Search Results (3,990)

Cell-wall polysaccharide O-acetylation contributes to cell-wall assembly, organ development, and plant–pathogen interactions, but the cucumber TBL gene family remains poorly characterized. Here, 37 CsTBL genes were identified genome-wide and analyzed using phylogenetic, syntenic, conserved-motif, gene-structure, promoter, protein-structure, Gene Ontology, and transcriptome approaches, followed by RT-qPCR analysis after powdery mildew inoculation. All CsTBL proteins contained the conserved GDS and DxxH motifs, whereas accessory motifs and predicted structural features varied among clades. Intraspecific analysis identified dispersed, WGD/segmental, and tandem duplication categories, and cross-species synteny was more extensive with melon than with Arabidopsis. Homology-derived annotations associated CsTBL genes with cell-wall polysaccharide metabolism, Golgi/endomembrane compartments, and O-acetyltransferase activity, including six genes assigned to xylan O-acetyltransferase-related annotations. Expression profiling revealed tissue- and developmental-stage-dependent patterns, whereas the publicly available powdery mildew RNA-seq dataset provided descriptive temporal expression profiles in Podosphaera xanthii-inoculated samples. Independent RT-qPCR analysis using time-matched mock controls revealed distinct post-inoculation responses among six selected genes. Relative to the corresponding mock controls, CsTBL2 was consistently repressed; CsTBL15 showed transient induction at 1 dpi followed by repression; CsTBL24 exhibited a biphasic response; CsTBL25 was induced at all sampled post-inoculation time points; CsTBL26 showed progressive induction; and CsTBL30 reached its highest observed expression level at 3 dpi. Integrated functional annotation and expression evidence highlighted CsTBL26 as a priority candidate for further functional characterization, while CsTBL24 and CsTBL25 represented fruit-associated candidates with distinct powdery mildew responses; CsTBL30 remained an additional strongly infection-responsive candidate. These findings provide an evolutionary and expression-based framework for the functional characterization of the cucumber TBL gene family. Full article

Auxin response factors (ARFs) are key transcriptional regulators of the auxin signaling pathway and play important roles in plant organogenesis and regeneration. However, the functions of ARF family genes in lily scale-derived bulblet regeneration remain largely unclear. In this study, 24 LdARF genes were identified from the genome of Lilium davidii var. unicolor. Phylogenetic analysis revealed that LdARF proteins showed evolutionary conservation with ARF homologs from other monocot species. Genome-wide identification, phylogenetic analysis, and expression profiling revealed functional divergence among LdARF genes during scale-derived bulblet regeneration. Among them, LdARF17 exhibited a distinct regeneration-associated expression pattern, characterized by rapid induction after scale excision and sustained high expression during subsequent bulblet initiation and formation. Subcellular localization analysis demonstrated that LdARF17 is localized in the nucleus. Transient overexpression of LdARF17 significantly promoted bulblet regeneration and was associated with increased expression of auxin-responsive and regeneration-related genes, including IAA14, LBD16, and LBD29. These findings suggest that LdARF17 acts as a positive regulator of lily scale regeneration and may influence auxin-responsive transcriptional processes associated with early cell proliferation, providing new insights into the molecular mechanisms underlying vegetative regeneration in lilies. Full article

Glycoside hydrolase family 1 (GH1) β-glucosidases (BGLUs) play diverse roles in plant development and stress responses. However, a comprehensive pan-genomic characterization of this gene family across diverse Brassica rapa accessions is still lacking. Here, we conducted a pan-genome-wide analysis of BGLU genes across 21 B. rapa accessions. A total of 1840 BGLU genes were identified and clustered into 57 orthologous gene groups (OGGs), comprising 22 core, 19 dispensable, and 16 private groups. Phylogenetic reconstruction assigned these OGGs to five subgroups, and duplication analysis revealed whole-genome duplication as the predominant driver of family expansion, accounting for 47.51% of duplicated genes. Expression profiling identified two core genes, BrBGLU10 and BrBGLU56, as specifically expressed in fertile floral buds and differentially regulated between fertile and sterile lines. CRISPR/Cas9-mediated knockout of BrBGLU10 resulted in approximately 36% pollen abortion and drastically reduced seed set upon self-pollination, supporting its important role in pollen development. Collectively, these findings establish BrBGLU10 as an important regulator of pollen development and a potential target for fertility-related applications via gene editing in B. rapa and related Brassica crops. Full article

Background: Autophagy plays a central role in maintaining cellular homeostasis, regulating growth and development, and responding to multiple stresses. Autophagy-related genes (ATGs) play critical roles in autophagy, yet their functional diversity in soybean (Glycine max) remains underexplored. Methods: Genome-wide identification of GmATG genes was performed using sequence similarity and domain-based searches against the Wm82.gnm4 reference genome, followed by characterization of physicochemical properties, chromosomal distribution, phylogenetic relationships, gene duplication, conserved motifs, gene structure, three-dimensional structural, and promoter cis-acting elements. Tissue-specific expression and multiple stresses response were examined using transcriptome data and profiled by RT-qPCR. Results: A total of 60 GmATG genes belonging to 20 subfamilies were identified in soybean. Gene family expansion was predominantly driven by fragment duplication (33 gene pairs), with the ATG8 family expanding to 12 members, and pan-genomic analysis uncovered prominent copy number variation (6–9 copies) in the ATG18 family. GmATG genes showed distinct expression patterns in response to multiple abiotic and biotic stresses. Specifically, GmATG18f was significantly induced by phosphorus deficiency in the low-phosphorus-tolerant soybean variety Nannong 94-156. GmATG8g, GmATG9d and GmATG13d showed a typical expression trend of initial increase followed by decrease, with expression levels peaking at 6–12 h after salt stress treatment. GmATG8g and GmATG9d were rapidly upregulated at the early drought stress stage, while GmATG13a maintained sustained upregulation. In response to Phomopsis stem rot, GmATG7a/8h/8i/11/13d/18e/18f displayed differential expression in resistant and susceptible soybean materials. Conclusions: This study systematically characterizes the composition, expansion and stress response patterns of the GmATG gene family, revealing functional differentiation among family members. The identified key candidate genes, including abiotic-stress-regulated GmATG8g/9d/13d/18f and biotic-stress-regulated GmATG7a/8h/8i/11/13d/18e/18f, provide valuable genetic resources for the molecular breeding of stress-tolerant soybean. Full article

Unusual DS-1-like G3P[8] rotavirus strains have emerged and spread rapidly across several countries. In Africa, however, reports of these strains and available whole-genome data remain limited, and their evolutionary relationships across the continent are not yet fully understood. In this study, we sequenced and characterized the complete genome of a DS-1-like G3P[8] strain (RVA/Human-wt/KEN/KCH1748/2020/G3P[8]) detected in a child with acute gastroenteritis in Kenya. Strain KCH1748 possessed an unusual genotype constellation: G3-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Phylogenetic analysis revealed that 10 of the 11 genomic segments of strain KCH1748 were closely related to those of other East African DS-1-like G3P[8] strains from Kenya and Tanzania within the globally circulating DS-1-like G3P[8] lineage, suggesting that it may be derived from this globally emerging lineage. In contrast, the VP1 gene of strain KCH1748 was closely related to those of Ghanaian G9P[4] strains, sharing a common branch with Beninese DS-1-like G3P[8] and G2P[4] strains, suggesting a VP1 intragenogroup reassortment event involving African RVA strains. This study provides the first comprehensive whole-genome evolutionary characterization of a DS-1-like G3P[8] strain identified in Kenya. Our findings contribute to understanding the evolutionary dynamics and genomic diversification of emerging DS-1-like G3P[8] strains in Africa. Full article

Background: The genus Anchusa L. includes plants used in Uyghur medicine for their anti-inflammatory and analgesic effects. However, in China, the botanical origin of HERBA ANCHUSAE (Niushecao, a Uyghur medicinal herb) is severely confused. Traditional identification methods and standard DNA barcodes do not work well for these close relatives. Chloroplast genomes are known to contain variable regions that can help distinguish species, yet no such study has been done for Anchusa. Therefore, We compared the complete chloroplast genomes of six Anchusa species and the main adulterants of Niushecao. Methods: We analyzed genome structure, repeat sequences, codon usage bias, and nucleotide diversity (Pi), as well as conducted comparative and phylogenetic analyses. Results: All genomes shared a typical ring-shaped quadripartite structure, ranged from 150,178 to 150,844 bp in size, and contained the same set of genes. Despite this overall conservation, we identified several highly variable spots, mostly located in non-coding intergenic spacer regions. Using two complementary approaches—sliding window analysis and mVISTA-based sequence visualization—we identified three overlapping regions (rbcL-psaI, petA-psbJ, and trnC-GCA-petN) as candidate DNA barcodes for species identification. Our phylogenetic tree showed that Anchusa strigosa Banks & Sol. is most closely related to the true medicinal species Anchusa azurea Mill. (Bootstrap support (BS) = 100%), while other look-alikes formed separate branches. Conclusions: These findings provide the first chloroplast genomic resources for this genus and offer potential molecular markers for authenticating Anchusa medicinal materials, laying a foundation for future development of molecular authentication methods. Full article

Carboxylesterases (CXEs) participate in diverse plant metabolic processes, including isoflavone biosynthesis. However, the soybean GmCXE subfamily remains poorly characterized, especially in relation to root isoflavone accumulation and the response to Fusarium oxysporum. Here, fifty-six putative GmCXE genes were identified in the soybean genome and classified into three major phylogenetic clades. Analyses of gene structure, conserved motifs, protein domains, and promoter cis-elements revealed conserved features as well as potential functional divergence among subfamily members. Collinearity and duplication analyses indicated that segmental duplication was the main driver of GmCXE subfamily expansion. Tissue-specific expression profiling and RT-qPCR validation selected five root-expressed genes as candidates associated with isoflavone accumulation. SNP variation analysis and allelic group analysis of 209 soybean accessions further prioritized GmCXE54 as a candidate gene for root isoflavone accumulation. Allelic groups defined by a putative promoter SNP, Chr.20-rs39215413, showed significant differences in root daidzein and total isoflavone contents, with accessions carrying the C allele exhibiting higher levels of both traits than those carrying the T allele. Functional analysis in soybean hairy roots showed that GmCXE54 overexpression increased daidzein and total isoflavone accumulation. At 3 h after F. oxysporum inoculation, GmCXE2, GmCXE39, and GmCXE54 were induced, with GmCXE54 showing the strongest response in the resistant accession ZD27. These findings clarify GmCXE subfamily evolution and identify GmCXE54 as a candidate gene associated with root isoflavone accumulation and early F. oxysporum response, offering new perspectives for improving soybean isoflavone-related traits and investigating root response mechanisms. Full article

Blastus Lour. is a taxonomically complex genus of Sonerileae (Melastomataceae), with unresolved infrageneric relationships and controversial boundaries among several species and varieties. In this study, we integrated morphological evidence with a broadly sampled internal transcribed spacer (ITS) dataset, an expanded nuclear ribosomal DNA (nrDNA) dataset, plastome data, and genomic single-nucleotide polymorphism (SNP) data to evaluate the phylogenetic relationships and classification within Blastus. The broadly sampled ITS and expanded nrDNA analyses supported the monophyly of the sampled Blastus accessions but provided limited resolution of relationships among closely related taxa. The plastome analysis did not recover the sampled Blastus accessions as monophyletic and revealed marked cytonuclear phylogenetic incongruence. The genomic SNP analysis strongly supported the monophyly of the sampled Blastus accessions and recovered the sampled members of the terminal inflorescence group as a monophyletic clade. However, the sampled members of the traditional axillary inflorescence group were not monophyletic because Blastus borneensis was recovered as sister to the terminal inflorescence clade. Within the terminal inflorescence clade, the sampled members of the B. pauciflorus and B. cavaleriei groups formed two strongly supported sister lineages. Morphological comparisons showed that inflorescence position and architecture, the distribution of yellow glands on the abaxial leaf surfaces, and calyx lobe morphology generally corresponded to the principal lineages recovered in the SNP tree, whereas indumentum characters varied considerably among individuals and populations. We therefore recommend retaining the axillary and terminal inflorescence groups as descriptive morphological categories and treating the B. pauciflorus and B. cavaleriei groups as two informal working subdivisions within the terminal inflorescence group. The broad circumscription of B. pauciflorus adopted in the Flora of China requires reassessment, whereas the boundaries of B. longiflorus var. apricus and B. dunnianus require broader population sampling before formal taxonomic changes are proposed. Full article

The post-anthesis sepal inflation forming a Chinese lantern in Physalis pubescens represents a striking morphological novelty, whereas in the related genus Solanum lycopersicum var. cerasiforme, the sepals remain non-enclosing, providing an ideal comparative system to study reproductive organ divergence. This study aimed to systematically compare the reproductive development between Physalis pubescens L. and Solanum lycopersicum var. cerasiforme. We integrated phylogenetic analysis, light and scanning electron microscopy, semi-thin sectioning, and quantitative RT-qPCR analysis of six MADS-box genes. Phylogenetic analysis placed P. pubescens in a clade with P. alkekengi (L.) and P. ixocarpa (Brot. ex Hornem.), distinct from tomato. Floral organs differed markedly in petal color, anther morphology, and dehiscence type. Microspore development was delayed before the tetrad stage but accelerated thereafter in P. pubescens; S. lycopersicum anthers exhibited pronounced connective tissue proliferation absent in P. pubescens. P. pubescens sepals expanded 6.92-fold by 17 days post anthesis and enclosed the fruit, while S. lycopersicum sepals grew minimally. Sepal expansion was driven by inner epidermal cell enlargement and intercellular space formation, producing a hollow structure with a trichome-free inner epidermis. Expression of six MADS-box genes exhibited diversity: PfMPF2 and PfAGL1 were upregulated during sepal growth, PfMPF3, PfSEP1 and PfSEP3 exhibited a high–low–high pattern with minima at peak growth, and PfAGL6 declined. These findings reveal that coordinated epidermal cell expansion, parenchyma cavity formation, and a dynamic MADS-box gene network govern the inflated sepal syndrome, and highlight key divergences in anther morphogenesis, providing a cellular and molecular framework for reproductive evolution in Solanaceae. Full article

Environmental temperature is a major ecological factor shaping physiological and molecular evolution in mammals. Fatty acid desaturase genes (FADS1 and FADS2) play essential roles in the biosynthesis of long-chain polyunsaturated fatty acids (PUFAs), which are critical for membrane structure and metabolic regulation. However, their evolutionary responses to climatic variation in wild mammals remain poorly understood. In this study, we analyzed 27 rodent species distributed across diverse climatic regions to investigate the relationship between environmental temperature and the evolutionary rates of the FADS1 and FADS2 genes. Phylogenetic comparative methods, including phylogenetic ANOVA, phylogenetic generalized least squares (PGLS), and branch model analyses, were applied to estimate ω (dN/dS) ratios and assess selection patterns. Branch-site model analyses were further performed to test for episodic positive selection acting on specific codons in low-temperature-associated lineages. Our results showed that species inhabiting lower-temperature environments exhibited significantly higher ω values for both FADS genes compared with those in warmer environments. PGLS analyses revealed consistent negative associations between temperature variables and evolutionary rates, particularly for BIO5, and branch model analyses further indicated elevated ω values in low-temperature-associated lineages relative to background branches. Branch-site analyses detected significant signatures of episodic positive selection in Spermophilus dauricus and Microtus oregoni, with candidate positively selected codons identified in both lineages. Similar temperature-associated evolutionary rate patterns were also observed in expanded mammalian datasets, suggesting a broader cross-taxa trend. Overall, these findings indicate that environmental temperature is associated with heterogeneous evolutionary rate patterns in FADS genes and suggest that lipid metabolism genes may be recurrently influenced by cold-related selective pressures across mammals. Full article

Feline kobuvirus (FKoV) has been linked to diarrheal disease in cats and has recently emerged in several Asian countries. This study aimed to investigate the epidemiological and genetic characterization of FKoV in domestic cats in northern Vietnam from 2022 to 2025. In total, 244 fecal samples were obtained from both healthy and sick cats in Hanoi, Hungyen, Bacninh, and Ninhbinh in the north of Vietnam. Of 244 fecal samples examined, eight (3.28%) samples were found to be positive for the FKoV genome by using the conventional PCR method. Viral genomes were identified in both healthy and sick cats. The highest FKoV-positive rate was 12.50% in 6–12-month-old cats, significantly higher than those detected in cats aged 3–6 months and >12 months. Eight positive samples were successfully sequenced and characterized for the partial 3D gene and full-length VP1 genes. Results showed that the level of nucleotide identity of the partial 3D gene and full-length VP1 genes among the FKoV strains in this study ranged from 95.86% to 100% and 94.09% to 99.73%, respectively. Phylogenetic analysis revealed that the eight Vietnamese viral strains obtained in this study formed a novel cluster within FKoV and are genetically related to Chinese FKoV strains. Two positive selections were found in the VP1 protein of the Vietnamese FKoV strains. Full article

β-D-Xylosidases (BXLs) are members of glycoside hydrolase family 3. They play essential roles in cell wall remodeling, plant development, and abiotic stress responses. BXL gene families have been systematically characterized in several crop species. However, a comprehensive analysis of BXL genes in cotton (Gossypium hirsutum), a globally important fiber and oilseed crop, is still lacking. In this study, we performed a genome-wide identification of BXL genes in allotetraploid cotton. A total of 25 GhBXL genes were identified and classified into six phylogenetic clades. Gene structure and conserved domain analyses showed that all GhBXL proteins possess the characteristic tripartite GH3 domain architecture. Chromosomal distribution and synteny analyses indicated that the expansion of the cotton BXL family may be associated with whole-genome duplication and allopolyploidization. Promoter cis-element analysis detected stress-responsive regulatory motifs in the GhBXL promoters, including STRE, W-box, DRE core, and as-1 elements. Under PEG-simulated drought and salt stress, expression profiling, independently confirmed by qRT-PCR, showed distinct temporal response patterns among GhBXL members. Weighted gene co-expression network analysis (WGCNA) further identified GhBXL-8, GhBXL-9, and GhBXL-20 as hub genes in stress-responsive modules. Their co-expressed partners were enriched in transcription factors, kinases, and stress-related proteins. These findings provide a systematic foundation for understanding the evolutionary dynamics and functional roles of BXL genes in cotton. They also highlight candidate genes for future functional investigation. Full article

Sulfur is an essential nutrient involved in plant growth, redox regulation, and responses to environmental stresses. Sulfate transporters (SULTRs) control sulfate uptake and distribution, thereby affecting sulfur availability for metabolic processes and stress adaptation. However, the characteristics and stress-responsive functions of SULTRs in the halophyte Sesuvium portulacastrum remain unclear. In this study, we identified and characterized the SULTR family in S. portulacastrum through phylogenetic analysis, gene structure comparison, conserved motif analysis, promoter characterization, synteny analysis, and expression profiling. A total of 22 SpSULTRs were identified and classified into three subfamilies. Most SpSULTRs contained conserved Sulfate_transp and STAS domains and were predicted to localize to the plasma membrane. Transcriptome analysis combined with qRT-PCR validation revealed that SpSULTRs displayed diverse tissue-specific expression patterns under salt, cadmium, and copper stresses. Of these, SpSULTR3;1 and SpSULTR3;2 showed strong responses to salt stress and were mainly expressed in leaves. Protein interaction predictions suggested that these two transporters may be associated with sulfur assimilation, antioxidant metabolism, and stress-related pathways. These results reveal the structural diversification and stress-responsive characteristics of the SULTR family in S. portulacastrum and provide a basis for further investigation of sulfur transport mechanisms underlying halophyte adaptation. Full article

Laccaria is a cosmopolitan genus of ectomycorrhizal fungi that plays an important role in forest ecosystems worldwide. To explore the species diversity of Laccaria in Asia, this study conducted morphological observations and multi-gene phylogenetic analyses on 12 specimens collected from China and Thailand. The results showed that these 12 specimens formed five distinct and well-supported clades, which, combined with morphological comparisons, were recognized as five new species: L. aurantirufescens, L. bisporus, L. jilongensis, L. longicystidiata, and L. yadongensis. The main diagnostic characteristics of each new species are as follows: L. aurantirufescens has small to medium-sized basidiomata, an orange-red to russet pileus, and a yellowish-brown to reddish-brown stipe surface; L. bisporus has small basidiomata, a pale orange to orange-white pileus, and a brown to yellowish-brown stipe surface, and it possesses cheilocystidia, pleurocystidia, and caulocystidia; L. jilongensis has large basidiomata, with a pileus reaching up to 11 cm in diameter, orange-red coloration, sparse lamellae, a stipe up to 15 cm long, and the presence of cystidia; L. longicystidiata has small basidiomata, a pale orange to grayish-orange pileus, a light brown to brown stipe surface, and long cheilocystidia; L. yadongensis has small to medium-sized basidiomata, a pinkish-brown to fleshy-brown pileus that is darker at the center, four-spored basidia with sterigmata extending up to 10 μm in length, and a pileipellis composed of inflated hyphae, some of which exhibit brown pigmentation. These characteristics distinguish them from their closely related species. These findings not only enhance our understanding of Laccaria species diversity in Asia but also highlight the increasingly important role that Asia is poised to play in global fungal diversity conservation and taxonomic research. Full article

Species of the genus Hepatozoon are among the most widespread haemogregarine parasites infecting reptiles; however, information regarding their occurrence in native snakes from Mexico remains scarce. This study investigated the molecular occurrence of Hepatozoon spp. in free-ranging Mexican black-tailed rattlesnakes (Crotalus molossus nigrescens) rescued within the Reserva Ecológica del Pedregal de San Ángel (REPSA), an urban protected area in central Mexico. Opportunistically sampled squirrels were also included to explore the occurrence of these parasites in sympatric mammals. Blood samples from 26 rattlesnakes, six Mexican gray squirrels (Sciurus aureogaster), and three rock squirrels (Otospermophilus variegatus) were screened by PCR targeting a partial fragment of the 18S rRNA gene. Hepatozoon spp. DNA was detected in six rattlesnakes (23.1%) and two Mexican gray squirrels (33.3%), whereas all rock squirrels tested negative. Phylogenetic analyses suggested the presence of two distinct Hepatozoon lineages: one showing phylogenetic affinity with Hepatozoon cf. ophiosauri, detected in all positive rattlesnakes and one squirrel, and another closely related to Hepatozoon griseisciuri, identified in a second squirrel. These findings represent the first molecular detection of Hepatozoon in C. molossus nigrescens, the first record of infection in S. aureogaster, and the first report of a H. griseisciuri-like lineage in Mexico. Although parasite identification was based exclusively on partial 18S rRNA gene sequences, this study expands current knowledge of Hepatozoon diversity in Mexican wildlife and provides important baseline information for future studies integrating molecular, morphological, and ecological approaches to better understand parasite diversity and transmission in protected urban ecosystems. Full article