Search Results (981)

NIN-like proteins (NLPs) are conserved, plant-specific transcription factors that play crucial roles in the nitrate signaling response, plant growth and development, and abiotic stress responses. However, their functions have not been explored in sweet potato. In this study, we identified 7 NLPs in cultivated hexaploid sweet potato (Ipomoea batatas, 2n = 6x = 90), 9 NLPs in the diploid relative Ipomoea trifida (2n = 2x = 30), and 12 NLPs in Ipomoea triloba (2n = 2x = 30) via genome structure analysis and phylogenetic characterization, respectively. The protein physiological properties, chromosome localization, phylogenetic relationships, syntenic analysis maps, gene structure, promoter cis-acting regulatory elements, and protein interaction networks were systematically investigated to explore the possible roles of homologous NLPs in the nitrate signaling response, growth and development, and abiotic stress responses in sweet potato. The expression profiles of the identified NLPs in different tissues and treatments revealed tissue specificity and various expression patterns in sweet potato and its two diploid relatives, supporting differences in the evolutionary trajectories of the hexaploid sweet potato. These results are a critical first step in understanding the functions of sweet potato NLPs and offer more candidate genes for improving nitrogen use efficiency and increasing yield in cultivated sweet potato. Full article

B-box (BBX) transcription factors, which are specific to the plant kingdom, play a crucial role in regulating light-dependent growth, development, secondary metabolite biosynthesis, and the response to biotic and abiotic stresses. Despite their significance, there has been a lack of systematic investigation into the BBX gene family in Ginkgo biloba. In the present study, we identified nine BBX genes within the G. biloba reference genome, distributed across seven chromosomes, and classified them into four groups based on their phylogenetic relationships with the BBX gene families of Arabidopsis thaliana. Our analysis of gene structure, conserved domains, and motifs suggests that GbBBXs exhibit a high degree of conservation throughout evolutionary history. Additionally, synteny analysis revealed that dispersed duplication events have contributed to the expansion of the BBX gene family in G. biloba. An examination of cis-regulatory elements indicated that numerous GbBBX genes contain motifs associated with light, hormones, and stress, suggesting their potential roles in responding to these signals and environmental adaptation. Expression profiles obtained from RNA-Seq data and quantitative Real-Time PCR (qRT-PCR) analyses of GbBBX genes across various organs, hormone treatments, and leaves with differing flavonoid content, as well as during both short-term and long-term water stress, demonstrated their potential roles in flavonoid regulation and responses to hormones and water stress. Subcellular localization studies indicated that the proteins GbBBX5, GbBBX7, GbBBX8, and GbBBX9 are localized within the nucleus. This study is the first thorough analysis of the BBX gene family in G. biloba, providing a valuable foundation for further understanding their evolutionary context and functional roles in flavonoid regulation and responses to water stress. Full article

Bats are great models for studying repetitive DNAs due to their compact genomes and extensive chromosomal rearrangements. Here, we investigated the repetitive DNA content of two phyllostomid bat species, Artibeus lituratus (2nn = 30♀/31♂) and Carollia perspicillata (2n = 20♀/21♂), both harboring a multiple XY₁Y₂ sex chromosome system. Satellite DNA (satDNA) libraries were isolated and characterized, revealing four and ten satDNA families in A. lituratus and C. perspicillata, respectively. These sequences, along with selected microsatellites, were in situ mapped onto chromosomes in both species and phylogenetically related taxa. SatDNAs showed strong accumulation in centromeric and subtelomeric regions, especially pericentromeric areas. Cross-species mapping with C. perspicillata-derived probes indicated terminal localization patterns in other bat species, suggesting conserved distribution. Microsatellites co-localized with 45S rDNA clusters on the neo-sex chromosomes. Additionally, genomic hybridization revealed a male-specific signal on the Y₁ chromosome, pointing to potential sex-linked repetitive regions. These findings confirm that bat genomes display relatively low amounts of repetitive DNA compared to other mammals and underscore the role of these elements in genome organization and sex chromosome evolution in phyllostomid bats. Full article

A strictly aerobic, straight-rod, motile Gram-negative bacterium, SDUM041083^T, was isolated from marine sediment in Xiaoshidao, Weihai, China, in the formation of yellowish-brown colonies. Its growing conditions are as follows: 20–40 °C, pH 5.5–9.5, and 0.5–11% (w/v) NaCl. Phylogenetic analysis of the 16S rRNA gene sequence showed that SDUM041083^T was related to members of the genus Microbulbifer. Strain SDUM041083^T showed the highest 16S rRNA gene sequence similarity (98.23%) with Microbulbifer okinawensis JCM 16147^T. The primary cellular fatty acids of SDUM041083^T were iso-C11:0 3-OH, iso-C11:0, and iso-C15:0. The respiratory quinone of SDUM041083^T was Q-8, and the polar lipids were phosphatidylglycerol, phosphatidylethanolamine, and one aminolipid. The genomic DNA G+C content of SDUM041083^T was 57.5 mol%. The phenotypic and genotypic characteristics of SDUM041083^T indicate that the strain should be classified as a new species representing the genus Microbulbifer, with the name Microbulbifer weihaiensis sp. nov. being proposed. The type strain was SDUM041083^T (=KCTC 8896^T = MCCC 1H01537^T). Comparative genomic analysis showed that the 32 Microbulbifer species shared 1446 core genes and differed mainly in terms of lipid metabolism, signal transduction and xenobiotic biodegradation and metabolism. Preliminary research showed that SDUM041083^T has the potential to degrade chitin. Biogeographic distribution analysis showed that the marine environments constitute the main habitat of the genus Microbulbifer. Full article

The WUSCHEL-related homeobox (WOX) gene family is integral to plant growth and development. Here, we identified 14 CcWOX genes from the Cinnamomum camphora genome and analyzed their phylogeny, conserved features, and expression patterns. Phylogenetic inference grouped CcWOX into the Ancient, Intermediate, and WUS clades, consistent with other plant lineages. Expression profiling across seven tissues/organs, together with qRT-PCR validation, revealed tissue-biased expression for several members (e.g., floral or root enrichment), suggesting gene-specific roles during development. Using AlphaFold3, we predicted monomeric structures for CcWOX proteins and an interface model compatible with an interaction between CcWOX3 and CcLBD33. Consistently, bimolecular fluorescence complementation (BiFC) in Nicotiana benthamiana detected nuclear YFP signals for cEYFP-CcWOX3 + nEYFP-CcLBD33 relative to appropriate negative controls, confirming a physical interaction in plant cells. While these findings support a putative WOX–LBD interaction module in C. camphora, the regulatory functions remain to be established. Overall, this work provides a framework for dissecting the CcWOX family in C. camphora and illustrates how AI-assisted structure prediction can be integrated with cell-based assays to accelerate hypothesis generation in plant developmental biology. Full article

Some bacterial species within the Enterobacteriaceae family possess different types of fimbrial (pili) adhesins that promote adherence to cells and colonization of host tissues. One of the well-characterized fimbrial systems is the pap operon, which encodes P fimbriae, a key virulence factor in urinary and systemic infections. One of the key regulators of P fimbriae is the transcriptional regulator PapB which plays a pivotal role as a master switch, not only by directing phase-variable expression of its own operon but also by influencing expression of heterologous fimbrial systems. This review explores the structural organization, biogenesis, and multi-tiered regulatory control of P fimbriae, with emphasis on PapB and homologous regulatory proteins such as SfaB, FocB, PixB, and PefB. Comparative genomics and phylogenetic analyses reveal that regulators belonging to the PapB family are evolutionarily conserved across π-fimbrial systems and also regulate other types of fimbriae. These regulators respond to epigenetic changes, host-derived signals, and global transcriptional cues to control levels of production of specific fimbriae in a bacterial population to dynamically modulate bacterial adhesion in different environmental niches. Optimally, understanding these mechanisms could lead to novel approaches to perturb PapB-family proteins and abrogate production of some types of fimbriae as a targeted strategy to prevent bacterial infections dependent on adherence mediated by PapB family regulators. Full article

Arginine vasotocin (AVT) is well known for its role in steroidogenesis and estradiol biosynthesis during early brain development in Epinephelus coioides. Despite its hormonal functions, the biological significance of AVT across different taxa remains poorly understood. Hence, the present study aims to unravel the evolutionary conservation and functional annotation of AVT in different taxa. Additionally, the antimicrobial properties of AVT were investigated across multiple conserved domains. From the sequence comparison results, AVT is highly conserved and a core motif across teleosts, mammals, plants, and bacteria, suggesting functional constraints under strong evolutionary selective pressure. Phylogenetic analyses highlighted AVT and its homologs evolved from a common ancestral gene. The functional enrichment analyses of the genes revealed different taxa that share an analogy with AVT genes. The major pathways for AVT and its homologs are identified in neuroendocrine, immune, and stress signaling. Importantly, a conserved AMP-like motif within the AVT sequence (GIRQCMSCGPGDRGR) was identified. The motif is predicted for its potential role in membrane permeabilization and antimicrobial defense. Physicochemical properties of this peptide showed cationic and amphipathic features, with cysteine residues conferring structural stability. Overall, the results underscore the pleiotropic role of AVT across different taxa, showing its evolutionary stability. AMP-like AVT motif was predicted as a promising candidate for synthetic peptide design. Experimental evaluation with peptides will determine their antimicrobial potential in infection models. Full article

Dehydration response element binding proteins (DREBs) have been identified as major regulators of cold acclimatization in many angiosperms. Cold stress is one of the primary abiotic stresses affecting kiwifruit growth and development. However, kiwifruit is currently one of the most widely consumed fruits worldwide because of its high nutritional value. 5-Aminolevulinic acid (5-ALA) is a nonprotein amino acid known for its distinct promotional effects on plant resistance, growth, and development. However, studies on the function of the kiwifruit DREB gene in alleviating low-temperature stress in its seedlings via exogenous 5-ALA have not been reported. Therefore, in this study, we performed a genome-wide identification of DREB gene family members in kiwifruit and analyzed the regulatory effects of exogenous 5-ALA on kiwifruit DREB genes under low-temperature stress. A total of 193 DREB genes were identified on 29 chromosomes. Phylogenetic analysis classified these genes into six subfamilies. Although there were some differences in cis-elements among subfamilies, all of them contained more biotic or abiotic stresses and hormone-related cis-acting elements. GO and KEGG enrichment analyses revealed that AcDREB plays an essential role in hormone signaling, metabolic processes, and the response to adverse stress. Under low-temperature stress, the application of exogenous 5-ALA inhibited the accumulation of APX and DHAR, promoted an increase in chlorophyll, and increased the accumulation of enzymes and substances such as 5-ALA, MDHAR, GR, ASA, GAH, and GSSH, thereby accelerating ROS scavenging and increasing the cold hardiness of kiwifruits. Functional analysis revealed that 46 differentially expressed DREB genes, especially those encoding AcDREB69, AcDREB92, and AcDREB148, which are involved in ethylene signaling and defense signaling, and, after the transcription of downstream target genes is activated, are involved in the regulation of low-temperature-stressed kiwifruits by exogenous 5-ALA, thus improving the cold tolerance of kiwifruits. Notably, AcDREB69, AcDREB92, and AcDREB148 could serve as key genes for cold tolerance. This study is the first to investigate the function of AcDREB genes involved in the role of exogenous 5-ALA in regulating low-temperature stress, revealing the regulatory mechanism by which DREB is involved in the ability of exogenous 5-ALA to alleviate low-temperature stress. Full article

The melon fly Zeugodacus cucurbitae (Coquillett) is a globally invasive pest responsible for substantial economic losses in the fruit and vegetable industries. Insulin-like peptides (ILPs) are evolutionarily conserved neuropeptides that play a crucial role in insect reproduction. In this study, six ZcILPs from the melon fly, designated as ZcILP1–6, were cloned. Phylogenetic analysis demonstrated a strong orthologous link with Dipteran ILPs. Spatiotemporal expression profiling revealed that ZcILP1 and ZcILP3 exhibit preferential enrichment in the adult female fat body, with their expression specifically and significantly upregulated in 5-day-old individuals. Their expression decreased 12, 24, and 48 h post-starvation and increased upon re-feeding. Silencing ZcILP1 and ZcILP3 resulted in reduced ovarian size by 51.42% and 69.17%, respectively. Furthermore, silencing ZcILP1 or ZcILP3 significantly decreased the transcriptional levels of genes downstream of the insulin signaling pathway (ISP), notably the target of rapamycin (ZcTOR) and Forkhead box O (ZcFOXO). Concurrently, the expression of Vitellogenin (ZcVg), a gene associated with reproduction, was significantly downregulated. These findings indicate that ZcILP1 and ZcILP3 regulate ZcVgs expression and ovarian development through ISP, suggesting them as potential targets for green control of Z. cucurbitae. Full article

The TIFY gene family participates in crucial processes including plant development, stress adaptation, and hormonal signaling cascades. While the TIFY gene family has been extensively characterized in model plant systems and agricultural crops, its functional role in Eucalyptus grandis, a commercially valuable tree species of significant ecological and economic importance, remains largely unexplored. In the present investigation, systematic identification and characterization of the TIFY gene family were performed in E. grandis using a combination of genome-wide bioinformatics approaches and RNA-seq-based expression profiling. Nineteen EgTIFY genes were identified in total and further grouped into four distinct subfamilies, TIFY, JAZ (subdivided into JAZ I and JAZ II), PPD, and ZML, based on phylogenetic relationships. These genes exhibited considerable variation in gene structure, chromosomal localization, and evolutionary divergence. Promoter analysis identified a multitude of cis-acting motifs involved in mediating hormone responsiveness and regulating abiotic stress responses. Transcriptomic profiling indicated that EgJAZ9 was strongly upregulated under methyl jasmonate (JA) treatment, suggesting its involvement in JA signaling pathways. Taken together, these results offer valuable perspectives on the evolutionary traits and putative functional roles of EgTIFY genes. Full article

The GLABROUS1 Enhancer Binding Protein (GeBP) gene family plays a crucial role in plant growth, development, and stress responses. In this study, 28 GeBP genes were identified in Brassica oleracea using HMMER and validated through multiple conserved domain databases. A phylogenetic tree was constructed based on the GeBP protein sequences from B. oleracea, Arabidopsis thaliana, Brassica rapa, and Brassica napus, dividing them into four evolutionary clades (A–D), which revealed a close evolutionary relationship within the genus Brassica. Conserved motif and gene structure analyses showed clade-specific features, while physicochemical property analysis indicated that most BoGeBP proteins are hydrophilic, nuclear-localized, and structurally diverse. Gene duplication and chromosomal localization analyses suggested that both segmental and tandem duplication events have contributed to the expansion of this gene family. Promoter cis-element analysis revealed a dominance of light-responsive and hormone-responsive elements, implying potential roles in photomorphogenesis and stress signaling pathways. Notably, the protein encoded by BolC01g019630.2J possesses both a transmembrane domain and characteristics of the Major Facilitator Superfamily (MFS) transporter family, and it is predicted to localize to the plasma membrane. This suggests that it may act as a molecular bridge between environmental signal perception and transcriptional regulation, potentially representing a novel signaling mechanism within the GeBP family. This unique feature implies its involvement in transmembrane signal perception and downstream transcriptional regulation under environmental stimuli, providing valuable insights for further investigation of its role in stress responses and metabolic regulation. Overall, this study provides a theoretical foundation for understanding the evolutionary patterns and functional diversity of the GeBP gene family in B. oleracea and lays a basis for future functional validation and breeding applications. Full article

Abscisic acid (ABA) is a key phytohormone involved in regulating plant growth and responses to environmental stress. As receptors of ABA, pyrabactin resistance 1 (PYR)/PYR1-like (PYL) proteins play a central role in initiating ABA signal transduction. In this study, a total of 30 PopPYL genes were identified and classified into three sub-families (PYL I–III) in the pan-genome of 17 Populus species, through phylogenetic analysis. Among these subfamilies, the PYL I subfamily was the largest, comprising 21 members, whereas PYL III was the smallest, with only four members. To elucidate the evolutionary dynamics of these genes, we conducted synteny and Ka/Ks analyses. Results indicated that most PopPYL genes had undergone purifying selection (Ka/Ks < 1), while a few were subject to positive selection (Ka/Ks > 1). Promoter analysis revealed 258 cis-regulatory elements in the PYL genes of Populus euphratica (EUP) and Populus pruinosa (PRU), including 127 elements responsive to abiotic stress and 33 ABA-related elements. Furthermore, six structural variations (SVs) were detected in PYL_EUP genes and significantly influenced gene expression levels (p < 0.05). To further explore the functional roles of PYL genes, we analyzed tissue-specific expression profiles of 17 PYL_EUP genes under drought stress conditions. PYL6_EUP was predominantly expressed in roots, PYL17_EUP exhibited leaf-specific expression, and PYL1_EUP showed elevated expression in stems. These findings suggest that the drought response of PYL_EUP genes is tissue-specific. Overall, this study highlights the utility of pan-genomics in elucidating gene family evolution and suggests that PYL_EUP genes contribute to the regulation of drought stress responses in EUP, offering valuable genetic resources for functional characterization of PYL genes. Full article

Background/Objectives: RAB11 (RABA) is a type of RAB GTPase. RAB GTPases are key components of membrane trafficking mechanisms, Rab11 is implicated in a variety of biological developmental processes and responses to biotic and abiotic stresses. Nevertheless, the role of Rab11 in the defense mechanisms of cotton against Verticillium dahliae (V. dahliae) remains to be elucidated. Methods: In the present study, by analyzing the transcriptome data of Gossypium hirsutum (G. hirsutum) infected with V. dahliae, in combination with gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, the research focused on endocytosis. Further, through bioinformatics approaches, the endocytosis-related gene Rab11 was identified. We conducted a genome-wide identification and analysis of Rab11 in G. hirsutum. In addition, by integrating transcription factor (TF) prediction, prediction of protein–protein interactions (PPI) and quantitative real-time polymerase chain reaction (qRT-PCR), the gene expression of Rab11 at different infection periods of V. dahliae (0, 24 and 72 hpi) were analyzed and validated. Results: The analysis of transcriptome data revealed that the endocytosis pathway is implicated in the stress response of cotton to V. dahliae. Additionally, three Rab11 genes were identified as being involved in this stress response. Phylogenetic analysis revealed that the 65 genes in the Rab11 family could be divided into four subgroups, each with similar gene structures and conserved motif patterns. Conclusions: The downregulation of Rab11 in G. hirsutum is closely linked to its defense against V. dahliae. TF prediction coupled with PPI offers a roadmap for dissecting the signaling pathways, functional validation, and network construction of the three GhRab11 genes. Full article

The Yucatán Black Hairless Pig (YBHP) is a native Mexican breed with cultural and agricultural importance in the Yucatán Peninsula. This study explored the genetic diversity and population structure of YBHP using a genome-wide single-nucleotide polymorphism (SNP) from the porcine GGP 50K chip, comparing it with native and cosmopolitan breeds worldwide. Genetic diversity analyses revealed an observed heterozygosity (HO) of 0.3602 ± 0.032 and an inbreeding coefficient (F_IS) of 0.1517 ± 0.076, indicating moderate diversity and a relatively low level of inbreeding for an endangered native breed. ADMIXTURE analyses revealed a predominant and distinctive ancestry component exclusive to YBHP, along with shared ancestry with European breeds, particularly those of presumed Iberian origin. Principal Component Analysis (PCA) and phylogenetic network clustering supported its genomic singularity while confirming ancestral proximity to traditional European pigs. These findings highlight the dual nature of the YBHP: a genetically distinct native breed shaped by local adaptation yet retaining ancestral signals from Old World lineages. This genomic insight provides a scientific basis for conservation planning, supports the breed’s recognition as a unique genetic resource, and promotes its sustainable use in regional production systems. Full article

Abiotic stresses increasingly threaten wheat (Triticum aestivum L.) productivity by impairing pollen development and fertilization, yet the molecular regulators that coordinate reproductive success with environmental resilience remain underexplored. Here, we present a comprehensive genome-wide analysis of the Pollen Olea europaea I (POEI) protein family in common wheat. A total of 104 TaPOEI genes were identified and classified into six phylogenetic clades, each sharing conserved exon–intron structures and key protein motifs. Promoter analysis revealed abundant cis-elements associated with phytohormone signaling and abiotic stress responses. Notably, TaPOEI 16-A was preferentially expressed in anthers, showing high expression during early anther development and responding to both high- and low-temperature stresses. Pairwise comparison between thermosensitive genic male-sterile wheat lines and fertile lines suggests a potential role for TaPOEI 16-A in regulating male fertility in response to temperature fluctuations. Our comprehensive analysis establishes a foundation for future functional studies of the TaPOEI family and provides insights into wheat fertility and stress resilience enhancement. Full article