Search Results (1,090)

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

Tree peony is an important horticultural plant with both ornamental and oil value. The tree peony genome and databases were used to search for calmodulin family genes to explore their function in the pollination of tree peony. The CaM gene family was identified, and then the basic protein characteristics of the family members, such as gene structure, isoelectric point, molecular weight, subcellular localization, and conserved protein domain, were analyzed. The expression levels of these genes in the pistil tissue of Paeonia ostii ‘Fengdan’ at different developmental stages after pollination were also analyzed. Further, qRT-PCR was used to detect the expression levels of six PsCaMs during the development process of the pistil under bee pollination conditions. The results showed that there were six CaM family members located on three chromosomes and one non-chromosome. There were a large number of hormone response and stress response elements on the gene promoter of this family. During the development of pistil tissue after pollination, CaM family gene expression showed a trend of first increasing and then decreasing, which may be related to its function during pollination. The purpose of this study is to identify the gene characteristics and expression patterns of the CaM family during pollination, and to lay a foundation for the functional study of the CaM family in tree peony pollination. Full article

Spinach is a dioecious vegetable and an excellent model for investigating plant sex differentiation. Exogenous gibberellin treatment induced sepal hypoplasia and sex reversal, converting 42% of stamens into pistils in male plants. Transcriptome analysis identified 112 male-biased genes enriched in stamen and pollen development, while hormone profiling revealed coordinated changes in GA, cytokinins, auxin, jasmonic acid, and abscisic acid. Functional assays demonstrated that silencing SpAMS or SpPGIP caused extensive carpelization, and in situ hybridization localized their expression to developing anthers. Dual-luciferase assays confirmed that SpAMS directly activates the B-class gene SpPI, and genomic mapping placed SpAMS in the pseudo-autosomal region of the Y chromosome. These results indicate that GA disrupts hormonal homeostasis and anther wall integrity, while the SpAMS–SpPI pathway regulates tapetal development to maintain male identity. Our findings identify SpAMS as a key male-promoting factor in spinach and provide a framework for elucidating sex determination mechanisms in dioecious plants. Full article

Chalcone Synthase (CHS) plays a vital role in flavonoid synthesis, influencing plant growth, development, and responses to both biotic and abiotic stress. In this study, 11 CHS genes were identified in Poncirus trifoliata using bioinformatics methods, with their distribution across five chromosomes and unassigned contigs. Each gene contains 2–3 exons and 3–8 conserved motifs. In silico prediction suggested that the PtrCHS proteins are localized in the cytoplasm. PtrCHS9 and PtrCHS11 share identical protein tertiary structures. Phylogenetic analysis classified the CHS family members into four subgroups. Synteny analysis revealed one set of collinear gene pairs within Poncirus trifoliata. Between Poncirus trifoliata and Arabidopsis thaliana, two sets of collinear gene pairs were identified, while one such set was found between Poncirus trifoliata and Oryza sativa. Promoter element analysis showed the presence of various hormone response and stress response elements within PtrCHS promoters. RNA-Seq data demonstrated tissue-specific expression patterns of PtrCHSs. RT-qPCR results indicated that all CHS genes, except PtrCHS11, respond to salt stress with dynamic, member-specific patterns. Additionally, four PtrCHSs (PtrCHS3, PtrCHS5, PtrCHS7, and PtrCHS10) were significantly upregulated in response to cold treatment. Notably, PtrCHS7 and PtrCHS10 maintained high expression levels at both 6 and 12 h, implying they may be key players in cold stress response in Poncirus trifoliata. Clones of PtrCHS7 and PtrCHS10 were obtained, and overexpression vectors were constructed in preparation for gene transformation. Overall, this study provides a solid foundation for future research into the functions of the PtrCHSs. Full article

CCCH zinc finger proteins play critical roles in plant growth, development and stress responses. Here, 56 CCCH genes were identified in Morus alba. These genes displayed wide variation in coding sequence (456–6318 bp) and protein length (151–2105 aa), with most proteins predicted to localize in the nucleus and a few in chloroplasts, the endoplasmic reticulum or cytoplasm. Chromosomal mapping showed uneven distribution across 14 chromosomes, with tandem clusters on chromosomes 1, 6 and 13. Phylogenetic analysis classified 53 MaC3Hs into 13 subfamilies, while three genes remained ungrouped. Synteny analysis revealed four segmental duplication events, suggesting segmental duplication as the major expansion mechanism, under purifying selection. Comparative collinearity showed higher conservation with Arabidopsis thaliana than with rice or maize. Promoter analysis identified 22 cis-acting elements, mainly related to phytohormones, followed by abiotic stress and developmental regulation. Expression profiling under drought stress revealed differential expression across tissues, with MaC3H33 showing strong induction (>200-fold in stems on day 6). Subcellular localization confirmed MaC3H33 is nuclear, and yeast assays indicated no self-activation. These findings provide comprehensive insights into the MaC3H gene family and lay a foundation for functional studies related to drought tolerance in mulberry. Full article

Background/Objectives: The eastern periphery of the Slavic expansion (the Volga-Oka region) is the most promising region for reconstructing interactions between Slavic and pre-Slavic populations of the East European Plain. Unlike most pre-Slavic tribes, its autochthonous population practiced inhumation instead of cremation, leaving us with some ancient DNA for analysis. Methods: The region’s modern and ancient Y-chromosome gene pools are dominated by the haplogroup R1a: its frequency reaches 56% in Ryazan Russians (n = 302) and 44% in the Finnic peoples of Mordovia (n = 633). This encouraged us to analyze its Y-SNPs and Y-STRs. Results: Using 2 independent methods of phylogeny analysis, we identified 10 informative Y-STR clusters within R1a, dating back 1600–2900 YBP. The clusters included 48% of modern Ryazan Russians, 40% of Mordovia’s Finnic populations, and ancient DNA samples from the Ryazan-Oka culture (6–7th centuries), Suzdal (12–13th centuries) and Vladimir (13th century). Such a unique combination and pre-Slavic TMRCA indicate that the informative clusters represent pre-Slavic Y lineages. The presence of ancient samples from Vladimir and Suzdal in the clusters suggests that the autochthonous tribes contributed to shaping the urban population of the Vladimir-Suzdal Rus. Some of the informative clusters are associated with the ancient population of the Baltics (2000–4000 YBP). Conclusions: About half of Russian R1a carriers in the Volga-Oka region are descended from a pre-Slavic population, suggesting that the Slavs did not fully replace the autochthonous population but rather mostly culturally assimilated the Meshchyora documented in the Russian chronicles and other local tribes. Full article

One of the critical steps in lignocellulosic deconstruction is the hydrolysis of cellulose by cellulases. Aspergillus oryzae can produce and secrete a large amount of various extracellular enzymes, including cellulases. However, due to the lack of a comprehensive characterization of the cellulase genes in A. oryzae, the development and application of A. oryzae cellulase are greatly limited. In this study, a total of 219 glycosyl hydrolase genes were systematically identified from the A. oryzae 3.042 genome and classified into 40 glycosyl hydrolase families. Among these glycosyl hydrolase genes, 26 genes encoding the cellulases of endoglucanase, exoglucanase, and β-glucosidase were identified and functionally characterized. The chromosome localizations, gene structures, functional domains, and subcellular localizations of these 26 cellulases were analyzed by bioinformatics. In addition, analysis of the expression patterns revealed that the expression of A. oryzae cellulase genes was time-specific, and most of the cellulase genes were inhibited under low- and high-temperature stress and high salt stress, which had important guiding significance for understanding the transcription patterns of A. oryzae cellulase genes. These findings lay a foundation for our subsequent modification of cellulase activity to realize the industrial applications of A. oryzae cellulase genes in cellulose biorefineries. Full article

Taraxacum kok-saghyz Rodin, an important rubber-producing plant, has emerged as a potential alternative crop for the natural rubber industry. Geranyl diphosphate synthase (GDS) catalyzes the condensation of dimethylallyl pyrophosphate and isopentenyl pyrophosphate into geranyl pyrophosphate in the mevalonate pathway in plants. However, its specific functions in natural rubber biosynthesis in T. kok-saghyz remain unclear. Methods: We conducted genome-wide analyses of TkGDS genes, followed by transient transformation assay, expression profiling, natural rubber quantification, and analysis of T. kok-saghyz photosynthesis. Results: Seven TkGDS genes are located on chromosomes A6 and A7 with an uneven distribution. All encoded TkGDS proteins contain FARM and SARM motifs. TkGDS1, TkGDS2, and TkGDS7 possess lspA domains, while TkGDS3, TkGDS4, TkGDS5, and TkGDS6 contain PLN02890 domains; both subgroups share similar domain architecture. TkGDS1, TkGDS2, and TkGDS7 exhibit interspecies collinearity with Arabidopsis thaliana; no intraspecies collinearity was detected. The putative cis-acting elements in promoter region of TkGDS genes mainly comprised abscisic acid responsiveness, anaerobic induction, light responsiveness, and MeJA responsiveness. Transient expression assays confirmed chloroplast localization of all TkGDS proteins. A strong positive correlation was observed between TkGDS1/TkGDS7 expression and natural rubber content, as confirmed by both transcriptome and qPCR analyses in T. kok-saghyz lines. Furthermore, overexpression of TkGDS1 and TkGDS7 improved photosynthetic efficiency and significantly increased natural rubber content (OE-TkGDS1: 6.08 ± 0.16%; OE-TkGDS7: 5.62 ± 0.32%; WT: 4.76 ± 0.28%). Conclusions: Our study elucidates the role of GDS1 and GDS7 in promoting growth and latex content, offering a genetic strategy for enhancing rubber accumulation in T. kok-saghyz. Full article

Small heat shock proteins play a pivotal role in maintaining protein homeostasis under abiotic stress conditions and are indispensable for plant viability. In the present study, a comprehensive characterization of this gene family in Allium sativum was conducted through genome-wide sequence identification, phylogenetic reconstruction, conserved motif analysis, promoter cis-element profiling, transcriptomic investigation, quantitative real-time PCR, subcellular localization, and yeast-based functional assays. A total of 114 small heat shock protein genes were identified across eight chromosomes and subsequently classified into ten phylogenetic subgroups. All encoded proteins conserved the α-crystallin domain, whereas their exon–intron architectures and promoter elements responsive to environmental stress or phytohormones exhibited considerable diversity. The predicted proteins range from 130 to 364 amino acids, with isoelectric points (pI) spanning 3.97 to 9.95 and GRAVY values from −1.131 to −0.014, indicating predominantly hydrophilic characteristics. Subcellular localization analysis revealed a broad distribution across the cytoplasm, chloroplasts, mitochondria, and other compartments, with the majority (74 proteins) localized in the cytoplasm. Synteny analysis uncovered two segmentally duplicated gene pairs (AsHSP20-80/31, and AsHSP20-81/32), both showing strong purifying selection (Ka/Ks = 0.0459 and 0.2545, respectively), suggesting functional conservation. Expression profiling demonstrated predominant transcript accumulation in bulbs and floral organs, with significant induction under heat, salinity, and jasmonic acid treatments. qRT–PCR validation further confirmed that several candidate genes, notably AsHSP20-94 and AsHSP20-79, were strongly and consistently upregulated across multiple stress conditions, underscoring their roles as core stress-responsive regulators. Subcellular localization experiments demonstrated that representative proteins are targeted to the cytoplasm, nucleus and chloroplasts. Furthermore, heterologous expression of AsHSP20-79 in yeast conferred marked thermotolerance. Collectively, these findings reveal extensive expansion and functional divergence of the small heat shock protein gene family in garlic and provide valuable candidate genes for improving stress resilience in this important crop species. Full article

Yak husbandry on the Qinghai–Tibetan Plateau relies on genetically resilient sire lines, yet the paternal ancestry of the locally prominent Jiuzhi breed has never been quantified. To resolve this gap, a 690 bp fragment of the Y chromosomal SRY gene was sequenced in 117 males spanning Jiuzhi (n = 12) and five neighboring Qinghai breeds and compared with three single individual public records that represent Qinghai Plateau, Tianzhu White, and Wild yaks. Alignment, haplotype calling, diversity indices, F_ST differentiation, AMOVA, multidimensional scaling, and TCS network analysis were performed. Thirty-two haplotypes were recovered; Jiuzhi yaks possessed twelve, and six of them had private alleles. Mean A + T content was 53.8%. Haplotype diversity was highest in Qinghai Plateau, Tianzhu White and Wild yaks and lowest in Larima yaks, while Jiuzhi diversity resembled that of Huanhu. Pairwise F_ST values indicated negligible differentiation between Jiuzhi and either Qinghai Plateau or Yushu yaks (F_ST ≈ 0) but pronounced divergence from Tianzhu White and Wild yaks (F_ST ≈ 0.97–0.99). AMOVA attributed 90.7% of molecular variance to among-breed differences, and multidimensional scaling clustered Jiuzhi with Jinchuan, Yushu and Huanhu. Network topology resolved two patrilineal clades, confirming dual paternal origins for Jiuzhi yaks. These data provide the first quantitative baseline for sire selection and conservation of Jiuzhi yaks and highlight close affinities with adjacent plateau breeds. Limitations include the use of single individual public sequences for Qinghai Plateau, Tianzhu White and Wild yaks (employed solely as phylogenetic anchors) and reliance on a single Y-linked locus; broader sampling and multilocus approaches will refine within-breed estimates. Full article

Insights into the state of individual cells within a living organism are essential for identifying diseases and abnormalities. The internal state of a cell is reflected in its morphological features and changes in the localization of intracellular molecules. Using this information, it is possible to infer the state of the cells with high precision. In recent years, technological advancements and improvements in instrument specifications have made large-scale analyses, such as single-cell analysis, more widely accessible. Among these technologies, imaging flow cytometry (IFC) is a high-throughput imaging platform that can simultaneously acquire information from flow cytometry (FCM) and cellular images. While conventional FCM can only obtain fluorescence intensity information corresponding to each detector, IFC can acquire multidimensional information, including cellular morphology and the spatial arrangement of proteins, nucleic acids, and organelles for each imaging channel. This enables the discrimination of cell types and states based on the localization of proteins and organelles, which is difficult to assess accurately using conventional FCM. Because IFC can acquire a large number of single-cell morphological images in a short time, it is well suited for automated classification using machine learning. Furthermore, commercial instruments that combine integrated imaging and cell sorting capabilities have recently become available, enabling the sorting of cells based on their image information. In this review, we specifically highlight practical applications of IFC in four representative areas: cell cycle analysis, protein localization analysis, immunological synapse formation, and the detection of leukemic cells. In addition, particular emphasis is placed on applications that directly contribute to elucidating molecular mechanisms, thereby distinguishing this review from previous general overviews of IFC. IFC enables the estimation of cell cycle phases from large numbers of acquired cellular images using machine learning, thereby allowing more precise cell cycle analysis. Moreover, IFC has been applied to investigate intracellular survival and differentiation signals triggered by external stimuli, to monitor DNA damage responses such as γH2AX foci formation, and more recently, to detect immune synapse formation among interacting cells within large populations and to analyze these interactions at the molecular level. In hematological malignancies, IFC combined with fluorescence in situ hybridization (FISH) enables high-throughput detection of chromosomal abnormalities, such as BCR-ABL1 translocations. These advances demonstrate that IFC provides not only morphological and functional insights but also clinically relevant genomic information at the single-cell level. By summarizing these unique applications, this review aims to complement existing publications and provide researchers with practical insights into how IFC can be implemented in both basic and translational research. Full article

Background/Objectives: Leaf sheath hairiness (LSH) is an adaptive trait in wheat that improves tolerance to biotic and abiotic stresses. Although trichome development has been extensively studied in model plants, the genetic basis of LSH in Triticeae crops remains poorly defined. Methods: In this study, the inheritance and genetic architecture of LSH were investigated. Two F₂ populations were used, derived from crosses between the glabrous lines ‘Shumai 830’ and ‘Shumai 2262’ and the hairy line ‘Zhongkelanmai 1’. BSA-seq was combined with KASP marker genotyping to map and refine the trait locus. Candidate genes were evaluated through comparative genomics; sequence variation; and subcellular localization prediction. Results: Phenotypic evaluation revealed that LSH is a dominant trait, segregating at a 3:1 ratio in F₂ populations. BSA-seq identified a major locus, QLsh.cwnu-4D, on chromosome 4DL. Fine mapping with KASP markers refined this region to a 1.67 Mb interval overlapping a 530 kb trichome-associated linkage disequilibrium block in Aegilops tauschii. Within this interval, TaSAIN1-4D, a salt-inducible protein unique to Triticeae, was identified as the strongest candidate gene. Extensive sequence variation among alleles (TaSAIN1-4Da; TaSAIN1-4Db; TaSAIN1-4Dc), including large insertions and multiple SNPs, indicated potential functional diversification. Predicted nuclear localization of TaSAIN1-4D supports a role in trichome regulation and stress adaptation. The co-dominant KASP marker K-cwnu-4D-502238348 was tightly linked to LSH and cosegregated perfectly, making it a reliable tool for marker-assisted selection. Conclusions: This study clarifies the genetic architecture of leaf sheath hairiness in wheat and identifies TaSAIN1-4D as a likely regulator. These findings provide a practical marker-assisted selection tool that can accelerate the development of improved wheat varieties with desirable leaf surface traits. Full article

Background: Mango is a tropical fruit that is deeply loved by consumers due to its unique flavor and taste. Different mango varieties have unique aromas, and the volatile components of mango are an important part of determining mango flavor. ATP-binding cassette (ABC) transporters are important in transporting plant volatile components. Although ABC transporters have been extensively studied in other species, little is known about the evolutionary characteristics and biological functions of the ABC family in mango. Results: In this study, a total of 119 MiABC genes were identified from the Mangifera indica genome and classified into eight subfamilies based on phylogenetic relationships. By analyzing the gene structure, subcellular localization prediction, chromosome localization, gene duplication events, and Ka/Ks ratios of MiABC genes, the MiABC gene functions were preliminarily determined. The expression profiles of MiABC genes at different stages of mango fruit harvesting indicate that MiABC genes are involved in the transport of volatile substances in mango fruit. The prediction of the transmembrane structure indicates that the MiABC genes have multiple transmembrane domains, and subcellular localization results show that the MiABC genes are mainly located on the cell membrane. Conclusions: In summary, this study conducted a comprehensive analysis of the ABC gene family in mango, laying an important theoretical foundation for the analysis of the transport process of volatile compounds in mango. Full article

KANADI (KAN) transcription factors are pivotal regulators of lateral organ polarity establishment in plants. Although extensively studied in herbaceous plants, the role of KAN genes in woody plant development remains unclear. This study conducts the first comprehensive analysis of 26 PmKAN genes in Prunus mume, elucidating their evolutionary trajectories, structural configurations, tissue-specific expression patterns and potential roles in root and fruit development. Phylogenetic analysis of four Rosaceae species and Arabidopsis thaliana clustered these PmKANs into five subfamilies, with conserved motif patterns supporting this classification. Chromosomal localization revealed that all PmKAN members are distributed across eight chromosomes, with tandem duplications events and syntenic relationships indicating functional diversification driven by gene family expansion. Cis-regulatory element analysis identified light-responsive, hormone-associated, stress-related, and developmental motifs, suggesting PmKAN genes are involved in regulating plant physiological processes and development. The qRT-PCR analysis revealed tissue-specific expression heterogeneity among PmKAN genes, with markedly elevated expression particularly observed in roots and fruits. Further expression profiling across fruit developmental stages suggests potential stage-specific functional divergence of PmKAN genes during fruit development. This study provides a theoretical foundation for further investigating the evolutionary relationships and molecular regulatory mechanisms of the PmKAN gene family. Full article

Sweetpotato displays diverse purple pigmentation due to anthocyanin accumulation. While current research on the underlying MYB activators has focused on IbMYB1 in purple-fleshed tubers, the color diversity suggests the involvement of other MYB activators. We previously identified IbMYB2 and IbMYB3 in leaf coloration. Here, we explored the chromosomal localization, phylogeny, and evolutionary scenario of IbMYB1/2/3 using four Ipomoea genomes. IbMYB1/2/3 are located adjacently as an anthocyanin MYB gene cluster, likely resulting from tandem duplications. All three IbMYBs induced anthocyanins in tobacco and activated the promoters of the key anthocyanin pathway genes IbCHS-D and IbDFR-B. Expression analysis across sweetpotato varieties indicated that IbMYB1 dominates purple tuber flesh, whereas IbMYB2/3 contribute to leaf and tuber skin coloration. Overexpression of IbMYB1/2/3 in sweetpotato all induced purple fibrous roots. Transcriptomics of IbMYB2-OX fibrous roots revealed upregulation of the entire anthocyanin pathway genes. Among the most highly upregulated transcription factors were IbMYB27 and IbHLH2. An inhibitory effect induced by IbMYB27 likely accounts for the faint pigmentation in IbMYB2-OX storage roots. The role of IbMYB2/3 in fine-tuning sweetpotato’s purple pigmentation was highlighted. This study supplements previous work on IbMYB1, providing valuable insights into the intricate anthocyanin regulatory network and supporting sweetpotato breeding efforts for improved nutritional and aesthetic qualities. Full article