Search Results (10,353)

Starch biosynthesis is a fundamental process influencing yield and fruit quality in banana, with ADP-glucose pyrophosphorylase (AGPase) serving as the rate-limiting enzyme catalyzing sucrose conversion into starch. However, the mechanisms underlying functional differentiation of AGPase family genes following polyploidization remain largely unexplored. In this study, eight AGPase genes, including large (MaAPL) and small subunit (MaAPS) members, were identified from the banana (Musa acuminata) genome, all harboring the conserved ADP-glucose pyrophosphorylase domain. Phylogenetic analysis traced their evolutionary origin to the ancient moss Physcomitrella patens, with polyploidization identified as the primary driver of gene family expansion. These genes exhibit conserved codon usage bias and have undergone strong purifying selection. Among them, MaAPS1 displayed distinct functional differentiation, increased intron number, enriched promoter cis-elements, and significantly elevated expression—features likely contributing to its adaptation for enhanced starch accumulation in fruit. Furthermore, the MaAPS1 protein was predominately localized in the chloroplast. Functional validation supported its regulatory involvement: transient silencing in banana fruit reduced starch content, while transient overexpression in banana fruit increased starch levels. Co-expression and molecular docking analyses revealed that transcription factors ERF1, C3H1, bZIP1, and bZIP3 may interact with the MaAPS1 promoter, indicating a multifactorial regulatory network. Overall, this study provides insights into polyploidy-driven functional innovation and transcriptional regulation of MaAPS1 in banana starch biosynthesis, providing valuable molecular targets for genetic improvement of yield and fruit quality. Full article

Riverine ecosystems represent critical nodes in the global carbon cycle, where the mechanistic role of viruses in modulating eukaryotic carbon cycling remains underexplored, particularly across heterogeneous landscapes. Here, we applied metatranscriptomics to dissect how multi-scale environmental factors and viral gene activity jointly regulate the spatial transcription of carbon cycling genes in riverine eukaryotic communities along the Yongding River, China. Our analyses reveal pronounced spatial heterogeneity in both viral gene expression—notably major capsid proteins of large eukaryotic DNA viruses—and carbon fixation, conversion, and metabolism pathways, peaking in agriculturally impacted plain regions. Multivariate statistics and network analyses demonstrate that land use enhances viral gene activity, serving as biological amplifiers that modulate host carbon metabolism and transformation. Structural equation modeling further identifies a cascade in which cropland coverage elevates viral gene expression, ultimately driving a 1.8-fold increase in TCA cycle gene transcription in plain regions, whereas nitrogen loading at the site scale suppresses viral activity and carbon fixation. Phylogenetic analysis corroborates that virus–host specificity underpins these spatial patterns. Collectively, these findings advance a new model in which viruses act as key intermediaries, transmitting multiscale environmental signals to shape riverine carbon cycling. Our study highlights the urgency of incorporating viral ecology into predictive frameworks of riverine biogeochemical cycling under accelerating environmental change. Full article

West Nile virus lineage 2 (WNV-2) is a growing public health concern in Europe causing West Nile fever or West Nile neuroinvasive disease (WNND) with substantial morbidity and mortality; however, genomic data from southern Italy are limited despite recent expansion of autochthonous transmission. The aim of the study was to characterize the phylogenetic and molecular features of the WNV-2 strain responsible for the first autochthonous human infection reported in Calabria (2023), and two more additional WNND cases detected in 2024. Full WNV-2 genomes were generated from the three cases. Phylogenetic analysis was performed using all publicly available WNV sequences up to September 2025. Amino acid changes in the polyprotein were compared with known WNV-2 lineage and sub-lineage signatures. The three sequences formed a monophyletic group within sub-lineage WNV-2a, clustering with strains circulating in Central-South-Eastern Europe and showing closest affinity to Hungarian sequences. Non-synonymous substitutions characteristic of the Hungary 578/10 strain (NS2B-119I, NS4B-14G, NS4B-49A, and NS5-298A) were identified and were absent from Central-Northern-Western European and previously reported Italian sequences. Additional substitutions (E-159T, E-399R, and NS3-249P) corresponded to signatures from a fatal WNV-2 infection in a Great Grey Owl in Slovakia. Our study provides the first report of Central-South-Eastern European WNV-2 circulation outside Eastern Europe, supporting its likely spread through the Balkans into Italy by 2022. These findings underscore the rapid spread of WNV-2 in newly affected areas and highlight the critical need for sustained molecular surveillance. Full article

Sorghum (Sorghum bicolor), a drought- and salt-tolerant staple cereal, supports over 500 million people globally as food, fiber, and fuel. Auxin/Indole-3-Acetic Acid (Aux/IAA) proteins regulate auxin signaling for plant growth and stress responses. However, the Aux/IAA gene family in sorghum has not yet been comprehensively analyzed. In this study, a total of 42 SbAUX genes were identified, and phylogenetic analysis revealed that the SbAUXs could be clustered into five subfamilies. Structural analysis further revealed that these subfamilies exhibit distinct structural features, while structures remain relatively conserved within each subfamily. The expansion of SbAUX genes has been mediated by multiple duplication types, with whole-genome duplication (WGD) events identified as the predominant driving force. Interspecific collinearity analysis revealed that AUX genes have undergone purifying selection. Promoter analysis revealed that the SbAUX gene promoters contain stress-responsive elements including as-1 and STRE, and transcriptome analysis combined with RT-qPCR data implied a potential involvement of SbAUX genes in the response to salt and PEG stresses. These findings provide a preliminary theoretical basis for exploring sorghum’s molecular responses to stress, and the SbAUX genes identified herein might represent potential candidate genes for genetic improvement in sorghum. Full article

The genus Scincella Mittleman, 1950 of the family Scincidae currently includes 50 species. However, due to challenges in sample collection, the taxonomy and phylogeny of this genus remain poorly resolved. This study conducted a taxonomic study of the genus Scincella based on three mitochondrial gene fragments (12S, 16S, COI) combined with morphological comparisons. The results indicated the specimens collected in Heishui County, Sichuan Province, China, represented a previously undescribed species. This new taxon is formally described as Scincella heishuiensis sp. nov. Phylogenetically, the new species is most closely related to S. wangyuezhaoi, which is another species recently described in Wenchuan County, Aba Prefecture, Sichuan Province. As a new species, the uncorrected genetic distance between this new species and its closest relative within the genus, as calculated based on 16S rRNA, is 5.45%. The new species can be distinguished from other closely related species by the following morphological characters: (1) 4 dorsal scale rows between dorsolateral stripes; (2) 5–7 superciliary; (3) 28 midbody scale-rows; (4) 24–25 gulars; (5) during the breeding season, the ventral scales and preanal exhibit a reddish-brown color; and (6) a black lateral stripe extends from behind the eye to the posterior third of the tail near the cloaca. In the phylogenetic analysis, the new species and S. wangyuezhaoi form an independent lineage, distinctly separate from all other taxa included in the study. The new species has currently been recorded and discovered in Heishui County in Sichuan Province, China. This description thus increases the number of members in the genus Scincella in China to 17 species. Full article

F-box-LRR (FBXL) proteins are crucial components of the SCF ubiquitin ligase complex, regulating diverse processes such as development and stress responses in plants. However, the FBXL family in tobacco (Nicotiana tabacum L.) remains poorly characterized. This study performed the first genome-wide analysis of the FBXL gene family in tobacco and identified 47 NtaFBXL genes. Phylogenetic analysis classified them into five clades, among which Clade III exhibited notable expansion. Promoter analysis revealed abundant stress- and hormone-related cis-elements. Expression profiling demonstrated tissue-specific patterns and strong responses to drought, ABA, IAA, and TMV infection. Importantly, six genes exhibited a significant negative correlation with TMV accumulation, suggesting their potential roles in antiviral defense. Moreover, both drought and TMV stress triggered a disturbance of redox homeostasis, a dynamic process that was closely associated with the expression of specific NtaFBXL genes, characterized by upregulated antioxidant enzymes (SOD, POD, CAT) and accumulated oxidative markers (H₂O₂, MDA). Collectively, this study provided a foundational resource for understanding the function of NtaFBXLs and identified key candidate genes for the genetic improvement of stress resistance in tobacco. Full article

Phytochelatin synthase (PCS) is crucial for synthesizing phytochelatins, cysteine-rich peptides vital for heavy metal detoxification in plants. Potato, a key staple crop in China, faces risks from soil heavy metal contamination, yet the genes involved in its detoxification, particularly PCS genes, remain underexplored. This study systematically identified and characterized the StPCS gene family in potato using genomic databases, uncovering five StPCS members distributed across three of the 12 potato chromosomes. Phylogenetic analysis classified StPCS proteins into three clades, while gene structure and motif analyses revealed high conservation in domain organization. Promoter region investigations identified stress-responsive elements in nearly all StPCS genes. Under cadmium (Cd) stress conditions, qPCR analysis indicated a significant upregulation of StPCS1 (5.73-fold) and StPCS2 (1.61-fold) transcript levels after 21 days compared to the control, whereas no obvious differences were observed at 7 days post-stress. Subsequent functional verification in yeast revealed that StPCS1 overexpression markedly improved Cd tolerance in transgenic yeast. In addition, analysis of cis-acting elements in the StPCS gene promoter combined with qPCR verification under MeJA and ABA stress conditions suggested that StPCS1 might be involved in Cd stress responses in potato through certain hormone signaling pathways. This study represents the first comprehensive analysis of the StPCS gene family in potato, clarifying its structural characteristics and characterizing the function of StPCS1 as a long-term Cd stress-responsive gene, which lays a solid foundation for investigating its role in heavy metal detoxification. Full article

Hepatitis E virus (HEV) is a global public health concern, causing over 20 million infections annually. It is primarily transmitted via the fecal–oral route, with wild boars and domestic swine as major reservoirs involved in zoonotic transmission. Bahía de Samborombón is an important natural reserve in Argentina characterized by a high population of wild boars, located in a livestock-intensive region near major urban centers. As part of a wild boar control program, 11 sampling campaigns were carried out between 2022 and 2023. Fecal, blood, and liver samples were systematically collected from 80 captured animals for the detection and characterization of HEV through antibody and RNA testing. Serological analysis revealed a positivity rate of 42.4%, whereas RT-qPCR detected HEV RNA in 9.1% of fecal samples and 12.5% of liver samples. From the positive samples, seven viral sequences were recovered using RT-nested PCR, including six from ORF1 and one from ORF2. Phylogenetic analysis clustered these sequences within zoonotic HEV genotype 3, showing a close relationship with human sequences from Buenos Aires and neighboring provinces. This study confirms the presence of HEV in wild boars from Argentina, highlighting the circulation of genotype 3, clade abchijklmno and the associated zoonotic risk. Full article

(1) Background. Parabuthus liosoma is one of the largest buthid scorpion species and is endemic to Saudi Arabia and Yemen. This study provides the first DNA barcoding and phylogenetic analysis of P. liosoma from Saudi Arabia, contributing to global efforts in arachnid molecular identification and biodiversity documentation. (2) Methods. The whole genome was extracted from nine adult individuals of P. liosoma, collected from Farasan Island, southwest of Saudi Arabia. A portion of the mitochondrial DNA, specifically, the cytochrome oxidase subunit I gene (COI) sequences, was amplified and sequenced and subjected to genetic and phylogenetic analyses. (3) Results. The DNA barcoding results revealed a high level of genetic variability within P. liosoma, aiding in species identification and supporting its utility as a molecular tool for scorpion taxonomy. In addition, our results reveal a monophyletic relationship among Parabuthus species, with a clear distinction between Arabian and African lineages. (4) Conclusions. This study highlights the effectiveness of DNA barcoding as a reliable tool for species identification and taxonomy and enhances our knowledge of the evolutionary history and geographic distribution of Parabuthus scorpions. However, further research is required to elucidate the complex phylogenetic relationships within this genus. Full article

WRKY transcription factors serve as key regulators in plants, playing important roles in growth and development, secondary metabolism, and stress responses. Here, a comprehensive genome-wide analysis identified 58 WRKY genes (LcWRKYs) in litchi for the first time. All LcWRKY proteins were predicted to be hydrophilic and localized in the nucleus. Phylogenetic analysis classified them into three major groups (Groups I, II, and III), with a pronounced expansion of Group II, which contained 42 members divided into five subgroups. Members within the same phylogenetic clade exhibited highly similar exon–intron structures and conserved motif compositions, indicating strong evolutionary conservation. LcWRKYs were unevenly distributed across the litchi chromosomes, with chromosome 3 showing the highest gene density. Collinearity analysis suggested that both segmental and tandem duplications contributed to the evolutionary expansion of this family. Notably, promoter cis-acting element analysis revealed that LcWRKYs are enriched with light-responsive, hormone-responsive (e.g., ABA, MeJA, SA), and stress-responsive elements, suggesting their potential involvement in integrating light signaling, hormonal pathways, and environmental stress responses. Integrative expression analysis further revealed that multiple LcWRKYs were significantly up-regulated during the middle and late stages of fruit development in cultivars such as ‘Feizixiao’ and ‘Nuomici’. Consistent with these patterns, qRT-PCR validation demonstrated a pronounced induction of four representative genes (LITCHI004628.m1, LITCHI018082.m1, LITCHI021964.m1, and LITCHI030932.m1) at 40 days post-anthesis, followed by gene-specific expression trajectories at later stages, indicating their potential involvement in regulating fruit development, particularly during the mid-developmental stage. Altogether, the results of this study provide insight into the expansion and potential functional diversification of WRKY transcription factors in litchi and identify candidate regulators associated with fruit development, offering valuable targets for future functional studies and genetic improvement. Full article

Leaf color mutants are key resources for uncovering the molecular mechanisms of chloroplast development and photosynthesis. Here, we identified a novel yellow-green melon mutant, ‘ygp2’, which displays yellow-green leaves and dwarfism throughout development. Genetic analysis indicated that the trait is controlled by a single recessive nuclear gene. Map-based cloning delimited the candidate region to an 805 kb interval on chromosome 11, within which only one missense mutation was identified in MELO13C_11G242690, encoding a triosephosphate isomerase (CmpdTPI). Phylogenetic analysis suggested its plastid localization, which was confirmed by transient expression of CmpdTPI-GFP in tobacco. The ‘ygp2’ mutant exhibited significantly reduced TPI enzyme activity and net photosynthetic rate. Transcriptome analysis revealed downregulation of genes related to light-harvesting complexes, cell division, and the cell cycle. These results demonstrate that the point mutation in CmpdTPI impairs chloroplast function and photosynthesis, leading to the yellow-green phenotype in melon. This study provides insight into the role of plastidial TPI in chlorophyll metabolism and chloroplast development. Full article

The regulatory role of zinc finger proteins is crucial for the development of extreme environmental tolerance in numerous species. Tardigrades, as multicellular animals capable of withstanding multiple extreme conditions, have yet to undergo systematic identification and analysis of their zinc finger proteins. This study first analysed the distribution characteristics of zinc finger proteins across four species of tardigrades. We systematically characterised the family features of C4-type ZFPs in these four species and explored their regulatory roles in extreme environmental adaptation. Statistical genomic investigation reveals a wide distribution of the C4-type ZFP family among tardigrades. Phylogenetically, they separate into six distinct groups, with Group 5 emerging as a functionally specialised branch enriched in stress-responsive promoter elements. Molecular evolutionary evidence points to tandem duplication as key to this branch’s expansion and functional innovation, while also highlighting the pervasive purifying selection across this family. Transcriptomic analysis revealed that a specific subset of C4-type ZFP genes belonging to phylogenetic Group 5 in both H. henanensis and H. exemplaris were downregulated after irradiation. Functional enrichment indicates that these genes are linked to nuclear receptor transcription factor activity and the negative regulation of NF-κB signalling. We propose that their coordinated downregulation may represent a conserved stress-adaptive response, potentially derepressing NF-κB and reprioritizing resources toward damage repair over growth. This study provides a foundation and key clues for research aimed at elucidating the functional mechanisms of C4-type ZFPs in tardigrade extremotolerance. Full article

Pseudomonas syringae pv. syringae (Pss) is an economically significant bacterial pathogen that causes canker in sweet cherry trees. In Chile, sweet cherry (Prunus avium L.) is a key crop whose exponential production growth has increased phytosanitary pressure. However, the genetic diversity and adaptive mechanisms of local Pss populations have remained poorly understood. This study characterized 41 Pss isolates from major Chilean production regions. Their genomes were sequenced and compared with 152 public genomes from the PG2 phylogenetic group. The analysis revealed a predominance of the PG2d subgroup among the Chilean isolates, with a population structure defined by at least 18 genomic clusters, some of which are exclusive to Chile. A characteristic feature of this entire PG2d subgroup is the presence of indole-3-acetic acid (IAA) synthesis genes (iaaM and iaaH). Furthermore, this subgroup displayed a marked increase in ancestral gene gain and loss events, indicating extensive remodeling of the shell genome and supporting a model of lineage-specific adaptive evolution. We also identified lineage-specific orthogroups, structural variants of the T-PAI pathogenicity island, and a differential distribution of Hop-type effector proteins. Furthermore, an extended copper resistance operon (cop and cus systems) was detected in a subset of strains, and a dominant lineage was found to have a dual i1-type of T6SS system. These findings highlight the local diversification of Pss in Chile, likely driven by agro-environmental pressures. This study provides crucial insights into the evolution, adaptation, and pathogenic potential of this important pathogen in a crop of high strategic value. Full article

Tick-borne viral infections, including severe fever with thrombocytopenia syndrome virus (SFTSV), are increasingly recognized as a significant threat to global public health owing to their rapid dissemination and high mortality rates. While isolated outbreaks within single species have been documented, reports of multi-host cluster cases remain scarce. This study describes a consecutive, cross-species outbreak of severe fever with thrombocytopenia syndrome disease between April and May 2024 on a remote island in Nagasaki Prefecture that involved four cats and four humans. An interdisciplinary investigation integrating molecular phylogenetic analysis of viral genomes—including previously identified Nagasaki strains of SFTSV—and haplotype network analysis provided insights into the infection dynamics. Despite the absence of confirmed direct contact between cats and humans, four animals and one patient succumbed to the infection. Genomic analyses demonstrated high similarity to circulating Nagasaki strains, whereas haplotype analysis indicated multiple viral introduction events and complex transmission pathways, reflecting diverse sources. These findings underscore the critical need for a One Health approach—integrating human, animal, and vector surveillance—to effectively monitor, understand, and control tick-borne viruses globally, in both endemic and emerging regions. Full article

Sarcocystis spp. (Apicomplexa: Sarcocystidae) are globally distributed protozoan parasites with an obligatory two-host prey–predator life cycle involving intermediate (IHs) and definitive hosts (DHs). Canids, including the red fox (Vulpes vulpes), often serve as DHs for species infecting various ungulates. This study identified Sarcocystis species in red foxes from Croatia, Lithuania, and Portugal. Between 2021 and 2024, 164 faecal samples (80 from Croatia, 50 from Portugal, and 34 from Lithuania) were analysed using nested PCR targeting the cox1 gene. Twelve Sarcocystis species were detected: S. arieticanis, S. capracanis, S. capreolicanis, S. cruzi, S. gracilis, S. hjorti, S. iberica, S. linearis, S. miescheriana, S. morae, S. rossii, and S. tenella. The overall prevalence was highest in Croatia (78%) and Lithuania (62%) and lowest in Portugal (30%). Phylogenetic and haplotype analyses revealed high homogeneity and absence of geographic structuring. These results confirm the red fox as a key DH for multiple Sarcocystis species infecting European ungulates and underscore its epidemiological importance in parasite transmission across diverse ecosystems. Full article