Search Results (430)

This narrative review synthesizes current knowledge on MADS-Box 27 (OsMADS27), a member of the AGL17 clade in rice that has emerged as a regulatory node linking nitrate signaling, root development, and abiotic stress tolerance. Because most functional and mechanistic studies on OsMADS27 to date have been conducted in rice, this review is centered on Oryza sativa, with cross-species comparisons used for evolutionary and comparative context. Specifically, we summarize the gene and protein structure, phylogenetic position, expression profile, upstream and downstream regulation, and emerging functional significance of OsMADS27. OsMADS27 is a typical MIKC-type MADS-box protein with root-preferential expression, and its activity is strongly influenced by nitrate availability and miR444-mediated regulation. Evidence from functional genomics, transcriptomics, ChIP-based studies, and transgenic analyses suggests that OsMADS27 contributes to the regulation of root architecture, nitrate uptake, hormonal crosstalk, and stress-responsive pathways. Notably, OsMADS27 enhances salt tolerance through nitrate-dependent activation of downstream targets such as OsHKT1;1 and OsSPL7, contributing to ion homeostasis and salinity tolerance. Recent findings also suggest roles in grain size regulation and yield improvement, expanding its significance beyond root biology. This review compares OsMADS27 with AGL17-clade genes and highlights its value for crop improvement aimed at salinity tolerance and nitrogen use efficiency. However, important research gaps remain, particularly the limited field-level validation, the absence of integrated multi-omics analyses, and the lack of functional studies of OsMADS27 orthologs in non-rice crops. Overall, OsMADS27 represents promising rice-centered target for future biotechnology applications, while its translational relevance to other cereals remains to be established through orthology analysis and field-level evaluation. Full article

Tamarindus indica L., a key economic tree species in tropical regions, suffers severely from postharvest decay. From 2023 to 2025, disease fruits exhibiting pericarp softening, pulp browning, and sticky exudates were collected in Yunnan, China. Pathogenicity tests following Koch’s postulates, combined with morphological characterization and phylogenetic analyses of the internal transcribed spacer (ITS), translation elongation factor 1-alpha (TEF 1α), and beta-tubulin (TUB) gene regions, identified the causal pathogen as Botryosphaeria fabicerciana (isolates ZWML-06, ZWML-44, ZWML-17). This is the first report of this postharvest disease on tamarind in Yunnan, filling an etiological gap. Additionally, an endophytic bacterium, designated BV-1, was isolated from asymptomatic pulp tissues. Whole-genome sequencing and phylogenetic analysis identified it as Bacillus velezensis. Strain BV-1 exhibited strong in vitro antagonistic activity against the pathogen, indicating promising biocontrol potential. Functional annotation revealed that BV-1 possesses a complex genetic system with developed transporter systems; its core metabolic network is dominated by nitrogen metabolism and redox processes, suggesting a potential “multi-target” antimicrobial mechanism. This study provides a theoretical basis and novel resources for the green control of postharvest diseases in tamarind. Full article

Sugarcane red rot is a critical constraint threatening the stability and sustainability of sugarcane production in Southwest China, where Yunnan and Guangxi Provinces are the core cultivation regions. To provide a scientific basis for targeted disease management and ensure sugarcane production security, 40 symptomatic red rot samples were collected from 10 sugarcane varieties across 7 locations in these two provinces. A total of 57 fungal isolates were obtained, and they were identified through morphological characterization, multigene phylogenetic analysis (ITS/ACT/TUB2 for Colletotrichum sp. and EF-1α/RPB2 for Fusarium sp.), and pathogenicity tests on the susceptible cultivar Yuetang 93-159 using three representative isolates per species. The results show that 36 isolates were identified as Colletotrichum falcatum and divided into light and dark morphotypes. Phylogenetic analysis revealed that Yunnan and Guangxi isolates clustered in Clade I and Clade II, respectively. The remaining 21 isolates were identified as Fusarium madaense, and no sequence polymorphisms were detected in either EF1α or RPB2 among these isolates, which clustered with the F. madaense strain isolated from sugarcane in Brazil. Pathogenicity tests on leaf midribs and stalks of this cultivar showed that the representative isolates of C. falcatum and F. madaense induced typical red rot symptoms consistent with field observations. Among the representative isolates tested, preliminary findings suggest that light-type C. falcatum isolates were more virulent than dark-type ones, and the C. falcatum isolates Cf16 and Cf1 showed higher stalk virulence than the tested F. madaense isolates. To our knowledge, this is the first report of F. madaense causing typical red rot symptoms on sugarcane in China. Full article

Phylogenetic reconstruction is a multi-step process that typically involves sequence retrieval, alignment, trimming, and tree inference, often requiring the integration of multiple independent tools. This fragmented workflow increases technical complexity and limits reproducibility, particularly in large-scale analyses. Here, we present phyloPipeR, an R package that provides an integrated and automated framework for end-to-end phylogenetic analysis and tree comparison within a unified environment. The phyloPipeR enables complete workflows from ortholog retrieval to tree inference and quantitative comparison, while also supporting modular execution of individual steps. The package implements multiple phylogenetic inference methods and supports both concatenation and coalescent strategies for multi-gene analyses. By integrating tree reconstruction and quantitative comparison within a single framework, phyloPipeR improves reproducibility, reduces technical barriers, and provides a scalable solution for systematic and integrative evolutionary studies. Full article

Perilla frutescens (L.) Britt., a medicinal and edible herb, is valued for its diverse leaf coloration, attributed to varying levels of anthocyanin accumulation. The primary anthocyanins in P. frutescens are acylated cyanidin glycosides; however, the enzymes facilitating the acylation process have yet to be characterized. BAHD acyltransferases, known to catalyze such modifications, remain uncharacterized in P. frutescens. To systematically identify potential genes that may be associated with this function, we performed a comprehensive genome-wide analysis of the BAHD acyltransferase family in P. frutescens. Our study identified 134 PfBAHD genes, which were subsequently analyzed for their physicochemical properties, phylogenetic relationships, conserved domains, motif compositions, and promoter cis-elements. Phylogenetic analysis categorized the PfBAHD genes into six clades, with Clade I being the primary candidate for anthocyanin-related activity due to its enrichment with members known to acylate flavonoids in other species. Promoter analysis indicated a significant presence of cis-elements associated with light, phytohormones, and stress responses. By integrating tissue-specific metabolomic and transcriptomic data, we established correlations between anthocyanin accumulation patterns and PfBAHD gene expression. Through the integration of multi-omics data, six candidate genes were prioritized, with PfBAHD05, PfBAHD77, and PfBAHD112 emerging as the most promising candidates. These genes demonstrated predominant expression in leaves, were induced under conditions of high light exposure, and were predicted to be localized in the cytoplasm. To further explore their potential functions, molecular docking analyses were conducted, suggesting that PfBAHD77 may have a preference for highly glycosylated anthocyanins, whereas PfBAHD05 and PfBAHD112 may favor substrates with lower levels of glycosylation. Collectively, these findings provide a preliminary foundation for understanding anthocyanin acylation in P. frutescens and identify several BAHD candidate genes that could be potentially targeted in future metabolic engineering efforts pending further biochemical and genetic validation. Full article

Callistosporiaceae is a recently established family within the suborder Tricholomatineae, encompassing tricholomatoid, collybioid or pleurotoid morphological forms. While most species of this family exhibit a saprotrophic lifestyle and have been predominantly documented in Europe and Americas, records from Asia remain comparatively sparse. In this study, Pulchragaricus rhodophyllus gen. et sp. nov., discovered in a Pinaceae and Fagaceae mixed forest in southwestern China, is described based on a comprehensive approach integrating both multigene phylogenetic analyses and morphological methods. A concatenated dataset comprising nuclear ribosomal DNA (ITS, LSU) and protein-coding genes (rpb2, tef1-α) provides robust statistical support for the placement of Pulchragaricus within Callistosporiaceae. Morphologically, this new taxon is characterized by a tomentose and yellowish-brown pileus, pink to pinkish lamellae, a solid and basally tapering stipe, broadly ellipsoid to ellipsoid basidiospores, sparse and subclavate cheilocystidia, and plentiful clamp connections. This discovery not only broadens the known diversity and distribution of the poorly documented Chinese Callistosporiaceae, but also offers a potential clue for understanding the evolutionary origins of the ectomycorrhizal symbiosis within the family. Full article

Sugarcane is a globally important crop, widely cultivated for sugar production and bioenergy. However, leaf spot disease leads to a reduction in its quality and yield. In this study, pathogen identification, biological characteristic analysis, and screening of antagonistic bacteria against the causal pathogens were done as a basis for epidemic prediction and green control of sugarcane leaf spot disease. The causal pathogens of sugarcane leaf spot disease were identified as Epicoccum latusicollum El532 and Fusarium sacchari Fs64, respectively, based on morphological characteristics, multi-gene phylogenetic analysis (ITS, TUB2, and RPB2 for El532; ITS, TEF1α, and RPB2 for Fs64), and pathogenicity tests. Biological characterization revealed that both pathogens exhibited optimal mycelial growth at 25 °C and under continuous darkness. However, light-dark cycles inhibited their growth. The optimal pH ranges for both isolates were 6–9 and 5–10, respectively. Maltose was the optimal carbon source for El532, whereas maltose, lactose, and starch were optimal for Fs64. Yeast extract served as the optimal nitrogen source for both. Isolation and screening of bacterial strains from healthy sugarcane roots, leaves, and rhizosphere soil yielded 13 antagonistic bacterial strains. Among them, six strains exhibited inhibition rates exceeding 57% against both pathogens. Bacillus subtilis A5 exhibited the highest antagonistic activity (68.85% against El532, 71.69% against Fs64), underscoring its potential as a promising biocontrol candidate. These findings provide a scientific basis for the diagnosis and management of sugarcane leaf spot disease. Full article

Thioredoxin (TRX) is an important redox-related protein, which plays a key role in maintaining redox balance in cells. However, the role of TRX in ammonia exposure of Oreochromis niloticus is still unknown. In this study, we successfully cloned the TRX gene (OnTRX) of O. niloticus and performed systematic bioinformatics analysis. The results of multi-sequence alignment and phylogenetic tree analysis showed that OnTRX is highly conserved in vertebrates, but exhibits low sequence similarity with TRX homologs from arthropods (crustaceans). The tissue distribution of OnTRX and its transcriptional response to ammonia challenge were determined by qRT-PCR, and we further investigated the relationship between OnTRX and the response of the Nile tilapia epithelial cell line (TSE-04) to NH₄Cl treatment. The results showed that OnTRX exhibited tissue-specific expression, with a relatively high expression level in gill tissue. Ammonia exposure could significantly induce the expression of OnTRX in the gill, head kidney, intestine, skin, liver, and spleen of tilapia. In TSE-04 cells, OnTRX overexpression was associated with reduced NH₄Cl-induced morphological damage, a lower proportion of apoptotic cells, and altered transcript levels of several stress-related genes. Collectively, these findings indicate that OnTRX is likely involved in the regulatory response of Nile tilapia to ammonia-induced stress, while the underlying molecular mechanisms thereof remain to be further elucidated. Full article

L-carnitine is a crucial quaternary ammonium compound widely used in the pharmaceutical, food, and feed industries. Microbial biosynthesis of L-carnitine, compared with chemical synthesis, offers milder conditions, higher stereoselectivity, and a lower environmental impact. However, highly efficient strains and mechanistic insights into the bioconversion of γ-butyrobetaine (γBB) to L-carnitine remain limited. This study focuses on strain WQ-1, a newly screened strain capable of converting γBB to L-carnitine. Based on morphological, physiological, and phylogenetic analyses of 16S rRNA and housekeeping genes, the strain was identified as Ensifer sp. WQ-1. Under the condition of 30 °C, initial pH 8.5, 10% inoculum, 6 g/L initial γBB, shake-flask fermentation reached molar conversion rate of 88%. In a 5 L bioreactor fed-batch fermentation, the L-carnitine titer achieved 13.98 g/L with a 78.7% molar conversion rate. Genomic analysis revealed a 6.97 Mb genome harboring 6568 protein-coding genes, including candidates for quaternary ammonium transport, CoA-dependent transformation, and transcriptional regulation. Comparative transcriptomics identified 58 differentially expressed genes, highlighting the significant upregulation of genes related to acyl-CoA activation, dehydrogenation, carnitine metabolism, and thioester hydrolysis in the presence of γBB. Multi-omics analyses support a putative CoA-dependent metabolic pathway for conversion of γBB to L-carnitine in Ensifer sp. WQ-1. Full article

The SHI-related sequence (SRS) transcription factors are vital plant regulators involved in development and stress responses. Given that biosynthesis of the valuable anticancer drug camptothecin (CPT) in Camptotheca acuminata is influenced by developmental and environmental cues, we hypothesized that SRS genes play key regulatory roles in the CPT biosynthetic pathway. To test this hypothesis and characterize the SRS family in this medicinally crucial plant, we performed a genome-wide identification of CaSRS genes and focused our analysis on their potential functional link to CPT biosynthesis. Eight distinct CaSRS genes were identified and classified into three phylogenetic subgroups. Comprehensive characterization—including phylogenetic relationships, gene structures, conserved motifs, chromosomal distribution, and synteny with Arabidopsis thaliana, Catharanthus roseus, and Ophiorrhiza pumila—provided foundational insights into the family. Crucially, integrated analysis of multi-tissue expression profiles revealed significant correlations between specific CaSRS genes (CaSRS2, CaSRS3, and CaSRS5) and key CPT biosynthetic genes. Promoter cis-regulatory element analysis further indicated that these CaSRS genes possess binding sites associated with stress and hormone responses known to modulate CPT production. These convergent lines of evidence strongly implicate CaSRS2, CaSRS3, and CaSRS5 as potential regulators of CPT biosynthesis. Collectively, this study first identifies specific CaSRS gene candidates for functional validation and provides a crucial foundation for understanding the role of the CaSRS family in regulating CPT biosynthesis in C. acuminata. Full article

Durian (Durio zibethinus Murr.), a renowned tropical fruit crop, is increasingly cultivated in the Hainan Province of China. In June 2025, symptoms of postharvest fruit rot were observed on durian fruits from a commercial orchard in Sanya City, Hainan Province, with a disease incidence of approximately 5.2%. Three fungal isolates were obtained and identified as Lasiodiplodia pseudotheobromae and L. lignicola based on morphological characterization and multi-locus phylogenetic analysis (combining ITS, TUB2, and EF1-α gene sequences). Pathogenicity assays confirmed both species as causal agents of durian postharvest rot, with rapid lesion expansion and eight tropical fruit hosts, including banana and mango, posing a threat to postharvest storage. Fungicide sensitivity tests showed imazalil and imazalil sulfate with mean EC₅₀ values of 0.07 µg/mL and 0.08 µg/mL as most effective, followed by prochloraz, iprodione, and prochloraz-Mn. L. lignicola was more sensitive to most fungicides than L. pseudotheobromae. These findings underscore the need for species-specific fungicide strategies in disease management. This is the first report of L. pseudotheobromae and L. lignicola causing durian postharvest rot in this preliminary study from Hainan. With Hainan emerging as a key production region, further research is essential to develop effective control measures against this economically significant disease. Full article

Background/Objectives: Acinetobacter baumannii is a critical opportunistic pathogen causing severe healthcare-associated infections, particularly in intensive care units. The global dissemination of carbapenem-resistant A. baumannii (CRAB) and its environmental persistence necessitate continuous genomic surveillance to monitor high-risk clones. Methods: We conducted whole-genome sequencing (WGS), core genome multi-locus sequence typing (cgMLST), and phylogenomic analyses on 26 CRAB isolates collected at the National Institute for Infectious Diseases (INMI) “Lazzaro Spallanzani” IRCCS (September 2023–September 2024). Antimicrobial resistance determinants, virulence-related genes, and capsular (KL) and lipooligosaccharide outer core (OCL) loci were characterized by interrogation of comprehensive bioinformatic pipelines. Results: All CRAB isolates displayed an extensively drug-resistant (XDR) phenotype, with a shared resistance pattern to carbapenems, aminoglycosides, fluoroquinolones, fosfomycin, and sulfonamides, while being susceptible only to colistin and cefiderocol. The carbapenemase gene bla_OXA-23 was detected in all CRAB isolates, together with clone-specific bla_OXA-51-like variants. For all isolates, the resistome profile fully matched the observed resistance phenotype. All isolates belonged to the International Clonal Lineage II (ICL II), Pasteur Sequence Type (ST) 2, and Oxford ST369, ST208, and ST455. Integration of cgMLST data with phylogenomic analyses and genome-based classification of KL and OCL loci revealed five distinct clusters, each one including nearly identical isolates, indicating both intra-hospital dissemination and possible inter-hospital transmission. Virulome profiling revealed heterogeneous repertoires of virulence-associated genes, resulting in cluster-specific patterns, while patristic analysis identified phylogenetic clusters linking the study isolates to other Italian and other European lineages. Conclusions: This study underscores the complex genomic landscape of CRAB in our setting, driven by the circulation of different ICL II clonal types, and reinforces the urgency of integrated genomic surveillance and robust antimicrobial stewardship to mitigate the spread of high-risk XDR A. baumannii clones. Full article

This study investigated Fusarium species associated with seven wild relatives of four economically important Rosaceae fruits in Sichuan Province, China, including wild strawberry (Fragaria sp. and Potentilla indica), wild raspberry (Rubus rosaefolius), wild cherry (Prunus sp., Maddenia sp. and Prunus leveilleana), and wild apple (Malus kansuensis). Based on multi-gene phylogenetic analyses and morphological characteristics, seven Fusarium species within the Fusarium tricinctum species complex (FTSC) were identified. Among these, four are described as new species (F. fragariae, F. potentillae, F. pruni and F. fructicola), while the remaining three represent new host records (F. avenaceum, F. diversisporum and F. paeoniae). In addition, phylogenetic and morphological evidence indicated that F. rosiradicicola is conspecific with F. diversisporum. Prioritizing the oldest epithet, we synonymized F. rosiradicicola under F. diversisporum. The pathogenicity of the isolates was evaluated on both their wild hosts and the corresponding cultivated fruits using detached, wound-inoculated assays. All tested isolates produced symptoms, showing pathogenic potential under experimental conditions. This study shows that selected wild Rosaceae fruits harbor several members of the FTSC and provides preliminary evidence of cross-host susceptibility under experimental conditions. However, further field-based investigations and non-wound inoculation studies are required to clarify their ecological roles, natural host susceptibility, and potential relevance in cultivated systems. Full article

Cudonia and Pleurocordyceps comprise a relatively limited number of species worldwide. In particular, Pleurocordyceps represents an ecologically important group of entomopathogenic fungi with considerable potential for medicinal applications. In this study, two novel species, Cudonia aurantiaca and Pleurocordyceps tianmushanensis, were collected from the National Nature Reserve of Mount Tianmu, Zhejiang Province, China. Detailed morphological descriptions and illustrations are provided, and genus-level phylogenetic relationships are inferred based on a combined multi-locus sequence dataset comprising the internal transcribed spacer (ITS), small subunit ribosomal RNA (SSU), large subunit ribosomal RNA (LSU), translation elongation factor 1-alpha (tef-1α), RNA polymerase II largest subunit (rpb1), and RNA polymerase II second largest subunit (rpb2) gene regions. This study contributes to a better understanding of the diversity and taxonomy of Cudonia and Pleurocordyceps. Full article

Sucrose synthase (SUS) is a key enzyme in plant carbon metabolism, catalyzing the reversible interconversion between sucrose + uridine diphosphate (UDP) and UDP-glucose (UDP-Glc) + fructose. It plays a central role in carbon flux allocation, cell wall and starch synthesis, as well as plant development and stress responses. SUS is encoded by a multigene family whose members exhibit significant functional diversification and expression specificity across species, tissues, and subcellular compartments. This review systematically summarizes the physiological functions of SUS in source–sink regulation, seed filling, and rapidly growing tissues; describes the organ-specific expression patterns and diverse subcellular localizations of different isoenzymes in Arabidopsis and major crops; and elucidates the phylogenetic pattern of the SUS gene family into three evolutionary clades—SUS I, SUS II, and SUS III—based on a comparative analysis of selected angiosperm species. Furthermore, it integrates the multi-level regulatory mechanisms of SUS, including transcriptional and post-transcriptional regulation, as well as the dynamic control of enzyme activity, stability, and subcellular localization through post-translational modifications such as phosphorylation and ubiquitination and protein interactions. Finally, this study identifies gaps in current research regarding ubiquitination mechanisms, metabolic network integration, and crop applications. It envisions SUS-centered molecular breeding strategies, informed by integrative regulatory genomics, multi-omics, and genome editing, to redirect crop carbon fluxes and thereby enhance yield, improve quality traits, and increase stress tolerance. Full article