Search Results (826)

As the second largest order of Insecta, Lepidoptera is an important component of the ecosystems. However, there are few data on the mitochondrial genomes of Saturniidae. Here, the complete mitochondrial genome of Cricula andrei was sequenced and characterized. It was 15,324 bp in length, containing 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs and a control region (AT-rich region). The control region had an AT content of 90.40%, and the conserved ATAGA sequence guided a 19 bp poly-T. Amino acid composition analysis showed that Ile, Leu, Phe and Asn were the most frequent amino acids, and codon usage analysis revealed a preference for A/U-ending codons. Phylogenetic trees constructed by Bayesian inference and Maximum likelihood methods indicated that C. andrei is grouped with C. trifenestrata and supported the current taxonomic placement of Cricula within the family. The enrichment of the mitochondrial genome database of Lepidoptera will help to better understand the genetic and evolutionary relationships of lepidopteran populations, as well as related taxonomic issues. Full article

After several revisions, Littorinimorpha has been classified as an order-level taxonomic unit under the subclass Heterobranchia of the class Gastropoda, but its suborder classification system remains controversial. In this study, high-throughput sequencing technology was used to obtain the complete mitochondrial genomes of three species from Stromboidea and Tonnoidea: Doxander vittatus, Tonna chinensis, and Phalium glaucum. Genome analysis revealed that the genomes of these three species are highly consistent in structure. They all contain 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes and lack a typical long non-coding control region. The phylogenetic tree constructed based on PCGs shows that Tonnoidea is a monophyletic group within Littorinimorpha, while Stromboidea is a paraphyletic group. Vermetoidea was identified as a separate evolutionary branch under this order. The present study clarifies the mitochondrial genomic characters of three species, D. vittatus, T. chinensis and P. glaucum and their positions in Littorinimorpha, which provides an important basis for evolutionary and phylogenetic studies of this order. Full article

Hosta ventricosa, also known as blue plantain lily, is an important traditional herbal medicinal and ornamental plant in China. Prior to this study, no virus has been reported to infect H. ventricosa plants. Based on RNA-seq, transmission electron microscopy, and RT-PCR analyses, we have demonstrated that the H. ventricosa plant showing leaf chlorosis, mottle, mosaic, and crinkling symptoms was co-infected with hosta virus X (HVX) and a novel luteovirus, which we tentatively named hosta ventricosa luteovirus (HVLV). The genome of HVLV is a 5723 nt long, positive-sense, and single-stranded RNA with seven open reading frames (ORFs). Phylogenetic analysis based on the amino acid (aa) sequence of the viral RNA-dependent RNA polymerase (RdRp) revealed that HVLV is clustered within the genus Luteovirus. The HVLV RdRp shares 9.75–45.17% aa sequence identity with the 14 closely related luteoviruses. The P1–2 and P3–5 proteins of HVLV were identified as potential viral pathogenicity determinants through the PVX heterologous expression in Nicotiana benthamiana plants. Moreover, P2, P5 and P3–5 proteins of HVLV have been found to exhibit RNA silencing suppression activities. Additionally, we have successfully constructed an infectious cDNA clone of HVLV and uncovered that this infectious cDNA clone can infect N. benthamiana plants through agroinfiltration. These findings have expanded our understanding of luteoviruses and their host range. Full article

Quantitative phylogenetics in historical linguistics has relied almost entirely on lexical cognate data. This study asks a different question: how much genealogical signal can be recovered from structural features extracted from annotated corpora, and whether it survives at deep time depths. We compute 29 structural features—including Shannon entropies of dependency direction and of dependency-relation distributions, relation-specific directionality ratios, dependency-distance measures, and constructional ratios—across 25 Transeurasian languages from the five proposed groups (Turkic, Mongolic, Tungusic, Japonic, and Koreanic) and three outgroups (Chinese, Vietnamese, and Hindi), 28 languages in all. Most of the Tungusic and Mongolic languages have no running-text corpus, so we built new Universal Dependencies treebanks for them by glossing example sentences from reference grammars; thirteen are used here. Each feature was tested for phylogenetic signal (Pagel’s λ and Blomberg’s K, with FDR correction) under four competing reference topologies, and the features that passed were used for tree inference (Bayesian inference in MrBayes, with Neighbor-Joining as a check). The same pipeline was first run on Indo-European in a companion study, where it recovers only individual subgroups and does not resolve a stable tree. At the depth proposed for the Transeurasian family (a Proto-Transeurasian root of about 9000 years before present), the structural signal was not enough to reconstruct the family’s internal relationships. The signal tests favoured a flat three-way division of the major branches (7 strict/20 relaxed features) over any nested hypothesis (≤2 strict features each), and the strongest signal lay in core word-order parameters (e.g., object direction, λ = 1.00, K = 6.06). But both Bayesian and distance-based inference returned near-complete polytomies: although the chains converged (ASDSF < 0.01), no branch reached a posterior probability above 0.75, and none of the three multi-language branches (Turkic, Mongolic, or Tungusic) was recovered. The outgroup test made the reason clear: Hindi, which is Indo-European but SOV, grouped with the head-final Transeurasian languages rather than with the other two (head-initial) outgroups, so the features are tracking typological similarity, not shared descent, at this depth. The study contributes 13 new treebanks for poorly documented languages, a reproducible framework for testing how much genealogical signal structural features carry, and direct evidence that, at Transeurasian time depths, this signal reflects typology rather than genealogy. Full article

Hexi cattle are a local cattle population endemic to the Hexi Corridor in Gansu Province, China, and exhibit strong adaptability to the region’s arid continental environment. However, comprehensive genomic investigations of this population are still lacking. In the present study, we integrated population genomic analyses with a genome-wide association study (GWAS) to dissect the genetic architecture of Hexi cattle. Whole-genome resequencing data were generated for 264 Hexi cattle, and public genomic datasets from six representative cattle breeds were obtained from the NCBI database for comparative analysis. Multiple analytical approaches—including principal component analysis (PCA), linkage disequilibrium (LD) decay analysis, neighbor-joining (NJ) phylogenetic tree construction, and ADMIXTURE analysis—were adopted to evaluate population structure and evolutionary relationships. A mixed linear model was then used to identify significant SNPs associated with five major body conformation traits in six-month-old cattle: body weight (BW), withers height (WH), hip height (HH), heart girth (HG), and abdominal girth (AG). Our results confirm the admixed nature of Hexi cattle, whose genome is derived primarily from Simmental cattle and secondarily from Mongolian cattle. A total of 69 trait-associated significant SNPs were identified and functionally annotated. Specifically, TBC1D31, DERL1 and MCPH1 were linked to BW; FSCN3 and PLBD1 to WH; MCPH1 to HH; NPAS3, TBC1D31, DERL1 and MCPH1 to HG; and SOX5, NTAQ1, FAM83A, TBC1D31, DERL1, CDH11, CPLX4 and ADAM18 to AG. This study deepens our understanding of the genetic basis of growth traits in Hexi cattle and offers valuable molecular resources for future selective breeding, genetic improvement, and long-term conservation of this indigenous cattle population. Full article

Pepper breeding in China faces challenges including narrow genetic backgrounds, variety homogenization, and authenticity issues in the seed market. The original SSR-based variety identification system (NY/T 2475-2013) has limitations such as low polymorphism and uneven marker distribution, failing to meet current efficiency requirements. In this study, 240 pepper varieties were used. Fluorescent capillary electrophoresis was employed to analyze issues in the original system. A total of 150 SSR primer pairs was screened using eight phenotypically distinct varieties, followed by rescreening with 96 varieties from different origins. After marker optimization, a new identification system was established, validated using 144 varieties, and a DNA fingerprint database was constructed. Phenotypic experiments were conducted to evaluate applicability. The new system comprises 26 core primer pairs: 12 newly selected and 14 retained from the original standard. These primers are evenly distributed across chromosomes, with annealing temperatures optimized to 57 °C and grouped into seven multiplex panels. Across 240 pepper varieties, the 26 primer pairs detected 153 allelic variants and 293 genotypes. Average polymorphism information content (PIC) increased from 0.43 to 0.49 compared to the original system, and the discrimination efficiency reached 99.975% among 28,680 pairwise variety combinations. Phylogenetic and population structure analyses divided the 240 pepper varieties into six groups. Varieties with molecular genetic distance approaching zero showed high phenotypic similarity. The newly developed SSR-based system demonstrated excellent performance and strong applicability. It can be used for authenticity and purity identification, parentage testing, and auxiliary selection in DUS testing, supporting new variety rights protection and providing technical support for standardized management of the pepper seed industry. Full article

Apple Valsa canker disease, caused by Valsa mali, is one of the most destructive diseases of apple trees in China and seriously threatens the sustainable development of the apple industry. VmSom1 acts as a core transcription factor in the cyclic adenosine monophosphate/protein kinase A (cAMP/PKA) signaling pathway and regulates vegetative growth, development and pathogenicity of this phytopathogen. Transcriptome analysis was performed using the VmSom1 deletion mutant and the wild-type strain sdau11-175, and a significantly differentially expressed transcription factor, VmGAL4, was identified. In this study, the single-gene deletion mutant ΔVmGAL4 and the double-gene deletion mutant ΔVmSom1/VmGAL4 were constructed via homologous recombination, aiming to preliminarily explore the interaction between these two genes. Sequence analysis revealed that the VmGAL4 protein contains a conserved fungal_TF_MHR domain spanning amino acids 164 to 614. Phylogenetic analysis indicated that VmGAL4 shares the closest phylogenetic relationship with homologs from Cytospora schulzeri and Cytospora chrysosperma. Phenotypic assays demonstrated that the VmGAL4 deletion mutant exhibited markedly reduced mycelial growth rate and fewer pycnidia production. Additionally, the mutant displayed enhanced sensitivity to cell wall inhibitors and osmotic stress agents, along with significantly increased capacity to utilize various carbon and nitrogen sources and decreased pathogenicity compared with the wild-type strain. Compared with the single deletion mutant ΔVmSom1, the double mutant ΔVmSom1/VmGAL4 partially rescued the growth defects and also alleviated the reduction in pathogenicity to a certain extent. Nevertheless, conidial production remained severely inhibited in the double mutant. Collectively, VmGAL4 is involved in the regulation of vegetative growth, asexual development, cell wall integrity, osmotic stress response, carbon and nitrogen source utilization, and pathogenicity in V. mali. Full article

The DUF538 gene family, harboring unknown functional proteins, has been reported to take active roles in plant development and response to adversities, while few studies of genome-wide identification and functional verification have been performed in cotton. Hence, two ancestral diploid species, G. arboretum and G. raimondii, and two cultivated tetraploid ones, G. hirsutum and G. barbadense, were chosen in this study to investigate the cotton DUF538 gene family, resulting in 37, 37, 70, and 70 members identified, respectively. A phylogenetic tree was constructed on these cotton DUF538 genes, together with 22 A. thaliana ones, which were divided into seven groups unevenly distributed across nearly all chromosomes. High-degree conservatism, while rich in diversity, was separately observed in gene structure and conserved motif analyses between the same groups and different groups, and a great number of gene-replication events were detected from intraspecific and interspecific collinearity analyses, implying this was the driving force for DUF538 family expansion. Multiple cis-acting elements relevant to adversity-stress responses were found in the promoter region, which were consistent with the transcriptome expression analyses in response to low-temperature and drought stress and Verticillium wilt infection. Coincidentally, GhDUF538-7 showed the core position in the protein–protein interaction network and was identified in the overlapping region of the interval of four reported VW resistance-related QTLs. The gene function of GhDUF538-7 was verified via gene cloning, relative expression-pattern detection, and virus-induced gene silencing (VIGS) experiment. The TRV:DUF538-7 plants showed more serious VW symptoms, significantly severe disease indices, relatively higher fungal biomass, and increased brown vascular bundles compared with TRV:00 plants. Significantly lower expression levels of marker genes PR4 and MYC2 in jasmonate signaling pathways indicated GhDUF538-7 as a potentially positive regulatory factor in plant defense via hormone signal transduction. This study not only broadened the research perspective of evolution and functional differentiation of the cotton DUF538 gene family, but it also revealed the cooperative relationship between DUF538-7 and the JA pathway for further molecular mechanisms of cotton resistance to VW infection. Full article

We develop a non-Archimedean framework for the representation and analysis of genomic sequences based on the arithmetic and geometric structure of the ring of 5-adic integers. The proposed approach associates RNA sequences with points in a compact ultrametric space through an injective symbolic-to-arithmetic embedding that transforms genomic information into a hierarchical geometric object. We prove that the embedding is a global isometry between a natural symbolic prefix metric and the induced 5-adic metric, and we show that its image forms a compact Cantor-type subset of ${\mathbb{Z}}_5$. Building upon this representation, we formulate a continuous-time evolutionary model governed by a Vladimirov pseudo-differential operator. The resulting non-Archimedean diffusion equation provides a mathematically rigorous mechanism for describing evolutionary transitions across hierarchical genomic scales and admits an explicit fundamental solution obtained through 5-adic Fourier analysis. We further introduce a finite-resolution projection onto quotient rings of ${\mathbb{Z}}_5$ and develop an alignment-free phylogenetic inference framework based directly on the 5-adic valuation. The induced distance function is ultrametric and naturally encodes hierarchical relationships through shared symbolic prefixes. The proposed construction establishes a bridge between p-adic analysis, ultrametric geometry, pseudo-differential operators, and computational phylogenetics. As an illustration, we discuss its application to Hantavirus genomic sequences, demonstrating how hierarchical evolutionary organization can be represented within a unified non-Archimedean mathematical framework. Full article

In this study, we constructed a comparative genomic framework encompassing 57 genome sequences from four key taxonomic groups—Bacillariophyta, Parmales, choanoflagellates, and Bacillus—all of which possess either siliceous cell walls or silicon-transporting vesicle structures. By comparing these genomes with those of non-silicified species, including Chlorophyta, Streptophytes, Rhodophyta, and Dinoflagellates, we systematically analyzed the evolutionary distribution patterns of genes involved in silicon transport, silicification, and related processes across eukaryotes. Through orthogroup clustering and phylogenetic analysis, we identified 75 orthogroups universally conserved across all 57 species (including representing siliceous and non-siliceous groups), and an additional 105 orthogroups consistently present across the four silica-bearing lineages (Bacillariophyta, Parmales, choanoflagellates, and Bacillus), which were predominantly enriched in fundamental metabolic pathways. Furthermore, by integrating 120 known siliceous cell wall-related protein sequences, we identified three orthogroups broadly distributed across the four major lineages, suggesting an ancient evolutionary origin of certain silicon-related genetic components. Our findings provide genomic insights into the evolutionary trajectory of siliceous cell wall-associated genes and offer a valuable resource for future studies on biomineralization in eukaryotes. Full article

Neurospora crassa is a widely distributed ascomycete with high genetic diversity, yet reliance on limited reference genomes has hindered a comprehensive understanding of its genetic landscape. To address this limitation, we integrated the functional annotation of the FGSC2225 genome with a comprehensive comparative genomic analysis of N. crassa strains. FGSC2225 gene and transposable element (TE) proportions mirrored those of FGSC2489, though TE levels were significantly higher than those in sister species Sordaria macrospora. Phylogenetic analysis resolved the N. crassa population into two primary lineages: Clade A (including FGSC2489 and FGSC2225) and Clade B (including FGSC4830), with the former exhibiting larger genome sizes. Leveraging de novo assemblies of 72 high-quality draft genomes, we constructed a comprehensive pangenome to investigate the molecular evolution of various gene families. For example, systematic phylogenetic analysis of the HET-domain-containing gene family and three stress-related families—heat shock transcription factor, basic leucine zipper, and Cytochrome P450—demonstrated varying degrees of conservation and presence/absence variation across the lineages. Addressing the limitations of current genomic resources, this work provides a pangenomic framework to detect rapid adaptive evolution in filamentous fungi. This methodology serves as a robust template for identifying transcription factors, effectors, and structural variations critical to stress response and virulence in diverse fungi. Full article

Dengue fever represents a significant public health challenge in Saudi Arabia, yet comprehensive molecular characterization of circulating serotypes remains limited. This study combines epidemiological and phylogenetic analyses to understand dengue virus (DENV) dynamics in the Kingdom. A systematic review and meta-analysis of dengue epidemiological data from Saudi Arabia (1992–2026) was the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. All available DENV envelope (E) gene sequences from Saudi human cases (1992–2023) were retrieved from GenBank and Global Initiative on Sharing All Influenza Data (GISAID). Phylogenetic trees were constructed using maximum likelihood with 1000 bootstrap replicates and best-fit models. Selection pressure was analyzed using SLAC, FEL, FUBAR, and MEME methods, while glycosylation sites were predicted with NetNGlyc and NetOGlyc. The pooled seroprevalence from 25 studies (n = 32,393) was 40.71% (95% CI: 26.96–56.10%). DENV-2 predominated (80.25%), followed by DENV-1 and DENV-3, with DENV-4 remaining rare (0.42%). Males (67–78%) and adults aged 25–44 years were most affected. Phylogenetic analysis of 50 Saudi isolates showed DENV-1 strains clustered within American–African (1994) and Asian (2004–2011) genotypes, all DENV-2 within the Cosmopolitan genotype, and all DENV-3 within Genotype III (bootstrap support 99–100%). Selection pressure analysis indicated pervasive positive selection in DENV-2, episodic selection across serotypes, and strong purifying selection in the E gene. Several amino acid substitutions with potential functional importance were identified. No DENV-4 E gene sequences from Saudi Arabia are publicly available. Dengue in western Saudi Arabia is characterized by DENV-2 predominance, co-circulation of three serotypes, and multiple introductions. The absence of DENV-4 sequences highlights critical surveillance gaps. Sustained molecular surveillance, expanded genomic sequencing, and data sharing are essential for effective prevention and vaccine preparedness. Full article

GRAS transcription factors are crucial regulators governing plant growth and stress adaptation, yet no systematic genome-wide investigation of the GRAS gene family has been reported for coriander, celery and carrot, three economically and medicinally important Apiaceae vegetables, which creates a critical research gap for comparative and functional genomics in Apiales. Here, we performed a multi-tiered bioinformatic pipeline integrating gene identification, phylogenetic classification, chromosomal mapping, gene duplication analysis, transcriptome profiling, co-expression network construction and large-scale evolutionary tracing across 406 plant genomes. In total, 87, 74 and 74 GRAS genes were identified from coriander, celery and carrot, respectively, which were divided into 13 subfamilies. WGD/segmental duplication drove GRAS expansion in coriander and carrot, while dispersed duplication dominated in celery. Tissue-specific expression and cross-TF regulatory networks uncovered core GRAS hub genes participating in developmental and stress pathways. Wide-range phylogeny further validated that GRAS genes originated from Zygnematophyceae algae and massively expanded in Penium margaritaceum. This study fills the research gap of GRAS family analysis in Apiaceae, provides abundant high-throughput data resources, and offers fundamental evolutionary clues for future functional verification and genetic improvement of horticultural crops. Full article

Vesicular stomatitis virus (VSV) causes clinical disease in livestock that mimics Foot-and-Mouth Disease, necessitating its status as a reportable pathogen to the World Organization for Animal Health. Given the importance of accurate classification for epidemiological surveillance, this study aims to update VSV taxonomic organization using whole-genome sequence criteria to better monitor disease dynamics. Using phylogenetic analysis and the Species Demarcation Tool (SDT), we analyzed pairwise identity across publicly available sequences, constructing a rooted maximum likelihood tree to cluster strains based on robust genetic identity scores. The results demonstrate that nucleotide divergences exceeding 30% define distinct species within the Vesiculovirus genus. Within a species, divergences between 10% and 30% successfully delineate genotypes, while differences between 6% and 10% identify specific subtypes. These quantitative benchmarks provide a precise framework for viral classification, significantly enhancing genomic surveillance and the ability to track the evolution and transmission of VSV genotypes and subtypes across diverse geographic regions. Full article

The glycine-aspartic acid-serine-leucine (GDSL) esterase/lipase family is a functionally diverse group of hydrolytic enzymes involved in multiple plant biological processes, including stress adaptation and development. However, its evolutionary patterns, functional conservation, and stress-responsive mechanisms in grasses remain not fully elucidated. In this study, a comprehensive comparative genomic analysis was performed on the GDSL gene family across nine representative grass species and Arabidopsis thaliana. Genome-wide identification, phylogenetic analysis, duplication pattern detection, synteny analysis, cis-regulatory element prediction, protein–protein interaction (PPI) network construction, and RNA-seq-based expression profiling were employed. A total of 1707 GDSL genes were identified, with substantial expansion in grasses, especially hexaploid wheat. Whole-genome and segmental duplications were the major drivers of family expansion, with most duplicated genes under strong purifying selection. A grass-specific clade (C3-2) was identified, and extensive syntenic conservation was observed among closely related grasses. Promoter analysis revealed enrichment of stress- and hormone-responsive cis-elements, and RNA-seq showed dynamic GDSL expression under low-temperature stress in rice and wheat. These findings demonstrate that the expansion of the GDSL gene family in grasses is driven by polyploidization and lineage-specific duplication, accompanied by the emergence of a grass-specific clade (C3-2) and regulatory diversification, collectively shaping stress-responsive evolutionary innovation in Poaceae. Full article