chloroplast genome of Eurya nitida Korthals. The complete chloroplast genome of Eurya nitida was sequenced and assembled using high-throughput sequencing technology. The genome spans 157,191 bp and exhibits a typical quadripartite structure, comprising a large single-copy region (LSC, 87,231 bp), a small single-...

Lutjanus bohar Forsskål 1775, a large reef-associated fish species, is widely distributed across tropical and subtropical waters and is recognized as a significant commercial fishery resource. Here, the complete mitochondrial genome of L. bohar was sequenced using next-generation sequencing technology, and its characteristics were comprehensively a...

The WRKY gene family plays a crucial role as transcriptional coactivators in plants. Pseudoroegneria libanotica, which serves as the maternal progenitor to various species within the tribe Triticeae, exhibits remarkable resistance to diverse adverse factors. Therefore, an investigation into its response mechanisms to abiotic stressors holds signifi...

Lilium leichtlinii var. maximowiczii, native to Northeast Asia, shows morphological differences between Korean and Japanese varieties. This study analyzed chloroplast (cp) genomes of three diploid L. leichtlinii groups: Korean (KR), Japanese broad-leaved (JB), and Japanese narrow-leaved (JN). Genome sizes ranged from 152,053 bp to 152,588 bp with G...

Telomeres, the nucleoprotein complexes that protect the ends of linear chromosomes, are essential for maintaining the stability of eukaryotic genomes. As telomeres generally consist of repetitive DNA associated with specifically bound proteins, telomeric repeat motifs (TRMs) are thought to be difficult to evolve. However, a recent study identified...

The complete mitochondrial genomes of Saussurella cornuta (Haan, 1843) and Saussurella longiptera (Yin, 1984) were sequenced and analyzed. The circular mitogenomes of S. cornuta and S. longiptera are 16,531 bp and 16,313 bp in length, respectively. The nucleotide compositions are significantly biased toward AT, with AT contents of 69.9% in S. cornu...

Tomato (Solanum lycopersicum) is a globally significant crop, vulnerable to a wide range of viral pathogens, among which begomoviruses (family Geminiviridae) are the most devastating. In recent years, the emergence of recombinant begomovirus strains has intensified the threat to tomato production, particularly in tropical and subtropical regions. T...

Tomato-infecting begomoviruses represent a significant threat to global tomato production, especially in tropical and subtropical regions. These viruses, belonging to the Geminiviridae family, are highly diverse and capable of rapid evolution through mechanisms such as mutation and recombination. In this study, we conducted a comprehensive phylogen...

Specimens of Singerocybe alboinfundibuliformis were collected from deciduous forests in district Swat. The species was identified using internal transcribed spacer region (ITS) sequences analysis as well as morpho-anatomical features. Detailed morphological description and illustrations are provided along with result of molecular phylogenetic analy...

Phylogenetic analysis strives to construct graphs, such as trees or networks, that encapsulate the historical structure of a set of terminal taxa. This process is based on comparative character data and an optimality criterion by which these graphs are evaluated. Whether there is structure in the data or not, phylogenetic analytical methods will pr...

The long-tailed ground squirrel (Urocitellus undulatus) is primarily distributed in various regions, including Xinjiang and Heilongjiang in China, as well as in Siberia, Mongolia, the Russian Federation, and Kazakhstan. In this study, we report the complete mitochondrial genomes of U. undulatus. The genome consists of 16,456 base pairs, including 1...

Canine parvovirus (CPV) is a highly contagious and lethal virus that primarily affects dogs. The virulence and transmissibility of this virus have intensified over time, posing significant challenges to the prevention and control of this pathogen. In this study, to investigate the epidemiology of CPV in China, 2,654 fecal samples were collected fro...

The S. heraclei (Takahashi) (Hemiptera: Aphididae) is a destructive pest of cultivated insectary plant Cnidium monnieri (L.) Cuss. However, to date, no S. heraclei-related genomic information has been reported. Here, we present the first chromosomal-scale genome assembly of S. heraclei approximately 440.3 Mb with contig N50 of 81.7 Mb. Using PacBio...

Wheat dwarf virus (WDV) poses significant threats to gramineous crops, making it crucial to explore its codon usage patterns and evolutionary dynamics for effective disease control. This study analyzed ten WDV isolates, including two from triticale (WDVT_117 and WDVT_118), using metrics such as relative synonymous codon usage (RSCU), effective numb...

Mahanarva (Ipiranga) Fennah, 1968, currently comprises nine described species. The subgenus is characterized by an inflated postclypeus with a convex profile, longer than wide tegmina, and male genitalia with a short, laterally compressed aedeagus with a pair of slender dorsal processes. In this study, a phylogenetic hypothesis based on morphologic...

Garra rufa, or doctor fish, is a small cyprinid known for its high-temperature tolerance and its use in ichthyotherapy. Recently, this trait has gained interest as a model for human diseases, including infections and cancer xenografts, though limited genomic resources hinder experimental use. In this study, we have generated a high-quality, chromos...

The family Rhabdoviridae comprises viruses with negative-sense RNA genomes. This family has four subfamilies, with the Betarhabdovirinae encompassing all plant-associated rhabdoviruses. Here, we report the creation of a new genus, Trirhavirus, within the subfamily Betarhabdovirinae to classify recently described trisegmented rhabdovirids. The trise...

Background Boletopsis is a genus of the family Bankeraceae with eight accepted species in the world. Species in the genus are ectomycorrhizal fungi and edible. In this study, we conducted a phylogenetic analysis of this genus, based on ITS and nrLSU sequences, using Maximum Likelihood and Bayesian Inference, along with morphological observations in...

In this study, we introduce two new records of Ascomycota, viz., Otidea bomiensis and Xylaria curta from Khyber Pakhtunkhwa, Pakistan. These specimens have been collected from district Abbottabad and district Swabi, Khyber Pakhtunkhwa, respectively during the monsoon season of 2022. Molecular phylogenetic analysis of internal transcribe spacer (ITS...

Amynthas bubonis Hong & James, 2001 is an earthworm species endemic to Korea. This species is typically found in mountainous forests at low altitudes. Specimens were collected from Mt. Deogyu in South Korea, and the complete A. bubonis mitogenome was sequenced, assembled, and annotated. The A. bubonic mitogenome is a 15,095 bp circular DNA molecule...

Background: Nirsevimab is a long-acting monoclonal antibody used to prevent respiratory syncytial virus (RSV) infection in infants and high-risk children. During the 2024 RSV season in Western Australia, 23,525 doses were administered to infants entering their first season, and 1,233 doses to at-risk children. In this context, the selection and spr...

Background Tianjin, a major hub in northern China, faces rising HIV-1 infections dominated by CRF01_AE and CRF07_BC. This study elucidated their divergent transmission patterns and drug resistance dynamics to guide targeted interventions. Methods This study included samples identified as CRF01_AE and CRF07_BC subtypes through various methods betwe...

This study aims to investigate the endogenous gibberellin levels and related genes analysis of noxious invasive weed Heracleum sosnowskyi. Genome-wide identification, phylogenetic analysis, conserved motif analysis, and gene structure characterization of GA-oxidases were performed. We analysed endogenous GAs levels and the expression of target HsGA...

Vesicular glutamate transporters are members of the solute carrier 17 (SLC17) family, and mammals express three closely related isoforms: vGluT1-3. While vGluT genes have been identified across various species in the Animalia kingdom, the evolutionary relationships and the natural history of vGluT members remain poorly understood. This study aimed...

Greenhouse whitefly, Trialeurodes vaporariorum Westwood (Hemiptera: Aleyrodidae) is a phytophagous insect that causes significant economic losses in agricultural production. This study aimed to investigate the genetic structure of T. vaporariorum populations collected from various provinces in Turkey, as well as their associated endosymbionts. Univ...

Background Infectious bronchitis virus (IBV) is a highly contagious evolving pathogen that causes respiratory, urinary and reproductive symptoms; threatening the poultry industry globally. Methods During this study, 90 tissue specimens were collected from various poultry flocks of seven Upper Egypt governorates from 2023 to 2024 for genetic charac...

The bovine respiratory disease complex causes significant morbidity and mortality with aetiological agents known to contribute to its development including several bacteria and viruses. In Albania there is limited information on the prevalence or genetic makeup of viral bovine respiratory disease complex pathogens, which limits mitigation strategie...

Kalops is a genus of early ray-finned fish in North America. It is distinguished from early actinopterygians by the combination of the following characters: subterminal mouth, rounded oval shaped lacrimal, multiple small supraorbitals and suborbitals. So far, it has been only excavated from the Serpukhovian (Late Mississippian) Bear Gulch Limestone...

Two freshwater tardigrade populations belonging to the genus Dactylobiotus were investigated using phase contrast microscopy, scanning electron microscopy, and molecular markers commonly employed in tardigrade phylogenetic studies (18S rRNA, 28S rRNA, ITS2, and COI). The population from Taiwan, discovered through social media, represents a new spec...

Plant genetic evaluation often faces challenges due to complex genetic structures. Ryegrass (Lolium), a valuable species for pasture-based agriculture, exhibits heterogeneous genetic diversities among base breeding populations. Partially overlapping datasets from incompatible studies and commercial restrictions further impede outcome integration ac...

Mutations are continuous source of new alleles and genetic diversity in populations. Domestication and selection influence the accumulation of alleles occurring across a range of deleteriousness. Evidence suggests that mildly deleterious mutations (DelMut) can be purged out of breeding populations, increasing favorable allele accumulation. We used...

We establish a new deep-sea tanaidacean family, Arthruridae n. fam., separated from the family Tanaellidae Larsen and Wilson, 2002, and based on a morphology-based phylogenetic analysis. This new taxon is supported by molecular evidence from a recent study of the newly described Caudalongidae Błażewicz & Bird 2024. Arthrurids resemble tanaellids su...

This study presents an optimized DNA extraction technique specifically tailored for Helichrysum species, which are known for their high content of secondary metabolites that often hinder DNA purity and yield. The method has been evaluated for its efficiency, cost effectiveness, and applicability across different Helichrysum taxa. Results demonstra...

This study presents the assembly and annotation of the full-length mitochondrial genome for the leafhopper species Empoasca fabae Harris, 1841. The mitogenome was obtained from a contig-level assembly with the identified mitochondrial genome being 14,873 bp in length. The base composition was A (38.8%), T (39.1%), C (11.7%), and G (10.4%). The mito...

While exploring the leaf litter fungal diversity in Doi Inthanon National Park, Northern Thailand, we discovered a previously unknown lineage within Niessliaceae. Muciflexus inthanonensisgen. et sp. nov. is therefore introduced to accommodate this new lineage. The link between the sexual and asexual morphs of Ochronectria thailandica is also establ...

Scale insects (Coccidae, Hemiptera) and whiteflies (Aleyrodidae, Homoptera) are diminutive, ubiquitous, sap-sucking plant parasites, many of which are serious agricultural pests. Over the course of several years, an investigation into entomopathogenic fungi affecting scale insects and whiteflies resulted in the collection of 13 novel species of Cla...

We report the complete genome sequences of four parechovirus-A3 (PeV-A3) isolates from Children’s Mercy Kansas City (CMKC), United States of America (USA): PeV-A3-MO-12-CMKC/CSF/MO/USA/2012 (isolated in 2012 from cerebrospinal fluid), PeV-A3-8C-CMKC/CSF/MO/USA/2022/ (isolated in 2022 from cerebrospinal fluid), PeV-A3-9C-CMKC/CSF/MO/USA/2022 (isolat...

Lumpy skin disease is a transboundary, emerging and a notifiable disease of cattle with huge economic impacts throughout the globe. In recent years, the disease has also been reported in Indian Gazelle, Camel, Banteng, Gaur, and Giraffe. This report provides an insight into the occurrence of LSD in red serow (Capricornis rubidus), a globally vulner...

The study of the fungus-growing termites genus Macrotermes in Africa remains notably limited, with the genus harboring hidden diversity that has eluded conventional taxonomy. Characterization of the mitochondrial genomes of these termite species represents an important biodiversity resource that could assist in resolving taxonomic ambiguities. The...

The genus Graphium belonging to order Microascales, comprises known wood pathogens that cause sapstain in timbers and wood degradation. However, this genus has been scarcely studied in Korea. Therefore, the current study was conducted to investigate the genus Graphium in freshwater environments as new habitat in Korea. Three strains, CNUFC PYW4-15,...

Super-enhancers (SEs) orchestrate high-level transcription by integrating multiple regulatory elements and signals. Although chromatin accessibility and transcription factor binding within SEs are extensively studied, the role of non-canonical DNA structures, particularly Z-DNA, remains underexplored. In this study, genome-wide predictions of Z-DNA...

The protein phosphatase 2 C (PP2C) plays a crucial role in the growth and development of plants. However, limited information on the PP2C genes in Chimonanthus spp. is available. Therefore, the comprehensive genome-wide identification and analysis of the PP2Cs gene family is necessary in Chimonanthus spp. to provide basic information for further st...

Increased demand of cultivated oyster mushrooms (Pleurotus species) in Aotearoa New Zealand has led to the importation of exotic species, which pose potential invasion risks. Gaps in taxonomic knowledge of this genus have complicated biosecurity decisions and cultivation efforts. To address this, we collected 84 wild and cultivated New Zealand Pleu...

Background Rotavirus A (RVA) is an important pathogen causing acute viral gastroenteritis in young children and various animals. RVA is also recognized as a common cause of gastroenteritis in piglets. Epidemiological studies of porcine RVA (PoRVA) conducted in different settings worldwide reported that the prevalence of PoRVA infection ranged from...

Turbo sazae, a commercially and ecologically significant marine gastropod traditionally found in Jeju Island and the southern coast of Korea, is experiencing a reported northward expansion into the East Sea, likely influenced by rising seawater temperatures. This study provides preliminary genetic insights into the genetic structure and connectivit...

Spotted fever group (SFG) rickettsioses are increasingly recognized worldwide as threats to public health. Rickettsia rickettsii, Rickettsia parkeri, and Rickettsia rickettsii subspecies californica cause spotted fever rickettsioses, including Rocky Mountain spotted fever. These disease agents are transmitted to humans by various tick vectors in th...

Aulandra H.J.Lam (Sapotaceae) has hitherto been treated as a genus of tropical forest trees native to Borneo. To test whether the genus is distinct from Palaquium Blanco, phylogenetic analysis using maximum likelihood was performed on target capture of nuclear data, including all species currently recognised as belonging in Aulandra. The results co...

Introduction Human papillomaviruses (HPVs) are well-known for causing both benign and malignant epithelial growths in humans, but their occurrence in non-human species is rarely reported. Expanding the understanding of HPV’s host range is essential for assessing its ecological and public health implications. Methods We investigated serum samples f...

Prototheca is an unusual genus of algae that lack chlorophyll and are obligate heterotrophs. To date, six paraphyletic pathogenic species have been identified in the context of vertebrates, principally in cattle-associated and human-associated infections. Together with the genus Auxenochlorella and Helicosporidium , rDNA sequence analysis currently...

Sessile plants exhibit diverse movement behaviors that have long intrigued the scientists. The legume plants display a rhythmic leaflet movement pattern characterized by horizontal opening during the day and vertical closure at night. However, the underlying mechanisms remain largely enigmatic. Here, we isolated a mutant designated as dlm1 (downwar...

Yunnan Province is rich in freshwater resources, providing a favorable environment for freshwater fungi. As a result, numerous new species have been described in recent years, further supporting the extensive diversity of freshwater fungi in this region. During an investigation of lignicolous freshwater fungi from the Dulongjiang River, six fresh i...

Based on observations of living plants of Hydrocotyle calcicola in the field, together with examination of herbarium specimens and descriptions of both H. calcicola and H. chiangdaoensis (including type material), we demonstrated that H. calcicola is a synonym of H. chiangdaoensis. The species was previously compared with H. sibthorpioides; our phy...

Genetic diversity is one level of biodiversity that is very importan for the resilience of biota in the face of environmental pressures such as cilmater change. However, information on the genetic diversity of red snapper in Kaimana water is still very limited. This study determines the genetic diversity of red snapper (Lutjanus erythropterus) in K...

A rich fossil record of teeth shows that many living shark families’ origins lie deep in the Mesozoic. Skeletal fossils of the sharks to whom these teeth belonged are far rarer and when they are preserved are often flattened, hindering understanding of the evolutionary radiation of living shark groups. Here we use computed tomography to describe tw...

Spinach is a globally cultivated leafy vegetable facing challenges in production, notably bolting, and the premature initiation of flowering. Hence, this study aims to provide genomic insights into spinach bolting through Tajima’s D test, transition-to-transversion rate analysis, Principal Component Analysis (PCA), and phylogenetic analysis. Ten sp...

Background Although methicillin-resistant Staphylococcus aureus (MRSA) transmission has traditionally been viewed separately in hospital and community settings, this distinction is increasingly blurred. We used whole-genome sequencing and epidemiologic analyses to characterize the movement of MRSA across these interfaces in a rural-urban population...

Key message Miconia predominantly accumulates Al regardless of soil saturation, though certain clades within this high-accumulating group may exhibit distinctly lower Al concentrations in their leaves. Abstract In acidic soils (pH < 5.0), aluminum (Al) occurs as Al³⁺, which is toxic to most plants. Tolerant species include Al avoiders and those th...

HIV exhibits significant genetic diversity, with genetic recombination being a major evolutionary process. The co‐circulation of HIV‐1/M and HIV‐1/O variants has led to the description of 20 HIV‐1/M+O dual infections since 1998. Despite the genetic divergence between these variants, HIV‐1/M+O dual infections have resulted in the emergence of HIV‐1/...

This study aimed to investigate the prevalence and phylogenetic characteristics of Human T-cell lymphotropic virus type 1 (HTLV-1) among blood donors in Jiroft Province, southeast Iran, a region previously under-studied regarding this virus. A total of 405 blood donor samples were collected from six cities within Jiroft Province. Serum samples were...