Search Results (2,420)

SHORT INTERNODE (SHI)-Related Sequence (SRS) transcription factors play crucial roles in plant growth, development, and stress responses and have been extensively studied in various plant species. However, the molecular functions and regulatory mechanisms of SRS genes in the economically important tropical fruit crop pitaya (Hylocereus undatus) remain poorly understood. This study identified 9 HuSRS genes in pitaya via bioinformatics analysis, with subcellular localization predicting nuclear distributions for all. Gene structure analysis showed 1–4 exons, and conserved motifs (RING-type zinc finger and IXGH domains) were shared across subclasses. Phylogenetic analysis classified the HuSRS genes into three subfamilies. Subfamily I (HuSRS1–HuSRS4) is closely related to poplar and tomato homologs and subfamily III (HuSRS6–HuSRS8) contains a recently duplicated paralogous pair (HuSRS7/HuSRS8) and shows affinity to rice SRS genes. Protein structure prediction revealed dominance of random coils, α-helices, and extended strands, with spatial similarity correlating to subfamily classification. Interaction networks showed HuSRS1, HuSRS2, HuSRS7 and HuSRS8 interact with functional proteins in transcription and hormone signaling. Promoter analysis identified abundant light/hormone/stress-responsive elements, with HuSRS5 harboring the most motifs. Transcriptome and qPCR analyses revealed spatiotemporal expression patterns: HuSRS4, HuSRS5, and HuSRS7 exhibited significantly higher expression levels in callus (WG), which may be associated with dedifferentiation capacity. In seedlings, HuSRS9 exhibited extremely high transcriptional accumulation in stem segments, while HuSRS1, HuSRS5, HuSRS7 and HuSRS8 were highly active in cotyledons. This study systematically analyzed the characteristics of the SRS gene family in pitaya, revealing its evolutionary conservation and spatio-temporal expression differences. The research results have laid a foundation for in-depth exploration of the function of the SRS gene in the tissue culture and molecular breeding of pitaya. Full article

High temperatures are one of the most important abiotic stressors affecting the survival and growth of American shad (Alosa sapidissima). Building on previous omics sequencing studies of A. sapidissima liver and gills under high temperature stress, this study focused on investigating the regulatory role of miR-1236-3p and its target gene hsp90b1. The results indicate that the full-length cDNA of the hsp90b1 gene is 2023 bp and comprises a 5’ end of 58 bp, a 3’ end of 84 bp, and a coding region of 1881 bp, encoding 626 amino acids. Sequence alignment and phylogenetic tree analysis reveal that the hsp90b1 sequence is highly conserved across species. In situ hybridization showed that hsp90b1 is mainly localized in the cytoplasm. Software prediction identified a potential binding site between miR-1236-3p and hsp90b1. Through the construction of wild-type and mutant 3’UTR hsp90b1 dual luciferase reporter plasmids, the targeted relationship between the two was confirmed. In addition, the spatiotemporal expression levels of the hsp90b1 was found to be highest in the multicellular stage and liver tissue at a cultivation temperature of 27 °C; miR-1236-3P was highly expressed in the hatching stage and heart tissue at 30 °C. These findings provide a theoretical foundation for further investigating the regulatory role of non-coding RNA in A. sapidissima heat stress and offer data for subsequent molecular breeding studies. Full article

Objective: This study conducted a comprehensive analysis of molecular transmission networks and pretreatment drug resistance (PDR) in newly diagnosed HIV-1 infections in Taizhou, China. Methods: From 2021 to 2023, we collected 1126 plasma samples from newly diagnosed HIV patients in Taizhou. The HIV pol gene was amplified, and the obtained sequence was used to construct a maximum likelihood (ML) phylogenetic tree and molecular transmission network. PDR-related mutations were analyzed based on the Stanford University HIV Resistance Database. We conducted genotyping analysis and analysis of factors related to the larger clusters (≥10). Results: We successfully amplified and sequenced the pol region from 937 (83.2%, 937/1126) treatment-naïve HIV-1 patients, each with comprehensive epidemiological documentation. Phylogenetic characterization revealed significant subtype heterogeneity, with CRF07_BC (42.1%, 395/937), CRF01_AE (27.6%, 259/937) and CRF08_BC (22.1%, 209/937) being the most prevalent. Notably, 11.4% of the sequenced population (107/937) presented detectable PDR mutations. Univariate analysis revealed that larger clusters (≥10) are more inclined to be aged ≥60, divorced or widowed, have high or technical secondary school education, and have sexual contact with homosexuality. Multivariate analysis revealed that age ≥60 years and not having a PDR mutation (p < 0.05) were factors associated with larger clusters (≥10). Conclusions: Molecular transmission networks suggest that CRF08_BC is spreading rapidly among the older male population. Consequently, targeted interventions aimed at this population are crucial for halting the ongoing rapid dissemination of this subtype. Full article

The increasing reliance on imported fish products in Kazakhstan raises concerns about the presence of fish-borne parasitic infections, particularly zoonotic helminths that pose risks to public health. This study aimed to assess the diversity and prevalence of helminths in commercially imported marine fish using both traditional and molecular diagnostic methods. A total of 670 specimens representing 17 fish species were collected from retail markets in Astana, Almaty, and Karaganda. Macroscopic inspection and muscle compression techniques were used to detect larval parasites, followed by DNA extraction and PCR amplification targeting the ITS-2, 5.8S, 18S rRNA, and mitochondrial COX gene regions. Sequencing and phylogenetic analysis confirmed the presence of cestodes (Eubothrium crassum, Hepatoxylon trichiuri, Nybelinia surmenicola), acanthocephalans (Echinorhynchus gadi), and nematodes, with a predominance of zoonotic species from the Anisakidae family, including Anisakis simplex, A. pegreffii, Pseudoterranova decipiens, and Contracaecum osculatum. The highest levels of infection were detected in Atka mackerel (97.1%), herring (96.0%), mackerel (92.0%), and blue whiting (88.1%), while the lowest rates were recorded in smelt (6.8%), flounder (10.2%), and haddock (16.0%). This is the first molecular-based survey of fish helminths in Kazakhstan and highlights the need to integrate genetic screening into food safety control systems to better protect consumers and improve parasite monitoring of imported seafood. Full article

Chicken infectious anemia virus (CIAV) causes immunosuppression in poultry, leading to substantial global economic losses through both vertical and horizontal transmission. Since 2014, frequent outbreaks have been reported in southern China; however, the epidemiology of CIAV in Guangdong Province remains poorly defined. Between July 2018 and March 2022, we collected 105 tissue samples and 786 serum samples from poultry in nine cities. PCR/qPCR assays targeting the VP1 gene confirmed CIAV infection, and positive tissues inoculated into MSB1 cells yielded four isolates (GDHZ1, GDHZ2, GDJM, GDLF). Phylogenetic analysis demonstrated that GDHZ1, GDJM, and GDLF clustered within clade A1, whereas GDHZ2 belonged to clade A2. All isolates shared glutamine (Q) at position 394, together with virulence-associated amino acid signatures (75V, 89T, 125L, 139K, 141Q, 144E). Serological testing indicated a high prevalence, with 627 of 786 samples positive (79.77%). The relatively low proportion of virus-positive tissues and successful isolations may reflect viral tropism or limitations in detection sensitivity. These findings enhance understanding of CIAV molecular epidemiology in Guangdong and provide evidence to inform surveillance, vaccination strategies, and control measures. Full article

Vitamin B6 is an essential coenzyme involved in various metabolic processes critical for plant growth and development. However, its biosynthesis and regulatory mechanisms remain poorly understood in the ancient gymnosperm Ginkgo biloba. In this study, we identified two members of the PDX2 gene family (Gb_34755 and Gb_34990) through genome-wide analysis and characterized their molecular and functional properties. Bioinformatic analysis revealed distinct physicochemical traits and subcellular localizations, with Gb_34755 predicted in the cytoplasm and Gb_34990 in both chloroplasts and cytoplasm. Both proteins contain the glutaminase-related PLN02832 domain, indicating involvement in VB6 biosynthesis. Chromosomal mapping placed the genes in transcriptionally active regions on chromosomes 6 and 9. Phylogenetic analysis showed close evolutionary relationships between Ginkgo PDX2 genes and those in ferns and gymnosperms, distinct from angiosperms. Promoter analysis revealed differential enrichment of cis-elements: Gb_34990 harbored low-temperature and salicylic acid-responsive elements, while Gb_34755 showed motifs related to development. Gene expression profiling indicated significant upregulation (p < 0.05) of both genes during the late developmental stages of Ginkgo kernels, coinciding with peak VB6 content. Functional validation via transient overexpression in Nicotiana benthamiana confirmed a positive regulatory role, with VB6 levels increasing from 3.38 μg/g to 12.17 μg/g (p < 0.05). This study provides the first comprehensive functional analysis of the PDX2 gene family in Ginkgo and confirms their critical role in VB6 biosynthesis. These findings enhance our understanding of vitamin metabolism in gymnosperms and present promising targets for metabolic engineering in plants. Full article

Background/Objectives: Miscanthus Andersson, a genus of perennial grasses that includes wild relatives of key crop species, remains poorly characterized in terms of genetic diversity and evolutionary relationships. The aim of this study was to elucidate the phylogenetic structure of Miscanthus through comparative genomic analysis of the chloroplast genomes of six Korean species. Methods: Complete chloroplast genomes were assembled and analyzed for six Miscanthus species. Informative nucleotide motifs and their associated gene locations were identified as potential markers, and their phylogenetic relationships with related crops were examined. Results: The chloroplast genomes exhibited a conserved quadripartite structure, with genome sizes and GC contents within typical ranges. Analysis of codon usage showed a preference for A/U-ending codons, consistent with patterns in other angiosperms. Simple sequence repeats and long repeats demonstrated non-random distributions, indicating their value as molecular markers for phylogenetic and population studies. Comparative analyses confirmed structural conservation across Miscanthus species, whereas variation in non-coding regions provided important phylogenetic signals. Phylogenetic reconstruction based on 21 chloroplast genomes revealed four major clades, corroborating previous findings and highlighting complex evolutionary relationships within Miscanthus, including close affinities between African and Himalayan species and the genus Saccharum L. Conclusions: This study provides complete chloroplast genomes of six Miscanthus species, contributing to enhanced understanding of the relationships within the subtribe Saccharinae. The findings support the inclusion of Miscanthus species in the Korea Crop Wild Relatives inventory and highlight their potential as a genetic resource for breeding programs aimed at enhancing crop resilience to environmental stress. Full article

The present study is focused on a newly isolated Fomitopsis strain obtained from black pine (Pinus nigra) from the Sredna Gora Mountains, Bulgaria. Molecular identification, based on ITS1-5.8S-ITS2 region sequencing, confirmed the strain as Fomitopsis pinicola with 99.84 BLAST percent identity. Phylogenetic analysis verified that the new fungal isolate belongs to the European F. pinicola clade. The morphological analysis of the strain revealed several distinctive structures that further support its identification. The influence of culture media composition on fungal development was evaluated by analyzing the mycelial growth kinetics using both the logistic growth model and the reversible autocatalytic model. Submerged cultivation was employed to produce fungal biomass, which was subsequently lyophilized and used for the assessment of the antimicrobial potential of the fungal strain. The results demonstrated notable antimicrobial effects against all tested bacterial strains. The most significant activity was observed for the aqueous extract against Escherichia coli and the hexane extract against Salmonella enteritidis, both with a minimum inhibitory concentration of 312.5 µg/mL. These findings highlight the promising potential of the newly isolated F. pinicola strain for future applications in the medical and pharmaceutical industries, particularly in developing drugs to combat multidrug resistance, based on the promising results of its water extracts. Full article

Safflower (Carthamus tinctorius L.) is a multipurpose economic crop. Flavonoid glycosides are its key bioactive constituents, and several glycosyltransferases involved in their biosynthesis have been identified. The glycosyltransferase 84 subfamily represents a specialized branch with diverse functions, involved not only in catalyzing flavonoid glycosylation but also in the biosynthesis of auxins, tannins, and other compounds. However, this subfamily remains poorly characterized in safflower. In this study, two UGT84 subfamily genes, UGT84A28 and UGT84B3, were screened based on expression patterns and phylogenetic evolution analysis. Recombinant proteins were induced and purified using prokaryotic expression systems. Functional characterization was subsequently conducted through enzymatic assays in vitro and transient expression in tobacco leaves. Molecular docking was employed to investigate the binding modes of UGTs with UDP-glucose. The results indicated that both UGTs demonstrated glycosylation activity at the flavonoid 7-OH position. Notably, when luteolin was employed as the aglycone, both enzymes also exhibited 3′-O-glycosylation activity. Combined with amino acid sequence alignment, we propose that residues A351/T343 and G263/F254, which affect spatial conformation and hydrogen bonding ability, may be one of the reasons for the functional differences between these two enzymes. These findings provide new insights into the catalytic diversity of glycosyltransferases. Full article

Utilizing the COI barcoding approach, cryptic diversity has previously been detected within the morphologically recognized Simulium (Gomphostilbia) trangense Jitklang, Kuvangkadilok, Baimai, Takaoka & Adler, 2008 and S. (G.) sheilae Takaoka & Davies, 1995, of the S. (G.) ceylonicum species-group. Here, an unknown black fly species belonging to the S. ceylonicum species-group from southern Thailand was discovered and described as a new species, S. (G.) sipoense sp. nov. In addition, S. (G.) trangense is herein fully redescribed based on specimens collected from its type locality. Based on an integrative taxonomic approach combining morphological and molecular data, the validity of the newly described S. sipoense sp. nov. and the redescribed S. trangense is confirmed. Comparative morphological characteristics and phylogenetic analysis, inferred from COI sequences, suggest that the new species is conspecific with the species redescribed as S. trangense, using specimens collected from Malaysia, and is morphologically and phylogenetically closely related to S. sheilae, particularly to the specimens from Indonesia. The redescribed S. trangense is genetically highly similar or even identical to the species that was apparently misidentified as S. sheilae from southern and western Thailand, and is morphologically very similar to the new species, from which it is clearly distinguished by the relative length of the female claw tooth, shape of the male ventral plate, and color of the larval body. A detailed information on the morphological characteristics separates the new species, and the redescribed S. trangense from all other known species of the same species-group in Thailand and neighboring countries is provided. Further studies are warranted to clarify the taxonomic status of several cryptic species recognized within the morphologically defined S. trangense and S. sheilae. Full article

Andrenidae is a major pollinator lineage with considerable ecological importance, yet limited molecular resources have impeded comprehensive understanding of its evolutionary history. This study sequenced and assembled five mitogenomes of Andrenidae, which were collected from Xizang, Tibet. Analyses included sequence size, nucleotide composition, Ka/Ks ratios, and gene rearrangements. The assembled mitogenomes ranged from 15,631 to 18,506 bp in length. AT content (%) varied between 74.46 and 79.85. Relative synonymous codon usage analysis revealed that AUU, UUA, UUU, and UUA were the most frequently preferred codons. All 13 protein-coding genes displayed Ka/Ks values below one, with ATP8 showing the highest ratio and COX1 the lowest. Gene rearrangements occurred in all mitogenomes, and three distinct tRNA rearrangement patterns were detected. This study provided more available molecular data for future evolutionary biology studies of Andrenidae. Additionally, 24 previously published Apoidea mitogenomes (three outgroups and 26 ingroups) were incorporated to infer phylogenetic relationships using Maximum Likelihood and Bayesian Inference methods. The results supported Melittidae as the basal lineage of bees, while Andrenidae was recovered as the sister clade to Halictidae + Colletidae. Full article

Wild carnivores are increasingly recognized as hosts or reservoirs of canine parvovirus (CPV), a major pathogen of dogs. To investigate CPV circulation in Central Europe, we examined 221 red foxes (Vulpes vulpes) and 53 European badgers (Meles meles) from seven Slovakian regions. Small intestines (n = 86), rectal swabs (n = 123), and feces (n = 65) were tested by real-time PCR, and positives were sequenced for the VP2 gene. Virus isolation was performed on MDCK cells. CPV was detected in 10.9% (30/274) of samples, with a prevalence of 10.9% (24/221) in foxes and 11.3% (6/53) in badgers. Phylogenetic analysis revealed co-circulation of CPV-2a, CPV-2b, and CPV-2c, with CPV-2b being prevalent (20/30, 66.7%) and CPV-2c detected in a single sample (1/30, 3.3%). CPV-2a/2b isolates clustered with European strains, while CPV-2c grouped within the “Asian” lineage. Several sequences carried “Asian-like” signatures (5G, 267Y, 324I, 370R), suggesting transboundary introduction and spillover into wildlife. Two infrequent substitutions were identified: S552I in CPV-2b and I447M in CPV-2a. Viable virus was isolated from all positives, with characteristic CPV-cytopathic effects. This study provides the first molecular and virological evidence of CPV in Central European wildlife. Our findings expand our understanding of CPV diversity in Europe, and underscore wildlife as an integral component of European ecology. Full article

Heat stress induces metabolic adaptations in fish, including the regulation of triglyceride (TG) synthesis/degradation to preserve cellular lipid balance and energy homeostasis. Diacylglycerol acyltransferase (DGAT) catalyzes the final step in TG synthesis. However, the molecular mechanisms by which DGAT regulates TG metabolism in heat-stressed fish remain unexplored. Our previous study suggested that miR-10c regulates dgat2 expression in genetically improved farmed tilapia (GIFT, Oreochromis niloticus) under heat stress. Here, we characterized the GIFT miR-10c precursor as a 65-nucleotide transcript yielding a 22 nt mature miRNA (oni-miR-10c). A phylogenetic analysis revealed a high level of miR-10c sequence conservation across species. A dual-luciferase reporter assay confirmed dgat2 as a direct target of miR-10c. Overexpression of miR-10c in vivo down-regulated dgat2 transcripts and DGAT2 protein. SiRNA-knockdown of dgat2 resulted in upregulation of cpt1α, fas, and lpl and downregulation of hsl, thereby reprogramming lipid metabolism in GIFT hepatocytes. Thus, the miR-10c-dgat2 regulatory axis facilitates TG hydrolysis and promotes fatty acid metabolism under heat stress. Our findings highlight miR-10c’s potential as a dgat2 inhibitor and its function in regulating lipid metabolism in heat-stressed GIFT. Our study reveals a key molecular pathway mediating thermal adaptation of energy metabolism in fish, providing novel targets for preventing heat-induced metabolic disorders. Full article

Carrot (Daucus carota L.) is an important root vegetable crop in the Apiaceae and is widely cultivated around the world. Expansins play crucial roles in the growth and development of plants. Here, a total of 35 carrot expansins were identified from carrot. Sequence alignment and phylogenetic analysis revealed that carrot expansins could be classified into four subfamilies, each with similar exon/intron structures and motif compositions, indicating that carrot expansins were relatively conserved during evolution. Chromosomal localization and gene duplication analysis indicated that DcEXP genes were unevenly distributed across carrot nine chromosomes and had evolved predominantly under purifying selection. Measurements of key agronomic characters of carrots at different developmental stages (30, 60, and 90 days after sowing) indicated significant positive correlations among root fresh weight, aboveground fresh weight, root–shoot ratio, root length, and root diameter. The period from 30 to 60 days after sowing was identified as the primary phase of taproot enlargement. Analysis of spatiotemporal expression patterns revealed that most DcEXP genes were specifically expressed in the taproots, and only one gene, DcEXP18, was specifically expressed in leaves. During the rapid growth period of carrot taproots (30 and 60 days after sowing), the genes DcEXP2, DcEXP3, DcEXP5, DcEXP8, DcEXP11, DcEXP13, DcEXP17, DcEXP19, DcEXP20, DcEXP22, DcEXP26, DcEXP28, and DcEXP33 exhibited high expression levels, suggesting that they played potential important roles in carrot taproot enlargement. These findings will advance our knowledge of the molecular mechanisms underlying expansin regulation of carrot growth and development. Full article

Universal Stress Protein (USP) plays crucial roles in plant stress adaptation, yet their evolutionary dynamics, regulatory mechanisms, and functional diversification in rice (Oryza sativa) remain poorly understood. This study aimed to conduct a genome-wide identification and characterization of the OsUSP gene family to elucidate its role in abiotic stress responses using integrated bioinformatics approaches. Here, we identified 46 OsUSP genes that are unevenly distributed across 11 rice chromosomes and exhibit significant divergence in protein length, molecular weight, and subcellular localization. Phylogenetic analysis classified OsUSPs into three subfamilies, with conserved motif and domain architectures within groups but distinct structural variations across subfamilies. Evolutionary analysis revealed strong collinearity between rice and other monocots, which suggests functional conservation in grasses, whereas limited synteny with dicots indicates lineage-specific divergence. Cis-regulatory element analysis showed enrichment in ABA, MeJA, drought, and hypoxia response motifs, implicating OsUSPs in hormonal and stress signaling. Expression profiling indicated tissue-specific patterns, with subfamily III genes broadly expressed, while subfamily II members were anther-enriched. Stress response profiling revealed that 24 OsUSPs were significantly induced, while LOC_Os02g54590 and LOC_Os05g37970 emerged as particularly notable due to their broad-spectrum responsiveness, being upregulated under all tested stress conditions. Protein–protein interaction (PPI) analysis indicated that OsUSP proteins potentially interact with Leo1/TPR-domain proteins and are involved in stress response and phosphorylation signaling pathways. This study yields key insights into OsUSP-mediated stress adaptation in rice and pinpoints promising candidate genes to facilitate the breeding of climate-resilient rice. Full article