GSDS 2.0: an upgraded gene feature visualization server

Genome-wide identification and analysis of the NF-Y transcription factor family reveal its potential roles in tobacco (Nicotiana tabacum L.)

Nuclear Factor Y (NF-Y) represents a group of transcription factors commonly present in higher eukaryotes, typically consisting of three subunits: NF-YA, NF-YB, and NF-YC. They play crucial roles in the embryonic development, photosynthesis, flowering, abiotic stress responses, and other essential processes in plants. To better understand the genome-wide NF-Y domain-containing proteins, the protein physicochemical properties, chromosomal localization, synteny, phylogenetic relationships, genomic structure, promoter cis-elements, and protein interaction network of NtNF-Ys in tobacco (Nicotiana tabacum L.) were systematically analyzed. In this study, we identified 58 NtNF-Ys in tobacco, respectively, and divided into three subfamilies corresponding to their phylogenetic relationships. Their tissue specificity and expression pattern analyses for leaf development, drought and saline-alkali stress, and ABA response were carried out using RNA-seq or qRT-PCR. These findings illuminate the role of NtNF-Ys in regulating plant leaf development, drought and saline-alkali stress tolerance, and ABA response. This study offers new insights to enhance our understanding of the roles of NtNF-Ys and identify potential genes involved in leaf development, as well as drought and saline-alkali stress tolerance of plants.

DlMYB1 positively regulates anthocyanin biosynthesis and contributes to red exocarp coloration in red-skinned longan

Red-skinned longan (Dimocarpus longan Lour.) varieties exhibit striking exocarp coloration and high potential market value. In this study, we characterized anthocyanin accumulation in the red-skinned longan RP1901 using high performance liquid chromatography (HPLC). The exocarp of RP1901 accumulated 264.2 μg g-1 fresh weight (FW) of petunidin 3-O-glucoside (Pt3G) and 28.2 μg g-1 FW of cyanidin 3-O-glucoside (Cy3G), whereas the common longan cultivar ShiXia showed no detectable levels of these pigments. Preliminary RNA-seq analysis suggested upregulation of anthocyanin pathway genes and DlMYB1 gene. RT-qPCR analysis indicated that F3'H, ANS, GST4, and DlMYB1 were significantly upregulated in the exocarp of RP1901 compared to ShiXia. Bioinformatic analysis revealed that DlMYB1 is structurally conserved across species but diverges by 12 amino acids from ShiXia (same species) and 16 amino acids from LcMYB1 in Litchi chinensis (different genus), indicating significant genetic variation between red-skinned and common longan varieties. Subcellular localization of a DlMYB1-eGFP fusion protein confirmed its nuclear localization, consistent with transcription factor function. Overexpression of DlMYB1 in Arabidopsis thaliana led to upregulated expression of AtPAL1, AtDFR, AtLDOX, and AtGST genes and significant accumulation of anthocyanin in transgenic plants. These findings demonstrate that DlMYB1 acts as a positive regulator of anthocyanin biosynthesis and plays a key role in the pigmentation of red-skinned longan RP1901.

Urban landscape lakes with backwater hide higher antibiotic resistance risk than living water

The pollution of antibiotic resistance genes (ARGs) in urban landscape lakes threatens the aquatic ecosystems and public health. However, a comprehensive understanding of the fate of ARGs in different types of park landscape lakes (i.e., backwater and living water) remains deficient. Here, we profiled the distribution, diversity, origin and potential spread risk to human of ARGs in backwater and living water using metagenomics and 16S rRNA gene sequencing. Our results showed higher antibiotic resistance risk presented in backwater due to higher ARG diversity, while higher resistance transfer risk occurred in living water due to higher mobile genetic elements (MGEs) diversity. Source tracking analysis revealed Yellow River water was the main the dominant source of ARGs in both backwater and living water, with an average contribution of 41.06 % and 65.82 %, respectively. Notably, nine high-risk ARGs (such as mdtM and msrA) significantly enriched in human feces, implying possible spread risk from environment to human. Metagenomics binning revealed that MAGs carrying ARGs mainly belong to Actinobacteria, while MAGs carrying MGEs belong to Proteobacteria. Our study highlights the significance of healthy management of park landscape lakes to prevent the spread of resistomes to the public.

Identification of grapevine BASIC PENTACYSTEINE transcription factors and functional characterization of VvBPC1 in ovule development

Seedless grapes are gaining increasingly attention in the market because of their desirable traits. Therefore, understanding the molecular genetic regulation of seed development and abortion is crucial for the advancement of seedless cultivars. Recent studies have shown that AGAMOUS-LIKE11 (VvAGL11), an ortholog of Arabidopsis SEEDSTICK (STK), plays a key role in grape ovule development, and amino acid substitution mutations result in seed abortion. However, the regulatory pathways involved in this process are poorly understood in grapevines. In this study, we identified four BASIC PENTACYSTEINE (BPC) genes in the grapevine (Vitis vinifera L.) genome and analyzed their evolutionary relationships, subcellular localization, and expression patterns. VvBPC1 was identified as an upstream regulatory factor of VvAGL11 in a yeast one-hybrid assay. Dual-luciferase assays confirmed that VvAGL11 is negatively regulated by VvBPC1, and the production of small seeds by heterologous overexpression of VvBPC1 in tomatoes results from the suppression of VvAGL11 expression. Furthermore, assays in yeast cells demonstrated that VvBPC1 interacts with VvBELL1. Taken together, this study not only establishes the foundation for further exploration of the molecular mechanisms of the VvBPC1-VvBELL1-VvAGL11 module in regulating grape seed development but also provides new insights into the genetic improvement of seedless grapes.

Evolutionary insights and poly(I:C)-induced changes in expression and m6A modifications of il17ra and il17rc in Miichthysmiiuy

Interleukin-17 receptor A (IL17RA) and IL17RC form a receptor complex critical for initiating IL-17A-mediated immune responses, a hallmark of T helper 17 (Th17) cells. In this study, il17ra and il17rc were identified in miiuy croaker (Miichthys miiuy) and bioinformatics analysis revealed their evolutionary and structural conservation, underscoring their roles in immunity. However, there has been little research on the IL-17 receptor family from the perspective of N6-methyladenosine (m6A) modifications. Using methylated RNA immunoprecipitation sequencing (MeRIP-seq), we identified strong m6A modifications on the last exons of il17ra and il17rc, validated by MeRIP-PCR. Poly(I:C) stimulation significantly upregulated il17ra and il17rc expression, while reducing their m6A modification levels, implicating these changes in antiviral immunity. Interestingly, cycloleucine (CL), a well-known methylation inhibitor, did not alter the expression of il17ra and il17rc but promoted the nuclear-to-cytoplasmic transport of il17ra mRNA, potentially influencing its translation process. These findings provide valuable insights into the regulatory roles of m6A modifications in il17ra and il17rc function and highlight their importance in the antiviral immune response.

Identification of pine SF3B1 protein and cross-species comparison highlight its conservation and biological significance in pre-mRNA splicing regulation

As a key component of the largest subunit of the splicing machinery, SF3B1 plays essential roles in eukaryotic growth and development. However, only a few studies have focused on the evolutionary features and functions of this protein in plants. In this study, with the assistance of a bioinformatic analysis, we determined the complete coding sequence of the gene encoding the pine SF3B1 protein using RT-PCR and DNA sequencing. The evolutionary features of SF3B1 proteins were further examined based on a phylogenetic tree of SF3B1 homologous proteins from different eukaryotes, along with comprehensive comparisons of their functional domains, conserved motifs, and cis-regulatory elements and the structures of the corresponding genes. Furthermore, the effects of the splicing modulator GEX1a on several plant species were analysed, confirming that the re-identified SF3B1, with a full-length HEAT repeat domain, is expressed and functions in pre-mRNA splicing regulation in pines. In summary, we conducted a systematic cross-species comparison of SF3B1 homologous proteins, with an emphasis on complete sequence determination and the functional confirmation of pine SF3B1, illustrating the conservation of homologous proteins in plants. This study provides a valuable reference for understanding functional and regulatory mechanisms, as well as the potential applications of SF3B1.

Genome-wide identification and expression patterns of uridine diphosphate (UDP)-glycosyltransferase genes in the brown planthopper, Nilaparvata lugens

Uridine diphosphate-glycosyltransferases (UGTs) are responsible for glycosylation by combining various small lipophilic molecules with sugars to produce water-soluble glycosides, which are crucial for the metabolism of plant secondary metabolites and detoxification in insects. This study presents a genome-wide analysis of the UGT gene family in the brown planthopper, Nilaparvata lugens, a destructive insect pest of rice in Asia. Based on the similarity to UGT homologs from other organisms, 20 putative NlUGT genes were identified in N. lugens. Sequence analysis revealed an average amino acid identity of 45.64 %; however, catalytic and sugar-binding residues, along with UGT signature motifs, were highly conserved. Phylogenetic analysis showed that the 20 NlUGTs were clustered into three main groups. The motif numbers ranged from 5 to 10, with motifs 1 and 4 being found in the functional domains of all 20 NlUGT proteins. Tandem and segmental duplication analysis identified one tandem duplication pair (UGT386K7 and UGT386K8) and two pairs of collinearity genes (UGT362C6/UGT386J4 and UGT386C2/UGT386G5) that expanded through segmental duplication within the UGT gene family of N. lugens. Combining the transcriptome and real-time quantitative PCR data showed that gut, antennae, integument, and ovaries were the tissues enriched with NlUGT gene expression. Six NlUGTs were present mainly in the gut, suggesting their putative roles in detoxification. This research provides valuable information on the molecular and genetic basis of NlUGTs, establishing a solid foundation for subsequent functional investigations of UGTs in planthopper, as well as paving the way for identifying potential targets to manage N. lugens effectively.

Genome-wide identification of aquaporin and their potential role in osmotic pressure regulation in Ruditapes philippinarum

Aquaporins (AQPs) are specialized membrane proteins that create selective water channels, facilitating the transport of water across cell membranes and playing a vital role in maintaining water balance and regulating osmotic pressure in aquatic animals. This study identified 9 aquaporin genes from the genome of R. philippinarum, and a comprehensive analysis was conducted on their gene structure, phylogenetic relationships, protein structure, and chromosome localization. RNA-seq data analysis revealed that aquaporin genes were differentially expressed at different developmental stages, in tissue distribution, and in response to salinity stress. In addition, qPCR results revealed that the expression levels of aquaporin genes (AQP1, AQP4d, and AQP3) were significantly elevated in response to both acute low and high salinity stress, suggesting their important role in osmotic pressure regulation in R. philippinarum. This study's results offer an important reference for further investigations into the regulation of osmotic pressure and salinity adaptation of aquaporin in R. philippinarum.

The ABC transporters and their epigenetic regulation under drought stress in chickpea

Chickpea (Cicer arietinum L.) is a globally essential pulse crop, providing dietary protein for millions. However, it suffers significant yield losses due to drought stress, therefore, identification of genes that confer drought tolerance is crucial. The ATP-binding cassette (ABC) transporters are vital proteins in plant growth and development, facilitating the transport of phytohormones like abscisic acid (ABA) that helps plants adapt to drought conditions. In this study, we identified 121 ABC transporter genes in chickpea, categorized into eight subfamilies. Consistent with other crops, the CaABCG family was the largest, with 48 members, while the CaABCE family had only one protein. Structural analysis revealed a conserved domain organization, including Walker A and B motifs and the ABC signature motif. Both segmental and tandem duplications were observed, with the highest duplication in the CaABCG and CaABCC subfamilies. Using RNA-seq and Whole Genome Bisulfite Sequencing (WGBS) data from the root tissues of two chickpea genotypes contrasting in drought tolerance, we found that DNA methylation at cytosine residues might regulate these genes under drought stress. Notably, the CaABCG41 gene was identified as drought-responsive, showing significant upregulation (p < 0.05) and hypermethylation (q < 0.01) in the drought tolerant genotype compared to the drought sensitive genotype under drought stress. CaABCG41 thus holds potential for developing drought-tolerant chickpea cultivars.

Genome-wide identification, evolution, and expression analysis of the bone morphogenetic protein gene family in Myxocyprinus asiaticus

Bone morphogenetic proteins (BMPs) are important growth factors belonging to the TGF-β superfamily. These factors not only play a vital role in skeleton formation in young fish but also regulate the morphological development of M. asiaticus, with Group II genes regulating morphology mainly during the juvenile stage. This study investigated how BMP genes regulate Myxocyprinus asiaticus development and function and explored the role of the BMP family in fish morphological development. In this study, 43 BMPs were identified and classified into five groups: BMP1/3/11/15 (Group I), BMP12/13/14 (Group II), BMP2/4/16 (Group III), BMP9/10 (Group IV), and BMP5/6/7/8 (Group V). Analyses of the gene structures and conserved motifs revealed the conservation of the BMP gene family in M. asiaticus. In M. asiaticus, gene fragmentation, duplication, and 4R whole-genome duplication events contributed to BMP gene family expansion. Furthermore, expression pattern analysis and qRT-PCR revealed that changes in M. asiaticus BMP gene expression during different developmental stages were due to body size alterations, highlighting the major impact of the BMP gene on body size variation in this species. Our study provides fundamental data for investigating the morphological development of M. asiaticus and lays the framework for understanding the genetic mechanisms of body size variation in scleractinian fishes, with potential applications in the artificial breeding and conservation of M. asiaticus.

AMHY and sex determination in egg-laying mammals

BACKGROUND

Egg-laying mammals (monotremes) evolved multiple sex chromosomes independently of therian mammals and lack the sex-determining gene SRY. The Y-localized anti-Müllerian hormone gene (AMHY) is the candidate sex-determination gene in monotremes. Here, we describe the evolution of monotreme AMHX and AMHY gametologues and for the first time, investigate their expression during gonad sexual differentiation in a monotreme.

RESULTS

Monotreme AMHX and AMHY have significant sequence divergence at the promoter, gene, and protein level, likely following an original allele inversion in the early stages of monotreme sex chromosome differentiation but retaining the conserved features of TGF-β molecules. We show that the expression of sexual differentiation genes in the echidna fetal gonad, including DMRT1 and SOX9, is significantly different from that of therian mammals. Importantly, AMHY is expressed exclusively in the male gonad during sexual differentiation consistent with a role as the primary sex-determination gene whereas AMHX is expressed in both sexes. Experimental ectopic expression of platypus AMHX or AMHY in the chicken embryo did not masculinize the female urogenital system, as does chicken AMH, a possible result of mammalian-specific changes to AMH proteins preventing function in the chicken.

CONCLUSIONS

Our results provide insight into the early steps of monotreme sex chromosome evolution and sex determination with developmental expression data strongly supporting AMHY as the primary male sex-determination gene of platypus and echidna.

Genome-wide identification, expression analysis, and stress response analysis of the RdbZIP gene family in Rhododendron delavayi

BACKGROUND

Basic leucine zipper (bZIP) gene family members represent one of the most diverse and largest groups of transcription factors in eukaryotes. Research has demonstrated that bZIP transcription factors play crucial roles not only in plant growth and development but also in response to various abiotic stresses. However, studies focusing on bZIP factors in Rhododendron delavayi (RdbZIPs) remain limited.

RESULT

In this study, a total of 59 RdbZIPs were identified using bioinformatics approaches, and these could be classified into 13 subfamilies based on the genomic data of R. delavayi. Members of the same RdbZIP subfamily exhibited similar gene structures and conserved motifs, and were unevenly distributed across the 13 chromosomes of R. delavayi. Collinearity analysis revealed a total of 20 duplication events, comprising 3 pairs of tandem duplications and 17 pairs of segmental duplications. Additionally, cis-acting element analysis indicated that RdbZIP family members may be involved in various biological processes, including transcription, development, hormone regulation, and responses to biotic and abiotic stresses. Transcriptomic analysis revealed that RdbZIP family genes were highly expressed in reproductive tissues. RT-qPCR expression analysis revealed that many selected RdbZIP genes were significantly upregulated under high salinity and drought conditions, suggesting their potential involvement in stress-responsive regulatory networks.

CONCLUSION

This study provides the first comprehensive characterization of the bZIP transcription factor family in Rhododendron delavayi, laying a foundational framework for functional studies of individual RdbZIP genes. The results highlight the pivotal role of RdbZIP genes in abiotic stress tolerance, which is crucial for understanding the adaptive mechanisms of R. delavayi. Future research should focus on the functional validation of key RdbZIP genes and elucidation of their regulatory pathways, which may contribute to the genetic improvement of Rhododendron species under adverse environmental conditions.

CLINICAL TRIAL

Not applicable.

In silico identification and functional annotation of universal stress protein (USP) gene family in Chenopodium quinoa

Quinoa is a resilient crop with significant genetic diversity, enabling it to thrive in various climates. This study focuses on the Universal Stress Protein (USP) gene family in quinoa. It helps plants maintain homeostasis in response to drought, high salinity, extreme temperatures, and scavenging reactive oxygen species. The research conducted a genome-wide analysis of C. quinoa USP genes (CqUSPs). The gene structure, distribution of motifs, phylogenetic history, and duplication of CqUSPs were analysed. Analysis of cis-elements, protein-protein interactions, and micro-RNAs that target CqUSPs revealed important insights into the regulatory mechanisms, functional associations and post-transcriptional control of these genes. We have identified 41 sequences inside the allotetraploid genome. Domain architecture helped us understand the multifunctional nature of CqUSPs. Analysis of transcriptome data has demonstrated that the CqUSP gene family plays a role in the defence response to drought and heat stress conditions in quinoa. Protein-protein interaction studies showed their roles in amino acid metabolism, chaperone activity, ubiquitination, and DNA repair mechanisms. This comprehensive study reveals the identification and characterisation of CqUSP genes, offering valuable insights for further exploration of abiotic stress tolerance in quinoa. Additional research, such as expression profiling, might assist in confirming the stress-specific transcriptional regulation of these genes. To the best of our knowledge this the first detailed study conducted on the identification and interaction network of USP gene family in quinoa.

Genome-wide identification and expression analysis of ACS and ACO gene family in Ziziphus jujuba mill during fruit ripening

The jujube (Ziziphus jujuba Mill.) cultivar 'Dongzao' is globally popular as a fresh fruit but faces challenges with shelf life, which is positively associated with ethylene production. The two key enzymes involved in ethylene biosynthesis, 1-Aminocyclopropane-1-Carboxylic acid Synthase (ACS) and 1-Aminocyclopropane-1-Carboxylic acid Oxidase (ACO), are encoded by ACS and ACO gene families, respectively. This study identified 7 ZjACS genes and 36 ZjACO genes in 'Dongzao' and revealed extensive evolutionary divergence between 'Dongzao' and Arabidopsis thaliana. Phylogenetic relationships were more apparent when analyzing genes with similar structures, motifs and subcellular localization predictions. Transcriptome profiling showed that a substantial number of the ZjACS and ZjACO genes displayed stage-specific expression tendency during fruit development. Co-expression analysis showed that 4 ZjACS and 9 ZjACO genes were linked to transcription factors (TFs) involved in fruit ripening. The diverse regulatory factors, including ERF, NAC and WRKY TFs and cis-acting regulatory elements, likely contribute to the complex roles of the ZjACSs and ZjACOs during ripening of jujube fruits. This study sheds light on the genetic regulation of ethylene biosynthesis in 'Dongzao' jujube ripening, providing insights for postharvest research in this economically important species.

RcPLATZ8 as a novel negative regulator of flowering in Rosa chinensis

KEY MESSAGE

Comprehensive analysis of the RcPLATZ gene family in Rosa chinensis reveals RcPLATZ8 as a novel negative regulator of flowering, offering insights for targeted breeding to manipulate flowering traits. Flowering regulation in Rosa chinensis is essential for improving ornamental and commercial traits, but its molecular mechanisms remain poorly understood. In this study, we identified and characterized ten members of the PLANT AT-RICH SEQUENCE AND ZINC-BINDING (PLATZ) protein family in R. chinensis through genome-wide analysis and protein domain validation using the Pfam database. Among these, we focused on RcPLATZ8, a novel negative regulator of flowering. Expression analysis via RT-qPCR revealed that RcPLATZ8 is predominantly expressed in floral organs, including stamens, pistils, and petals, and exhibits significant responsiveness to key plant hormones, such as abscisic acid (ABA), gibberellins (GA), and jasmonic acid (JA). Functional assays showed that overexpression of RcPLATZ8 in Arabidopsis resulted in delayed flowering and increased leaf number, whereas silencing RcPLATZ8 in R. chinensis led to early flowering. Furthermore, Weighted Gene Co-expression Network Analysis (WGCNA) identified that RcPLATZ8 is part of the 'red module,' which is strongly associated with flowering-time regulatory genes, including SHORT VEGETATIVE PHASE (SVP). These findings provide new insights into the molecular regulation of flowering in roses, demonstrating that RcPLATZ8 may plays a key role in integrating hormonal signals and floral development. Our study not only expands the functional understanding of the PLATZ family but also offers potential strategies for molecular breeding aimed at improving flowering traits for horticultural applications.

Comprehensive structural, evolutionary and functional analysis of superoxide dismutase gene family revealed critical role in salinity and drought stress responses in chickpea (Cicer arietinum L.)

Superoxide dismutase (SOD), a metalloenzyme, catalyses the dismutation of superoxide anions (O2•‾) into molecular oxygen (O2) and hydrogen peroxide (H2O2), perform crucial roles in plant growth, development, and responses to multiple abiotic stressors. Present study attempted to explore the SOD gene family in chickpea and their key role in salinity and drought tolerance. Computational analysis of SOD gene family in chickpea revealed 10 SODs (4 Cu/ZnSODs and 6 Mn/FeSODs) and explored their chromosomal location, evolutionary relationships, structure, conserved motifs, promoter analysis, tissue specific expression analysis, protein-protein interactions and docking of CaSODs with their predicted interacting partners. GO (gene ontology) and KEGG analysis revealed association of CaSODs in ROS signalling, metal binding, and catalysis, which contribute in stress tolerance and cellular homeostasis. Further, transcriptomic analysis revealed that CaSODs showed differential expression pattern under salinity and drought conditions. qRT-PCR was performed to analyse the response of CaSODs in salinity ICCV2 (tolerant), JG62 (susceptible) and drought ICC4958 (tolerant), ICC1882 (susceptible) genotypes. A comparative analysis of gene expression in ICCV2, JG62, ICC4958 and ICC1882 revealed number of CaSODs, such as CaCSD3, CaCSD2, and CaCSD4, showed high expression in response to salinity and drought stress, suggesting their involvement in stress response pathways as predicted by GO analysis. miRNA analysis revealed that CaCSDs and CaMSDs were targeted by miRNAs (CaCSD4-miR398a/b/c, and CaMSD-miR747). Additionally, the study found SNP variation in two CaSODs (CaMSD5 and CaMSD6) promoter regions, which could affect expression pattern of these genes. Our findings provide the basis to understand the functional roles of CaCSD3/CaCSD4 in salinity tolerance and CaCSD3 for drought tolerance by reducing oxidative stress, offer important information for future research with the objective of improving chickpea stress tolerance using breeding or genetic engineering technologies.

Integrative Identification of Chloroplast Metabolism-Related RETICULATA-RELATED Genes in Soybean

As a globally important leguminous crop, soybean (Glycine max L.) serves as a vital source of edible oils and proteins for humans and livestock. Oils in leaves can help crops combat fungal infections, adapt to temperature changes via fatty acid modulation, and support resource recycling during leaf senescence. However, accumulating oils in leaves is a fundamental challenge due to the need to balance the inherently competing photosynthesis and fatty acid biosynthesis processes within chloroplasts. RETICULATA-RELATED (RER), known to regulate chloroplast function and plastid metabolism in Arabidopsis, plays an essential role in leaf development. Here, 14 non-redundant GmRER genes were identified in soybean and phylogenetically classified into four subclades. Most Arabidopsis RER genes were evolutionarily preserved as gene duplicates in soybean, except for GmRER5 and GmRER6. RNA secondary structures spanning the coding sequences (CDSs), the 5'- and 3'- untranslated regions (UTRs) of GmRERs, displayed exceptional structural plasticity in CDSs, while exhibiting limited conservation in UTRs. In contrast, protein structures retained conserved folds, underscoring evolutionary constraints on functional domains despite transcriptional plasticity. Notably, GmRER4a and GmRER4b represented an exceptional case of high similarity in both protein and RNA structures. Expression profiling across fourteen tissues and three abiotic stress conditions revealed a dynamic shift in expression levels between leaf-predominant and root-enriched GmRER paralogs after stress treatments. A comparative transcriptome analysis of six soybean landraces further revealed transcriptional polymorphism in the GmRER family, which was associated with the expression patterns of lipid biosynthesis regulators. Our comprehensive characterization of GmRERs may offer potential targets for soybean breeding optimization in overall plant oil production.

Genome-Wide Identification, Phylogeny and Expressional Profiles of Mitogen Activated Protein Kinase Gene Family in Blakeslea trispora

In eukaryotes, the mitogen-activated protein kinase (MAPK) cascade pathway is a highly conserved cell signaling mechanism that is essential for stress response, growth, and development. MAPK cascade genes have currently been identified and characterized in a wide range of fungi, although they have not been fully understood in early divergent fungal lineages like the Mucoromycota, which contains Mucoromycotina, Glomeromycotina, and Mortierellomycotina. In this study, a genome-wide investigation of Blakeslea trispora (Mucorales, Choanephoraceae) revealed a total of 19 MAPK cascade genes, including 9 BtMAPKKKs, 4 BtMAPKKs, and 6 BtMAPKs genes. Using phylogenetic analysis, it was found that the kinase domain sequences and motif composition of the three MAPK, MAPKK, and MAPKKK lineages are substantially conserved in fungi. Whole genome duplication analysis indicated that B. trispora has four and nine duplication pairs in the MAPK and MAPKKK genes, respectively, which are expanded by segmental replication events. BtHog2, the orthologous protein of Hog1, exhibits a substantial rise in transcription levels under blue light irradiation, indicating its function in light signal response and transduction. Several sets of interacting protein pairs were found using molecular docking analysis and yeast two-hybrid assay, providing a comprehensive MAPK cascade signaling network in B. trispore. Furthermore, MAPK cascade proteins show varying transcription levels in response to blue light and sex hormone stimulation, as well as variable treatment duration. BtMAPKKK9 and BtBck1 are strongly induced during sexual interaction, indicating their involvement in the response to trisporic acid and the subsequent alterations in hyphal cell wall structure. These findings shed light on the evolution of MAPK cascade genes and the functional mechanisms underlying MAPK cascade genes in response to light and sex hormone signaling pathways in B. trispore.

Genome-wide identification and expression profiles of NAC transcription factors in Poncirus trifoliata reveal their potential roles in cold tolerance

BACKGROUND

Citrus, a globally vital economic crop, faces severe challenges due to extreme climatic conditions and diseases/pests attack. Poncirus trifoliata is closely related to citrus and shows unique cold tolerance, making it a crucial material for unraveling genes involved in cold tolerance. NAC (NAM, ATAF1/2, CUC2) transcription factors play important roles in plant growth, development, and stress responses. However, their evolution patterns and gene functions in citrus remain poorly studied. This study aims to elucidate the genomic characteristics and evolution of the NAC genes in P. trifoliata, and to analyze their expression patterns and conduct functional validation under cold stress.

RESULTS

Genome-wide analysis identified 135 PtrNAC genes in P. trifoliata with non-random chromosomal distribution, including 20 gene clusters. 57.78% of the NAC genes are located in the chromosomes 3, 4 and 5. Gene duplication analysis revealed that proximal and tandem duplications as primary expansion mechanisms, with tandem repeats specifically driving gene expansion in citrus lineages (subfamilies IV, V, and VII). Collinearity analysis showed that 24.44% of the PtrNAC genes were retained in homologous regions, and Ka/Ks ratio analysis further confirmed that purifying selection dominated their evolutionary process. Transcriptome landscapes revealed that Pt5g024390 (PtrNAC2) was induced to the greatest degree under the cold stress. Meanwhile, expression level of PtrNAC2 in tetraploid was more than two folds higher compared to diploid counterpart in the presence of cold stress. Virus-induced gene silencing of PtrNAC2 led to significantly enhanced cold tolerance, implying that it plays a negative role in regulation of cold tolerance.

CONCLUSION

This study systematically elucidated the global distribution and evolutionary patterns of NAC genes in P. trifoliata. In addition, the NAC gene exhibit adaptive expansion driven by tandem duplications. The identification of PtrNAC2, a negative regulator of cold tolerance in P. trifoliata, provides valuable insights into unravelling potential candidates for engineering cold tolerance in citrus.

Durum wheat nuclear factor Y (NF-Y) a subfamily: structure, phylogeny, and expression analysis in response to hormones and abiotic stresses

Nuclear factor-Y (NF-Y) transcription factors are heterotrimeric complexes that are widely distributed in eukaryotes and play essential roles in many biological processes. Although NF-YA proteins have been characterized in numerous plants, their contribution to the response of durum wheat (Triticum turgidum ssp. durum) to environmental factors has not been reported. Thus, this study was aimed at identification and characterization of Triticum turgidum TtNF-YA family members through genome-wide analysis. Twelve NF-YA genes were discovered in Triticum turgidum. Discovered genes were distributed across eight chromosomes, while their encoded proteins were localized in cell nucleus. Structure and motif pattern analyses revealed that the TtNF-YA genes were relatively conserved. The expression of TtNF-YAs genes was significantly induced by several stressors and their expression profiles differed in various tissues and at various development stages. Notably, TtNF-YA2 A-1 and TtNF-YA2B-1 exhibited the greatest increase in response to Polyethylene glycol, while TtNF-YA4 A and TtNF-YA4B-1 showed the highest increase under salt stress. Additionally, TtNF-YA5B-1 and TtNF-YA6 A-1 displayed pronounced upregulation when exposed to exogenous Abscisic acid, suggesting that TtNF-YA are involved in a series of cellular and developmental events. This finding was corroborated by the recognition of several cis-regulatory elements in the TtNF-YAs promoter region, associated with the applied treatments. Overexpression of TtNF-YA2 A-1, TtNF-YA2B-1, TtNF-YA4 A, TtNF-YA4 A-1, TtNF-YA4B-1, and TtNF-YA5 A-2 genes in Saccharomyces cerevisiae showed that these genes increase cell tolerance to multiple stresses. Our results will facilitate subsequent functional analysis of TtNF-YAs genes, which emerge as promising targets for genetic engineering for increasing wheat tolerance to multiple stresses.

Genome-Wide Identification of bZIP Gene Family in Lycium barbarum and Expression During Fruit Development

Wolfberry (Lycium barbarum L.) is a valued traditional medicinal plant and dietary supplement in China. The basic leucine zipper (bZIP) transcription factor (TF) family is a multifunctional group of regulatory proteins critical to plant biology, orchestrating processes such as growth and development, secondary metabolite biosynthesis, and stress responses to abiotic conditions. Despite its significance, limited information about this gene family in wolfberry is available. In this study, a total of 66 LbabZIP genes were identified, exhibiting a non-uniform distribution across all 12 chromosomes. Phylogenetic analysis divided these genes into 13 subgroups based on comparison with Arabidopsis bZIP proteins. Analysis of gene structures and conserved motifs revealed high similarities within individual subgroups. Gene duplication analysis indicated that dispersed duplication (DSD) and whole-genome duplication (WGD) events were the primary drivers of LbabZIP gene family expansion, with all duplicated genes subject to purifying selection. Cis-regulatory element (CRE) analysis of LbabZIP promoter regions identified numerous elements associated with plant growth and development, hormone signaling, and abiotic stress responses. Gene Ontology (GO) annotation further indicated that the LbabZIP genes are involved in transcriptional regulation, metabolism, and other biological processes. Transcriptome data and quantitative real-time PCR (qRT-PCR) analysis demonstrated tissue-specific expression patterns for several LbabZIP genes. Notably, LbaZIP21/40/49/65 showed significant involvement in wolfberry fruit development. Subcellular localization assays confirmed that these four proteins are nucleus-localized. This comprehensive analysis provides a theoretical foundation for future studies investigating the biological functions of LbabZIP genes, especially their role in wolfberry fruit development.

Genome-Wide Characterization of WRKY Gene Family in Camellia chekiangoleosa Identifies Potential Regulatory Components in Pigment Biosynthesis Pathways

The WRKY gene family is essential for controlling a variety of plant physiological functions, yet the involvement of specific WRKY members in pigment biosynthesis and accumulation in Camellia chekiangoleosa remains unexplored, particularly in anthocyanins and carotenoids, which play crucial roles in the pigmentation of C. chekiangoleosa. This study systematically identified 87 WRKY genes across 15 chromosomes in C. chekiangoleosa through bioinformatic approaches. Further structural and phylogenetic analyses of these TFs enabled their classification into six different subgroups. WRKY family expansion was shown to be mostly driven by tandem duplication. W-box elements, which can be binding sites for WRKY transcription factors, were present in a number of biosynthetic genes in the pigment production pathway. Yeast one-hybrid assay confirmed that five WRKY transcription factors (CchWRKY15/24/33/47/76) directly bind to the promoter regions of two key biosynthetic genes, CchPSY1 and Cch4CL1. Intriguingly, among the five WRKYs tested, the expression levels of CchWRKY15, CchWRKY33, and CchWRKY47 showed the strongest positive associations with flavonoid accumulation (p < 0.05, Pearson correlation analysis).These findings provide novel insights into the evolutionary patterns, transcriptional regulation, and functional characteristics of CchWRKYs, while elucidating their possible regulatory mechanisms in the fruit coloration of C. chekiangoleosa.

Transcriptome profiling and alternative splicing analysis of skeletal muscle in Pseudocaranx dentex: insights into slow-twitch and fast-twitch muscle specialization

Alternative splicing (AS) plays a crucial role in regulating muscle type specialization characteristics in mammals but has been rarely explored in teleost. In this study, we combined Iso-Seq and RNA-Seq technologies to profile the transcriptome and AS landscape of slow-twitch muscle (SM) and fast-twitch muscle (FM) in a migratory teleost, Pseudocaranx dentex. We identified 24,096 full-length transcripts and 14,346 isoforms in SM, and 18,483 full-length transcripts and 10,541 isoforms in FM, revealing extensive transcript and isoform diversity. The 3086 differentially expressed transcripts (DETs) were found to contribute to metabolic and contractile differences between SM and FM. Additionally, we detected 5761 AS events in SM and 4543 in FM, with skipped exons (SE) and intron retention (IR) being the predominant AS types. Furthermore, 325 differentially AS genes (DASGs) were found to regulate differences in metabolic processes, organelles organization, cellular component organization, and microtubule-based processes. Importantly, transcripts of tnni2, capzb, neb, and pdlim5 produced by AS with significant expression differences between SM and FM were determined to associate with sarcomere assembly. This study provides the first comprehensive view of transcriptome complexity and splice variants in teleost skeletal muscle and sheds light on the molecular mechanisms underlying muscle type specialization through post-transcriptional regulation.

Genome-Wide Identification and Expression Profiling of Phosphatidylethanolamine-Binding Protein (PEBP) Genes in Helianthus annuus L

The phosphatidylethanolamine-binding protein (PEBP) gene family is critical for regulating plant growth, development, and flowering. Sunflower (Helianthus annuus L.) is the fourth most important oilseed crop globally. However, the genomic structure and functional diversity of PEBP genes in sunflower remain unexplored. Leveraging the recently assembled telomere-to-telomere (T2T) sunflower genome, a genome-wide analysis of the HaPEBP family was carried out. A total of 12 PEBP genes were identified in sunflower and categorized into three subfamilies: TFL1-like, FT-like, and MFT-like. Phylogenetic and synteny analyses revealed that tandem duplication events have substantially contributed to the evolution and expansion of the HaPEBP gene family. Furthermore, the analysis of the promoter regions revealed 77 distinct cis-acting elements, including 35 related to light signaling and growth regulation, highlighting their potential involvement in the regulation of flowering and development in sunflower. Expression profile analysis using RNA-seq data across various tissues indicated that FT-like and TFL1-like HaPEBP genes may be the key regulators of flowering time and plant architecture in sunflower varieties. This study offers valuable insights into the structural, evolutional, and functional dynamics of the HaPEBP gene family and holds significant implications for sunflower breeding strategies aimed at optimizing flowering time and plant architecture traits.

Genome-wide analysis of the laccase gene family in tossa jute (Corchorus olitorius): insights into stem development, lignification, and responses to abiotic stress

Tossa jute (Corchorus olitorius) dominates global jute cultivation but has a high lignin content (13-14%) in its fibres, making them coarse and limiting their industrial applications. Reducing the lignin content requires a deeper understanding of the lignification process and the associated genes. Laccase (EC 1.10.3.2) is a key enzyme in the final step of lignin biosynthesis. A genome-wide analysis of the 361 Mb C. olitorius genome identified 46 laccase genes (ColLACs) from a total of 28,479 genes. In-silico analysis revealed that ColLAC genes are distributed across seven chromosomes, encode proteins ranging from 7.98 to 173.99 kDa, with 74 to 1548 amino acids and 10 conserved motifs. Additionally, 48.83% of ColLACs are predicted to be transmembrane proteins. Phylogenetic analysis classified them into eight groups, with GO term assignments suggesting their involvement in lignification. Tissue-specific expression analysis showed that 43.47% of ColLAC genes are predominantly expressed in roots, aligning with RNA-seq data. ColLAC gene expression varied across the developmental stages, from seedling to fibre harvest, and was influenced by heavy metal copper and abscisic acid (ABA) treatments. This variation correlated with upstream cis-acting elements. Ath-miR397 target sites were identified in 14 ColLAC genes, indicating potential post-transcriptional regulation. Further expression analysis in X-ray-induced bfs (bast fibre-shy) mutant tossa jute lines suggested that ColLAC34 is involved in both lignification and structural development, while ColLAC22, ColLAC40, and ColLAC46 play key roles in lignification. This study presents the first comprehensive genome-wide identification and characterization of the LAC gene family in jute. Understanding ColLAC functions could facilitate the development of low-lignin jute fibres, meeting the growing industrial demand for high-quality natural fibres of jute.

HsGA20ox1, HsGA3ox1, and HsGA2ox1 Are Involved in Endogenous Gibberellin Regulation Within Heracleum sosnowskyi Ovaries After Gibberellin A3 Treatment

This study aims to investigate the endogenous gibberellin levels and related genes analysis of noxious invasive weed Heracleum sosnowskyi. Genome-wide identification, phylogenetic analysis, conserved motif analysis, and gene structure characterization of GA-oxidases were performed. We analysed endogenous GAs levels and the expression of target HsGAoxs in response to GA3 within H. sosnowskyi developing ovaries. Twenty-seven HsGAoxs genes were identified, distributed across eleven chromosomes. Phylogenetic analysis classified proteins into the HsGA20ox, C19-HsGA2ox, and HsGA3ox subfamilies, facilitating functional predictions. Among the thirteen HsGA2ox protein members, there were no C20-GA2ox subfamily that distinguish H. sosnowskyi from other model plant species. The analysis of gene structure and conserved motifs confirmed the phylogenetic grouping and suggested that the evolutionary pattern was maintained within these subfamilies. The observed increase in precursor and bioactive GA levels provides evidence that they play a crucial role in promoting fruit growth. Ovary phenotypes reflected the timing of peak gibberellin levels, specifically during the cell expansion period. Exogenous GA3 treatment promoted HsGA3ox1 expression within both the central and lateral regions of the umbel ovaries. Overall, the results show that GA levels are precisely regulated by multiple HsGAox genes for stable early fruit development, and that disturbances in this stability affect fruit development. This opens up the possibility of investigating the role of GA in H. sosnowskyi fruit formation and developing measures for invasion control.

Long-read sequencing reveals novel isoform-specific eQTLs and regulatory mechanisms of isoform expression in human B cells

BACKGROUND

Genetic variations linked to changes in gene expression are known as expression quantitative loci (eQTLs). The identification of eQTLs helps to understand the mechanisms governing gene expression. However, prior studies have primarily utilized short-read sequencing techniques, and the analysis of eQTLs on isoforms has been relatively limited.

RESULTS

In this study, we employ long-read sequencing technology (Oxford Nanopore) on B cells from 67 healthy Japanese individuals to explore genetic variations associated with isoform expression levels, referred to as isoform eQTLs (ieQTLs). Our analysis reveals 17,119 ieQTLs, with 70.6% remaining undetected by a gene-level analysis. Additionally, we identify ieQTLs that have significantly different effects on isoform expression levels within a gene. A functional feature analysis demonstrates a significant enrichment of ieQTLs at splice sites and specific histone marks, such as H3K36me3, H3K4me1, H3K4me3, and H3K79me2. Through an experimental validation using genome editing, we observe that a distant genomic region can modulate isoform-specific expression. Moreover, an ieQTL analysis and minigene splicing assays unveils functionally crucial variants in splicing that splicing prediction software did not assign a high prediction score. A comparison with GWAS data reveals a higher number of colocalizations between ieQTLs and GWAS findings compared to gene eQTLs.

CONCLUSIONS

These findings highlight the substantial contribution of ieQTLs identified through long-read analysis in our understanding of the functional implications of genetic variations and the regulatory mechanisms governing isoforms.

Genome-wide identification of YABBY genes and functional characterization of CRABS CLAW (AktCRC) in flower development of Akebia trifoliata

As a representative species of basal eudicots, Akebia trifoliata has a unique unisexual flower development model, while the internal mechanism of its transition from a bisexual to unisexual flower is still lacking. Here, 6 AktYABs genes were firstly identified from A. trifoliata and divided into five clades: YAB2, FIL/YAB3, INO, CRC, and YAB5. Collinearity analysis and structure analysis proved that AktYABs members were highly conservative. Promoter cis-acting element analysis and RT-qPCR indicated that AktYABs were relative to various development, environmental stress, and hormone response events. All AktYABs members were located in the nucleus and membrane, but only AktYAB2 showed transcriptional activation activity. GUS staining manifested that the AktCRC transcript was strongly accumulated in the leaf, flower meristem, carpel, and tip of mature silique in Arabidopsis. Heterologous expression of AktCRC in Arabidopsis crc-1 mutants could significantly rescue the short siliques phenotype and the defect of apical carpel fusion. The AktCRC regulated carpellary development by affecting the expression levels of auxin synthesis, transport-related genes YUC4, TRN2, and floral meristem homeostasis regulation factor WUS. These results reveal the function of AktCRC in regulating the development of unisexual flowers in A. trifoliata and also lay a foundation for understanding the evolutionary status of the YABBY family in basal eudicots.

Genome-wide analysis of the BoBZR1 family genes and transcriptome analysis in Brassica oleracea

The BRASSINAZOLE-RESISTANT 1 genes play a crucial role as key regulators in Brassinosteroid (BR) signaling, which affects various plant developmental and stress-responsive aspects. Understanding regulatory mechanisms via BZR1 in modulating target genes has become a main point in research on plant BR signaling networks. Despite this, the BZR1 functioning in B. oleracea is not elucidated. A complete genome-wide analysis identified 12 BZR1 genes in B. oleracea, categorized into three groups based on their gene motif and structural features. These BoBZR1s were found on eight different chromosomes. Synteny analysis between B. oleracea, Arabidopsis, and potato provided perception into their evolutionary characteristics. Promoter regions of BoBZR1 family genes in B. oleracea have shown specific cis-elements associated with hormones, stress, and plant development. The expression analysis toward cuticular wax biosynthesis revealed that BoBZR1-1, BoBZR1-6, BoBZR1-7, and BoBZR1-10 were upregulated in response to cuticular wax biosynthesis. Differential expressions of BoBZR1 genes were observed for all seven different tested tissues. The whole study involved systematic characterization of the BoBZR1 family, and expression patterns, in BR signaling and its extensive involvement in developmental processes in B. oleracea. Results establish a theoretical foundation for deeper investigation of BoBZR1 structure and functions in B. oleracea, specifically toward regulating plant stress.

Evolution and comparison of the expression of TCP genes in the benincaseae and cucurbiteae tribes

TCP genes are plant-specific transcription factors that play essential roles in plant growth, development, metabolism, and responses to biotic and abiotic stresses. However, the roles of TCP genes in Cucurbitaceae species remain unknown. In this study, 111 and 119 TCP genes were identified in the Benincaseae (C. melo, C. sativus, C. lanatus and L. siceraria) and Cucurbiteae (C. maxima, C. moschata and C. pepo) tribes, respectively, and were analyzed. Segmental duplication, tandem duplication, and whole-genome duplication (WGD) were identified as the major driving factors in the expansion of TCP genes in Cucurbitaceae species, with the majority of TCP genes undergoing purifying selection. Using the melon genome as a reference, an integrated map containing 29 loci across nine chromosomes was constructed, 28 of which were shared by seven Cucurbitaceae species. Gene structure analysis revealed that their function was conserved. The result of promoter sequence analysis indicated that TCP genes have many phytohormone-related cis-regulatory elements. GO term enrichment analysis showed that TCP genes were the major regulators of many downstream transcriptional networks and primarily functioned in the nucleus. Transcriptome analysis of different tissues and developmental stages of the Cucurbiteae tribe revealed tissue-specific spatial and temporal expression patterns of TCP genes, suggesting that TCP genes play an important role in the growth and development of Cucurbitaceae. Gene expression profiling demonstrated that TCP genes are involved in the responses of plants to abiotic and biotic stresses. In conclusion, this is the first systematic analysis of TCP genes in Cucurbitaceae, which provides deeper insights into their evolutionary dynamics and functional properties, which may be crucial for the genetic improvement of Cucurbitaceae.

BEL1-like homeodomain transcription factor SAWTOOTH1 (MdSAW1) in Malus domestica enhances the tolerance of transgenic apple and Arabidopsis to zinc excess stress

In recent years, the phenomenon of zinc pollution in orchards has become increasingly serious, and the safety of apple production is facing a major risk. Therefore, exploring excellent genes for zinc tolerance has a positive effect on apples. Up to now, there is still a lack of attention on genes related to zinc stress tolerance in apples. In this study, the apple transcriptome map under zinc stress (1000 μM ZnSO4) was generated based on high-throughput sequencing. Through transcription factor analysis and association network prediction, TALE superfamily SAWTOOTH 1 was found to have an important role in 32 up-regulated core transcription factors. Further, BEL1-like homeodomain MdSAW1 gene from Malus domestica was overexpressed in Arabidopsis seedlings ('Col-0'), apple callus tissues ('Orin'), and apple plants ('GL-3'), and the results showed that the transformed lines carried obvious tolerance to zinc stress, which was reflected in the significant reduction of relative dielectric leakage, malondialdehyde, O2- and H2O2 content. The interaction between protein and DNA confirmed that MdSAW1 binds to natural resistance-associated macrophage protein NRAMP2 promoter to inhibit its transcription and thus regulate zinc ion homeostasis. In addition, overexpression of MdSAW1 increased the activity of antioxidant enzymes (superoxide dismutase, catalase, and glutathione peroxidase) and caused differences in metabolites in plants. MdSAW1 endows plants with strong tolerance to Zn stress, therefore, this study provides valuable reference for genetic improvement and environmental adaptation of fruit trees.

Camellia sinensis WIP domain protein 3 (CsWIP3), a C2H2 zinc finger protein, mediates lignin content and regulates plant growth in tea plants

The WIP proteins are essential for plant development, but their functions in tea plants (Camellia sinensis) remain poorly understood. In this study, six WIP members were identified in the tea plants and conducted a systematic analysis of their structure characteristics, expression patterns, promoter cis-acting elements, and functional roles. Sequence alignment and phylogenetic analysis revealed that the CsWIP family contains members with characteristic C2H2 zinc finger domains. Expression analysis across different tissues revealed a constitutive expression pattern. Promoter cis-acting element analysis identified several key regulatory elements associated with growth, development, and stress responses, highlighting the potential regulatory roles of CsWIP genes. Subcellular localization studies showed that CsWIP proteins primarily localize in the nucleus. Overexpression of CsWIP3 in Arabidopsis thaliana led to stunted growth, reduced leaf size, and increased lignin content, indicating its role in plant growth and lignification, with its function also validated in Solanum lycopersicum. Additionally, yeast two-hybrid assays identified interactions between CsWIP3 and CsTTG, CsAim32, and CsDUF1005, all of which are involved in regulating plant development, flower formation, and lignin biosynthesis. This study provides new insights into the functions of the CsWIP gene family in tea plants, revealing their functional diversity and potential applications in enhancing growth and development in tea plants.

Genome-wide identification and expression analysis of glutamate receptor-like genes in three Dendrobium species

Glutamate receptor-like (GLRs) genes play essential roles in plant growth and development, and in coping with environmental stresses; however, information on GLR genes in Dendrobium species is lacking. We identified 25 GLR genes in three Dendrobium species, which were classified into three subfamilies based on their phylogenetic relationships. These genes have been relatively conserved during evolution. Analysis of cis-acting elements and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes annotations revealed the complexity and diversity of GLR gene regulation and functions. Further, gene expression analysis showed that different GLR members exhibited different expression patterns during Dendrobium growth and development, and some were involved in pathogen infection and in response to hormones. These results provide important information on the GLR gene family of Dendrobium, and a foundation for further functional, and trait regulation and improvement studies.

ZjMAPKK4 Interacted With ZjNAC78 Regulates Cold Tolerance Response in Jujube

Jujube (Ziziphus jujuba Mill.) holds great importance as a fruit tree in China, with strong tolerance to drought and saline stress, but its growth is limited by vulnerability to cold stress. Consequently, the role of MAPK cascades in mediating jujube cold stress response remains unclear, with the specific function of ZjMAPKK4 in this context yet to be fully elucidated. Thus, in the current study, it was found that ZjMAPKK4 was significantly upregulated compared with other ZjMAPK cascade genes after cold treatment. Heterologous transformation of ZjMAPKK4 in Arabidopsis, VIGS-induced ZjMAPKK4 transiently silencing and overexpression of ZjMAPKK4 in jujube callus assays demonstrated that ZjMAPKK4 positively regulated the cold resistance of jujube. Furthermore, to elucidate the molecular regulation mechanism behind ZjMAPKK4 under cold stress, 25 key DEGs were screened out by transcriptome analysis. Yeast screening cDNA library, yeast two-hybrid, LCA and Co-IP analysis showed ZjMAPKK4 interacted with ZjNAC78 and VIGS-induced ZjNAC78 silenced sour jujube plants showed cold sensitivity and the expression level of cold response genes were downregulated after cold stress. All the results demonstrated that ZjMAPKK4 could interact with ZjNAC78 to regulate the downstream ZjICE-ZjCBF genes to regulate the cold tolerance of jujube.

Genomic and Methylomic Signatures Associated With the Maintenance of Genome Stability and Adaptive Evolution in Two Closely Allied Wolf Spiders

Pardosa spiders, belonging to the wolf spider family Lycosidae, play a vital role in maintaining the health of forest and agricultural ecosystems due to their function in pest control. This study presents chromosome-level genome assemblies for two allied Pardosa species, P. laura and P. agraria. Both species' genomes show a notable expansion of helitron transposable elements, which contributes to their large genome sizes. Methylome analysis indicates that P. laura has higher overall DNA methylation levels compared to P. agraria. DNA methylation may not only aids in transposable element-driven genome expansion but also positively affects the three-dimensional organisation of P. laura after transposon amplification, thereby potentially enhancing genome stability. Genes associated with hyper-differentially methylated regions in P. laura (compared to P. agraria) are enriched in functions related to mRNA processing and energy production. Furthermore, combined transcriptome and methylome profiling has uncovered a complex regulatory interplay between DNA methylation and gene expression, emphasising the important role of gene body methylation in the regulation of gene expression. Comparative genomic analysis shows a significant expansion of cuticle protein and detoxification-related gene families in P. laura, which may improve its adaptability to various habitats. This study provides essential genomic and methylomic insights, offering a deeper understanding of the relationship between transposable elements and genome stability, and illuminating the adaptive evolution and species differentiation among allied spiders.

Unveiling role of HSP70 genes for development and survival of Indian malaria vector Anopheles culicifacies

Heat shock proteins (HSPs) play a pivotal role in maintaining cellular homeostasis and mediating stress responses across diverse organisms. Among them, the HSP70 family is crucial for protein folding and stress regulation. However, its functions remain underexplored in mosquito species, particularly in major Indian malaria vectors such as Anopheles culicifacies (Ac). This study aims to contribute to mosquito control by investigating the role of HSP70 in An. culicifacies. Given the persistent global challenge posed by malaria, understanding the regulatory mechanisms of HSP70 is essential for developing effective control strategies. In this study, we identified seven HSP70 genes in An. culicifacies and analyzed their expression profiles across different life stages. Six of these HSP70 genes (1, 2, 3, 5, 6, and 7) exhibited significant upregulation during the third instar larval stage, emphasizing their critical role in larval development. Using specific HSP70 inhibitors, quercetin and KNK437, we observed that KNK437 displayed potent larvicidal activity, comparable to the widely used insecticide temephos. Additionally, we successfully purified and characterized recombinant AcHSP70-1, which demonstrated unique interactions with adenosine triphosphate (ATP) and its co-chaperone AcHSP40, distinguishing it from other HSP70 systems. Through a combination of confocal microscopy, qRT-PCR analysis, and inhibitor assays, we further established the essential role of HSP70 in both larval development and adult female mosquitoes during blood meal acquisition. These findings provide novel insights into the functional diversification and regulatory mechanisms of HSP70 genes in An. culicifacies. This study not only enhances our understanding of their developmental roles but also highlights innovative targets for the development of mosquito control strategies.

Evolutionary trajectories and subfunctionalization of 2 key methyltransferase regulator subfamilies in plants

DNA methylation, a conserved epigenetic mark in both plants and animals, plays a critical role in growth, development, and adaptability. This study explores the origin, evolution, and functional diversification of 2 key methyltransferase regulators, DNAJ-domain-containing protein 1/2/3 (DNAJ1/2/3) and SU(VAR)3-9 HOMOLOG 1/3 (SUVH1/3), in plants. By analyzing genomic data from 21 algae and 86 land plants, we discovered that DNAJ1/2/3 originated within Magnoliopsida, while SUVH1/3 emerged in ferns and evolved through retrotransposition. Both protein families have undergone multiple duplication events and positive selection throughout plant evolution, resulting in their expansion and functional divergence. In dicotyledons, DNAJ1/2/3 diverged into 3 subclades, whereas SUVH1/3 underwent a common duplication event in its ancestral lineage, resulting in 2 subgroups. Structural domain analysis revealed that the evolution of PHD fingers in DNAJ1/2/3 and AT domains in SUVH1/3, under selective pressure, enhanced their interaction capabilities and contributed to the formation of complexes involved in DNA methylation and demethylation regulation. Expression profile analysis across various plant taxa demonstrated tissue-specific expression patterns, with higher expression levels observed in meristematic tissues and active cell regions. These findings elucidate the evolutionary patterns of DNAJ1/2/3 and SUVH1/3 and offer insights into their functional diversification in plants.

RNAi-mediated down-regulation of the endogenous GhAIP10.1 and GhAIP10.2 genes in transgenic cotton (Gossypium hirsutum) enhances the earliness and yield of flower buds

Armadillo BTB Arabidopsis protein 1 (AtABAP1) plays a central role in the cell cycle. ABAP1-interacting protein 10 (AtAIP10, a Snf1 kinase interactor-like protein) is a protein that interacts with AtABAP1. Down-regulation of the AtAIP10 gene in A. thaliana resulted in an altered cell cycle and increased photosynthesis, chlorophyll content, metabolites, plant growth, root system, seed yield, and drought tolerance. Herein, aimed to test whether the down-regulation of GhAIP10 genes can stimulate the cotton plants in a manner similar to those observed in A. thaliana. Cotton transgenic events containing transgenes carrying RNA interfering (RNAi) or artificial miRNA (amiRNA) strategies were successfully generated to down-regulate the endogenous GhAIP10.1 and GhAIP10.2 genes. From these 15 transgenic events, five RNAi-based transgenic lines and five amiRNA-based transgenic events were selected for further analyses. The down-regulation of the GhAIP10.1 and GhAIP10.2 genes was confirmed by real-time RT-PCR. Phenotypic and physiological analyses revealed that these transgenic lines exhibited earlier production and opening of flower buds, increased vegetative growth over time and root biomass, no reduction in susceptibility to root-knot nematodes, and improved drought tolerance indicated by a higher photosynthetic rate and better intrinsic water-use efficiency. Based on the high identity of amino acid sequences, motifs, domains, subcellular localization, tertiary structure, down-regulation of GhABAP1 (partner of GhAIP10), up-regulation of GhCdt1 (a marker of the ABAP1 network), up-regulation of GhCyclinB1 (a marker of the cell cycle), up-regulation of GhAP3 (involved in vegetative to reproductive transition), and the up-regulation of CAB3, NDA1, DJC22, and DNAJ11 genes (involved in plant resilience) suggested that GhAIP10.1 and GhAIP10.2 proteins may act in cotton similarly to the AtAIP10 protein in A. thaliana. Furthermore, GhAIP10.1 and GhAIP10.2 genes are suggested as biotechnological targets for cotton genetic engineering based on genome editing.

Identification and Functional Exploration of the ALKBH Gene Family in Oriental Melon Fruit Ripening

N6-methyladenosine (m6A) methylation functions as a vital post-transcriptional and epigenetic modification in higher plants regulated by α-ketoglutarate-dependent dioxygenases (ALKBH). However, the role of ALKBH genes in oriental melon (Cucumis melo L.) fruit ripening has not been explored. Therefore, we treated oriental melon with an exogenous m6A demethylase inhibitor (mechlorfenamic acid) then analyzed endogenous ethylene production and ripening-related indicators to explore the effects of m6A methylation on ripening. Bioinformatics and real-time quantitative PCR analyses were used to determine the impact of ALKBH genes on key ethylene synthesis gene expression. Treatment effectively inhibited endogenous ethylene production, firmness changes, and soluble solid contents, thereby extending fruit ripening. Eight ALKBH gene family members belonging to five major groups were identified in the melon genome. All members were expressed in ripening fruits, with different expression patterns during ripening. CmALKBH6, CmALKBH7, and CmALKBH8 expression was inhibited by an ethylene inhibitor (1-methylcyclopropene). The transient overexpression (OE) of CmALKBH8 in oriental melon led to the increased expression of the ethylene synthesis genes CmACS1, CmACS2, and CmACO1. In summary, the ethylene-regulated gene CmALKBH8 may participate in oriental melon fruit ripening regulation by modulating the methylation levels of ethylene synthesis-related genes. These findings help us better understand how m6A methylation regulates melon ripening.

Molecular characterization and expression analysis of interleukin-1 beta in Japanese eel (Anguilla japonica)

Interleukin 1-beta (IL-1B) is a key proinflammatory cytokine involved in disease resistance. In recent years, il-1β genes from several teleosts have been cloned. The Japanese eel (Anguilla japonica) is an evolutionarily primitive fish widely farmed in East Asia. The il-1β gene has not yet been cloned from Japanese eel. In this study, the complete cDNA of il-1β was successfully sequenced from peripheral leukocytes through the rapid amplification of cDNA ends. The il-1β gene consists of five exons and four introns, and the full-length cDNA spans 1204 bp, comprising a 99-bp 5' untranslated region, a 750-bp coding sequence, and a 355-bp 3' untranslated region. The deduced amino acid sequence includes a consensus IL-1 family signature but lacks both a signal peptide and an IL-1 converting enzyme cleavage site, similar to other teleost IL-1B proteins. Homology analysis revealed that Japanese eel IL-1B is highly conserved within the order Anguilliformes, sharing the highest similarity with American eel (Anguilla rostrata), followed by conger eel (Conger myriaster). Tissue expression analysis showed that il-1β is constitutively expressed in multiple tissues, with high expression in peripheral leukocytes and the spleen; moderate expression in the gill, liver, head kidney, trunk kidney, and intestine; and low expression in the heart, stomach, skin, and muscle. In vitro stimulation with zymosan, polyinosinic-polycytidylic acid, and lipopolysaccharide upregulated il-1β expression in peripheral leukocytes.

Genome-wide identification of the Medicago sativa L. MYB family and its transcriptional dynamics during pollen development

BACKGROUND

The myeloblastosis (MYB) gene family plays crucial roles in the development of anthers and the establishment of pollen morphology during plant growth. However, little is known about the role of MYB transcription factors in pollen development in alfalfa (Medicago sativa L.).

RESULTS

In this study, we identified 161 MsMYBs in the alfalfa genome, including 34 1R-MYBs, 123 R2R3-MYBs, 3 3R-MYBs, and 1 4R-MYBs (categorized by the number of repeats). These were classified into six subfamilies based on the phylogenetic analysis, conserved structural domains, and gene structures. All MsMYBs were predicted to be hydrophilic and localized in the cell nucleus. The promoter regions contained three classes of cis-regulatory elements related to pollen development, as well as a variable set of functionally diverse elements, including hormone responsiveness, growth and development, and stress responsiveness elements. A transcriptome and qRT-PCR analysis revealed 12 MsMYBs with anther-specific expression and exhibited distinct expression patterns. Some MsMYBs showed a close phylogenetic relationship with Arabidopsis MYBs related to pollen development, such as MsMYB49 and MsMYB100, were found to be localized in the nucleus upon subcellular localization analysis. This genetic proximity suggests a potential role for these MsMYBs in the developmental processes of pollen.

CONCLUSIONS

This study provides a comprehensive understanding of MsMYBs in alfalfa and elucidates their potential roles and expression patterns in pollen development.

Analysis of the Genes from Gibberellin, Jasmonate, and Auxin Signaling Under Drought Stress: A Genome-Wide Approach in Castor Bean (Ricinus communis L.)

Castor bean (Ricinus communis L.) can tolerate long periods of dehydration, allowing the investigation of gene circuits involved in drought tolerance. Genes from gibberellins, jasmonates, and auxin signaling are important for crosstalk in the developmental and environmental adaptation process to drought conditions. However, the genes related to these signals, as well as their transcription profiles under drought, remain poorly characterized in the castor bean. In the present work, genes from gibberellins, jasmonates, and auxin signaling were identified and molecularly characterized. These analyses allowed us to identify genes encoding receptors, inhibitory proteins, and transcription factors from each signaling pathway in the castor bean genome. Chromosomal distribution, gene structure, evolutionary relationships, and conserved motif analyses were performed. Expression analysis through RNA-seq and RT-qPCR revealed that gibberellins, jasmonates, and auxin signaling were modulated at multiple levels under drought, with notable changes in specific genes. The gibberellin receptor RcGID1c was downregulated in response to drought, and RcDELLA3 was strongly repressed, whereas its homologues were not, reinforcing the suggestion of a nuanced regulation of gibberellin signaling during drought. Considering jasmonate signaling, the downregulation of the transcription factor RcMYC2 aligned with the drought tolerance observed in mutants lacking this gene. Altogether, these analyses have provided insights into hormone signaling in the castor bean, unveiling transcriptional responses that enhance our understanding of high drought tolerance in this plant. This knowledge opens avenues for identifying potential candidate genes suitable for genetic manipulation in biotechnological approaches.

Iron-binding transferrins regulate immunity and reproduction via tissue-specific iron redistribution in Spodoptera exigua

Transferrins are a multifunctional family of proteins that are essential for diverse physiological processes through their binding and transport of iron. Although previous studies have indicated that transferrins play crucial roles in insect antibacterial immunity and reproduction, the molecular mechanisms by which they regulate these essential processes remain poorly understood. Here, we identified and characterized transferrins in the beet armyworm, Spodoptera exigua (Hübner), an economically important agricultural pest, and elucidated their roles in innate immunity and reproduction. Four putative transferrin-coding genes were identified in the S. exigua genome, and structural analysis revealed that iron-binding domains were present exclusively in SeTsf1. Following infection with the entomopathogenic fungus Metarhizium anisopliae, SeTsf1 expression increased 3.2-fold, whereas iron levels decreased by 57.9 % in the hemolymph but increased by 51.6 % in the fat body. SeTsf1 knockdown significantly enhanced the susceptibility of S. exigua to M. anisopliae infection and abolished the hypoferremic response. Additionally, SeTsf1 silencing reduced egg production and hatching rates by 26 % and 28 %, respectively, and was accompanied by a 31 % decrease in ovarian iron content. Taken together, these findings demonstrate that SeTsf1 regulates immunity and reproduction through tissue-specific iron redistribution in S. exigua.

Genome-Wide Reidentification and Expression Analysis of MADS-Box Gene Family in Cucumber

MADS-box transcription factors play a crucial role in plant growth and development. Although previous genome-wide analyses have investigated the MADS-box family in cucumber, this study provides the first comprehensive reannotation of the MADS-box gene family in Cucumis sativus using updated Cucurbitaceae genome data, offering novel insights into the gene family's evolution and functional diversity. The results show that a total of 48 CsMADS-box genes were identified in the V3 version of cucumber, while 3 of the 43 genes identified in the V1 version were duplicated. The V1 version actually has only 40 genes. Additionally, we analyzed the variability in protein sequences and found that the amino acid sequences of 14 genes showed no differences between the two versions of the database, while the amino acid sequences of 29 genes exhibited significant differences. The further analysis of conserved motifs revealed that although the amino acid lengths of 15 genes had changed, their conserved motifs remained unchanged; however, the conserved motifs of 12 genes had altered. Furthermore we found that motif1 and motif2 were present in most proteins, indicating that they are highly conserved. Gene structure analysis revealed that most type I (Mα, Mβ) MADS-box genes lack introns, whereas type II (MIKC) genes exhibit a similar structure with a higher number of introns. Chromosomal localization analysis indicated that CsMADS-box genes are unevenly distributed across the seven chromosomes of cucumber. Promoter region analysis showed that the promoter regions of CsMADS-box genes contain response elements related to plant growth and development, suggesting that CsMADS-box genes may be extensively involved in plant growth and development. Different CsMADS-box genes exhibit specific high expression in roots, stems, leaves, tendrils, male flowers, female flowers, and ovaries, suggesting that these genes play crucial roles in the growth, development, reproduction and morphogenesis of cucumber. Moreover, 26, 18, 8, and 10 CsMADS-box genes were differentially expressed under high temperature, NaCl and/or silicon, downy mildew, and powdery mildew treatments, respectively. Interestingly, CsMADS07 and CsMADS16 responded to all tested stress conditions. These findings provide a reference and basis for further investigation into the function and mechanisms of the MADS-box genes for resistance breeding in cucumber.

Genome-wide identification and expression analysis of epigenetic regulator gene families in the medicinal mushroom Ganoderma lucidum

Epigenetic regulator (ER) genes, crucial for fungal growth and development, remain largely unexplored in Ganoderma lucidum, a medicinal mushroom valued for its bioactive compounds. This study identified 81 ER genes in G. lucidum, distributed across 12 chromosomes and classified into six families: 3 chromatin remodelers, 4 DNA methyltransferases, 7 histone acetyltransferases, 22 histone deacetylases, 23 histone methyltransferases, and 22 histone demethyltransferases. Comparative and phylogenetic analyses with other species revealed conserved orthologs and species-specific clusters. Gene duplication analysis suggested whole-genome duplication expanded ER gene families, primarily histone demethyltransferases under purifying selection. Additionally, gene structure, motif, and domain analyses revealed family-specific intron/exon organization and conserved domains. Transcriptome profiling across four developmental stages (mycelium, primordia, young and mature fruiting body) revealed dynamic stage-specific expression patterns, suggesting their developmental significance. The result of qRT-PCR validated the expression patterns for 18 ER genes, laying foundation for future research exploring epigenetic regulation in fungal development and bioactive compound production.

Identification and characterization of Spätzle in Myzus persicae and its role during microbial infection

As a Toll receptor ligand, Spätzle (Spz) plays a crucial role in activating the Toll pathway and participating in the innate immune response of insects. However, the immune function of Spz in Myzus persicae remains poorly understood. In this study, we identified and cloned 7 Spz genes from M. persicae, all containing a Spz domain (cystine-knot domain). Phylogenetic analysis revealed that the 7 different MpSpzs were divided into 6 groups within a single cluster with each Spz of Drosophila melanogaster and Acyrthosiphon pisum. These genes were mainly expressed in 1st-instar nymphs, hemolymph, and embryos and showed varying levels of positive response to infection with Escherichia coli, Staphylococcus aureus, and Beauveria bassiana. After gene-silencing of MpSpzs by RNA interference with injection of target gene-specific double-stranded RNA, microbial infection significantly increased the mortality of M. persicae compared to control groups. Further studies revealed that the suppression of MpSpz resulted in a significant reduction in lysozyme expression. The present study offers novel insights into the role of Spätzle in the innate immune response against microbial infection in M. persicae.

Genome-Wide Identification of the Defensin Gene Family in Triticum durum and Assessment of Its Response to Environmental Stresses

Plant defensins (PDFs) are a group of cationic antimicrobial peptides that are distinguished by their unique tertiary structure and play significant roles in physiological metabolism, growth, and stress tolerance. Defensins are key components of plant innate immunity; they can target a wide variety of microorganisms. This study aimed to identify and investigate the role of Triticum durum PDFs (TdPDFs) in response to environmental stresses. Prior to this, in silico analyses of TdPDF genes were conducted to assess their chromosomal locations, conserved motifs, exon-intron distribution, and cis-regulatory elements in the promoter regions. Additionally, bioinformatic analyses were performed to characterize the structure of TdPDF proteins, evaluate their phylogenetic relationships, predict their subcellular localization, and estimate their physicochemical properties. Docking studies were conducted to assess the interactions between TdPDF proteins and the fungal plasma membrane. A total of 28 TdPDF genes were identified in durum wheat based on their conserved domain PF00304 (gamma-thionin). These genes are distributed across all chromosomes of the durum wheat genome, except for chromosomes 4A and 7A. Analysis of the promoters of these genes revealed numerous elements associated with development, hormone responsiveness, and environmental stress. The majority of TdPDF proteins were predicted to be located extracellular. In addition, TdPDF proteins were classified into three clusters based on sequence similarity. Phylogenetic analysis suggested that TdPDF proteins share ancestral similarities with the PDF sequences of other monocotyledonous species. Molecular docking studies revealed that TdPDF proteins interact with fungal plasma membranes, suggesting that they play a critical role in the resistance of plants to pathogen infections. Expression analysis underlined the crucial role of nine TdPDF genes in the defense responses of durum wheat against both pathogenic and environmental stressors. Overall, our findings underscore the potential of TdPDF genes in host-plant resistance and highlight opportunities for their application in crop improvement toward stress tolerance.

Genome-Wide Identification and Expression Analysis of m6A Methyltransferase Family in Przewalskia tangutica Maxim

N6-methyladenosine (m6A) RNA modification plays important regulatory roles in plant development and adaptation to the environment. However, there has been no research regarding m6A RNA methyltransferases (MT-A70) in Przewalskia tangutica Maxim. Here, we performed a comprehensive analysis of the MT-A70 family in Przewalskia tangutica (PtMTs), including gene structures, phylogenetic relationships, conserved motifs, gene location, promoter analysis, GO enrichment analysis, and expression profiles. We identified seven PtMT genes. Phylogeny analysis indicated that the seven PtMT genes could be divided into three groups; two MTA genes, three MTB genes, and two MTC genes, and domains and motifs exhibited similar patterns within the same group. These PtMT genes were found to contain a large number of cis-acting elements associated with plant hormones, light response, and stress response, suggesting their widespread regulatory function. Furthermore, the expression profiling of different tissues was investigated using RNA-seq data, and the expression of seven genes was further validated by qPCR analysis. These results provided valuable information to further elucidate the function of m6A regulatory genes and their epigenetic regulatory mechanisms in Przewalskia tangutica.

Genome-Wide Analysis of Tea FK506-Binding Proteins (FKBPs) Reveals That CsFKBP53 Enhances Cold-Stress Tolerance in Transgenic Arabidopsis thaliana

FK506-binding proteins (FKBPs) belong to the peptidyl-prolyl cis/trans isomerase (PPIase) superfamily and are involved in a wide range of biological processes including protein folding, hormone signaling, plant growth, and stress responses. However, the FKBPs and their biological functions have not been identified in tea plants. In this study, 21 FKBP genes were identified using the conserved FK506-binding domain (PF00254) in the tea-plant genome. Their phylogeny, classification, structure, motifs, interactors, and expression patterns were analyzed. Comprehensive qRT-PCR analysis revealed distinct expression patterns of CsFKBPs in different tissues and in response to low temperature. Through a comprehensive genome-wide analysis, we characterized the low-temperature expression dynamics of the CsFKBP53 gene family and demonstrated that its overexpression significantly enhances cold tolerance in Arabidopsis. Notably, the transcript levels of CsFKBP53 exhibited pronounced variability across distinct tea (Camellia sinensis) cultivars under cold-stress conditions. These findings not only underscore the functional conservation of FKBP-type immunophilins across plant lineages but also highlight the biotechnological potential of CsFKBP53 as a genetic modulator of low-temperature resilience in crops. By integrating comparative genomics and functional validation, our study establishes a foundation for leveraging conserved stress-response mechanisms to engineer climate-resilient plants.

CsMYB1-CwINV6 Module Involves in the Promotion of Soluble Sugar Accumulation in Citrus Fruits Under Drought Stress

Drought can promote soluble sugar accumulation in fruits by increasing the fruit sink strength. Cell wall invertase (CwINV) plays a pivotal role in determining sink strength by regulating sucrose partitioning into the extracellular matrix. Research has demonstrated that drought stress significantly increases the transcript level of citrus CwINV6, but the transcriptional mechanisms governing its regulation under drought conditions remain elusive. In this study, we characterised the MYB transcription factor gene CsMYB1 from the citrus genome. CsMYB1 is localised in the cell nucleus, and CwINV6 is localised in the cell wall. Furthermore, the transcript levels of both CsMYB1 and CwINV6 significantly increased in 'Nanfeng' tangerine fruits (Citrus reticulata) in response to drought or ABA treatment. Transient overexpression of CsMYB1 or CwINV6 promoted the accumulation of glucose and fructose in 'Nanfeng' fruits. Conversely, transient VIGS of CsMYB1 or CwINV6 resulted in the opposite trend. Additionally, stable overexpression of CsMYB1 or CwINV6 significantly increased the soluble sugar content in the fruits of the 'Micro-Tom' tomato lines. Y1H and luciferase assays confirmed that CsMYB1 can bind to the CwINV6 promoter and positively regulate its expression. Taken together, our findings reveal that drought promotes soluble sugar distribution in citrus fruits by increasing sink strength via the CsMYB1-CwINV6 module.