Search Results (1,072)

Cadmium (Cd), a highly mobile and phytotoxic heavy metal, threatens plant growth and food safety and has increased interest in woody plant-based phytoremediation. However, the genome-wide characteristics of the NAC transcription factor family and its role in Cd tolerance remain largely unknown in pomegranate (Punica granatum L.), a stress-tolerant woody plant. In this study, 121 PgNAC genes were identified from the chromosome-level genome of the pomegranate cultivar ‘Tunisia’. Phylogenetic analysis classified these genes into two major groups and 16 subgroups. PgNAC genes were unevenly distributed across the eight chromosomes and showed evident clustered distribution patterns. Synteny and Ka/Ks analyses further revealed that segmental and tandem duplication jointly shaped the expansion of the PgNAC family, while the duplicated pairs have largely evolved under strong purifying selection. Conserved motif and gene structure analyses showed that PgNAC proteins possessed a highly conserved N-terminal NAM domain, whereas their C-terminal regions were relatively divergent. Promoter analysis further identified abundant hormone- and stress-responsive cis-elements, suggesting diverse regulatory roles of the PgNAC family. Transcriptome profiling identified PgNAC87, a member of the NAP subfamily, as a Cd-responsive candidate gene that was consistently upregulated in both roots and leaves under Cd stress. Heterologous overexpression of PgNAC87 in tobacco significantly enhanced Cd tolerance, as reflected by alleviated growth inhibition, increased antioxidant enzyme activities and osmotic adjustment substances, and reduced oxidative damage. Collectively, our results clarify the evolutionary features of the PgNAC family and its involvement in Cd-induced transcriptional regulation, while highlighting PgNAC87 as a potential genetic target for enhancing Cd tolerance in pomegranate and related woody species. Full article

Verticillium wilt (VW), caused by the soil-borne phytopathogen Verticillium dahliae, is a devastating vascular disease that severely threatens global cotton production and causes substantial economic losses. Jasmonic acid (JA) signaling plays a crucial role in plant innate immunity; however, the molecular mechanisms governing JA biosynthesis during cotton defense responses to V. dahliae infection remain largely elusive. In this study, we identified that GhAOS1 (allene oxide synthase 1), a key rate-limiting enzyme-encoding gene in the JA biosynthetic pathway, was rapidly and significantly induced by V. dahliae infection and exclusively localized in chloroplasts. Functional analysis in GhAOS1-silenced cotton and overexpressing Arabidopsis plants demonstrated that GhAOS1 positively regulates resistance to V. dahliae. Transcriptome analysis of GhAOS1-silenced cotton plants showed that DEGs are significantly enriched in phenylpropanoid biosynthesis, flavonoid biosynthesis, and α-linolenic acid metabolism pathways. Consistent with these findings, silencing GhAOS1 significantly reduced endogenous JA levels and suppressed the expression of defense-related genes and JA biosynthetic genes in cotton. Furthermore, we identified that the transcription factor GhWRKY70 directly binds to the W-box cis-acting element in the GhAOS1 promoter through Y1H, LUC, and EMSA, which activated GhAOS1 transcription. Silencing GhWRKY70 in cotton significantly enhanced plant susceptibility to V. dahliae and suppressed the expression of JA signaling pathway-related genes. Collectively, our results elucidate that GhWRKY70 positively regulates cotton resistance to VW by activating GhAOS1-mediated JA biosynthesis, revealing a novel GhWRKY70-GhAOS1 regulatory module that integrates JA signaling to coordinate cotton immune responses against V. dahliae. This study provides new insights into the molecular mechanism of JA-mediated defense and offers potential targets for molecular breeding of VW-resistant cotton. Full article

The GRAS transcription factor family plays a pivotal role in plant stress adaptation, yet its systematic characterization and the underlying drought-responsive mechanisms remain poorly elucidated in Populus deltoides. Here, a genome-wide identification and analysis of GRAS genes in P. deltoides was performed, and a total of 92 family members were identified and classified into 12 distinct subfamilies through phylogenetic analysis. Evolutionary analysis revealed a high degree of conservation between the GRAS proteins of P. deltoides and those of Arabidopsis thaliana, Oryza sativa, and Solanum lycopersicum. Genomic duplication events, including 90 segmental and 11 tandem duplications, were identified as the primary drivers of GRAS family expansion. Promoter cis-element analysis uncovered an enrichment of stress-responsive elements (MBS, ABRE) and phytohormone-related motifs (e.g., TATC-box). Transcriptomic profiling further revealed distinct drought-inducible expression patterns of GRAS genes: PdeGRAS49 exhibited rapid upregulation at the early stage of drought exposure (1–3 h), whereas DELLA subfamily members PdeGRAS51 and PdeGRAS59 reached their expression peaks at 6–9 h, and PdeGRAS34 and PdeGRAS77 maintained sustained activation throughout 12–24 h. Moreover, the drought-inducible expression patterns of five DELLA genes were confirmed by qRT-PCR validation. Collectively, this study provides crucial genomic insights into the GRAS family and valuable candidate gene resources, which lay a foundation for molecular breeding of drought-tolerant P. deltoides cultivars via manipulating GRAS-mediated regulatory mechanisms. Full article

GRAS transcription factors are essential for plant growth and stress adaptation, yet they remain uncharacterized in the medicinal herb Coptis chinensis. To address this gap, we performed a genome-wide identification of the GRAS family and investigated its transcriptional responses to temperature and light stress, integrating comparative transcriptomics with promoter analysis to explore potential co-expression with bZIP factors. A total of 48 CcGRAS genes were identified and found to be unevenly distributed across nine chromosomes. Expression profiling revealed that CcGRAS genes are markedly more responsive to varying light intensities (476, 8340 lx) than to temperature stresses (15, 35 °C), relative to controls (2060 lx for light, 25 °C for temperature). Co-expression analysis uncovered an underground tissue-specific module in which CcbZIP16 is upregulated with four CcGRAS genes (CcGRAS11, CcGRAS12, CcGRAS43, CcGRAS48) that are coordinately upregulated specifically under low-light conditions. The promoters of these co-expressed genes are significantly enriched in canonical light-responsive cis-elements, providing correlative evidence for their coordinated transcriptional control. Together, these findings identify a tissue-specific GRAS-bZIP co-expressed gene set under light stress and suggest a candidate regulatory framework for dissecting light adaptation mechanisms. This work also provides a foundation for targeted genetic improvements in stress tolerance and alkaloid biosynthesis in this important medicinal plant. Full article

Fruit endocarp and seed coat are essential protective structures that influence key agronomic and mechanical traits in species with lignified protective tissues, yet their regulatory mechanisms remain incompletely understood. Here, we conducted a comprehensive genome-wide analysis of the MADS-box gene family in four angiosperm species: Juglans sigillata, Carya illinoinensis, Macadamia integrifolia, and Ricinus communis. A total of 58, 55, 57, and 57 MADS-box genes were identified, respectively, and systematically characterized through phylogenetic, structural, and evolutionary analyses. Comparative results revealed that MIKCc-type genes are highly conserved and primarily expanded via segmental duplication under strong purifying selection. Co-expression network analysis identified MADS-box genes as high-connectivity hub candidates that are strongly associated with genes involved in tissue specification, hormone signaling, and secondary cell wall biosynthesis. Promoters analysis indicated that these genes contain diverse cis-regulatory elements; however, these results are based on sequence prediction and do not demonstrate functional regulatory interactions. Across species, MADS-box genes exhibited analogous temporal expression dynamics during lignified endocarp and seed coat development, consistent with a potentially conserved transcriptional framework. Collectively, this study provides new insights into the evolutionary diversification and putative functions of MADS-box genes, and proposes a putative hierarchical regulatory framework for lignified endocarp and seed coat development. These findings supply valuable candidate target genes for future molecular breeding aimed at improving shell thickness, hardness, and related agronomic traits in woody nut and oilseed species. Full article

Choy Sum (Brassica rapa subsp. chinensis var. parachinensis), also known as flowering Chinese cabbage, is an important stalk vegetable in Asia. However, the unique regulatory mechanism governing its “easy-bolting yet susceptible to premature bolting” trait remains poorly understood. The phosphatidyl ethanolamine-binding protein (PEBP) family serves as a central regulator of bolting, flowering, and growth development in plants. But this gene family has not been systematically identified and studied in Choy Sum yet. Therefore, this study systematically identified and analyzed the members of the PEBP gene family in Choy Sum using bioinformatics, transcriptomics, real-time fluorescence quantification, subcellular localization, and transgenic techniques. A total of 12 BcPEBP genes were identified and categorized into three subfamilies: FT-like, TFL1-like, and MFT-like. Phylogenomic analyses revealed family expansion through whole-genome duplication with strong purifying selection. Most members have highly conserved core motifs and gene structures. Protein sequence alignment showed that BcFT-2 and BcTFL-2 underwent non-synonymous mutations at key residues. The analysis of cis-acting elements suggests that the BcPEBP gene may be influenced by complex hormone and light regulatory networks. Expression profiling demonstrated leaf-specific upregulation of BcFT-1/2 during development and shoot apices-predominant expression of BcTFL1 genes, and the expression between homologous genes of BcTFL1-1/3 is more refined. Subcellular localization confirmed dual nuclear and plasma membrane targeting of BcFT-1/2 proteins. Overexpression of BcFT-1/2 in transgenic Arabidopsis promotes flowering. These findings establish BcPEBP genes as key bolting regulators and provide molecular targets for breeding-improved varieties. Full article

Basic leucine zipper (bZIP) transcription factors are widely involved in plant growth, development, environmental adaptation, and secondary metabolism. However, the bZIP gene family in Taxus yunnanensis has not been systematically characterized, and its potential involvement in shading-responsive regulation of paclitaxel biosynthesis remains unclear. In this study, a genome-wide analysis was performed to identify and characterize the bZIP family in T. yunnanensis. Phylogenetic analysis, conserved motif and domain identification, promoter cis-element analysis, chromosomal localization, and expression profiling were conducted to investigate their structural features and regulatory potential. A total of 18 TyubZIP genes were identified and classified into 10 subfamilies. These genes exhibited variation in physicochemical properties but showed conserved structural features and nuclear localization. Promoter analysis revealed abundant light-responsive, hormone-related, and stress-related cis-elements. Expression profiling indicated tissue-specific expression patterns and diverse responses to shading treatment. WGCNA further identified candidate TyubZIP genes potentially associated with paclitaxel biosynthesis. Among them, TyuHY5 was selected for functional analysis. Subcellular localization and transcriptional assays demonstrated that TyuHY5 can bind to the promoter of TyuDBTNBT and positively regulate its activity. These findings provide the first genome-wide characterization of the bZIP family in T. yunnanensis and identify TyuHY5 as a shading-responsive candidate regulator of paclitaxel biosynthesis, providing insights that may inform the genetic improvement and cultivation strategies of Taxus for enhanced paclitaxel production. Full article

SMXL proteins serve as central regulators of strigolactone (SL) and karrikin (KAR) signaling pathways, orchestrating key developmental processes including shoot branching, floral transition, photomorphogenesis and stress responses. However, the SMXL gene family has not been systematically characterized in Lavandula angustifolia. We identified 37 LaSMXL genes in the lavender genome. Phylogenetic and synteny analyses classified these proteins into four subgroups (Groups I–IV) and indicated that family expansion in lavender was mainly driven by whole-genome and segmental duplications, with most duplicated pairs evolving under strong purifying selection. Gene structure and motif analyses revealed high conservation within each subgroup. Promoter cis-element analysis suggested that LaSMXL genes are integrated into light-, hormone- and stress-responsive regulatory networks. RNA-seq profiling showed that most LaSMXL genes are weakly expressed, but a small subset displays pronounced tissue specificity and clear transcriptional responses to low temperature. Protein–protein interaction predictions and co-expression network analysis further placed highly expressed LaSMXLs within conserved SL/KAR and chloroplast/light-associated modules, alongside D14, KAI2, MAX2, CCD7/CCD8, and CYP711A. Together, these findings provide the first comprehensive overview of the SMXL gene family in lavender and identify candidate LaSMXL genes for future functional studies aimed at optimizing plant architecture and inflorescence-derived essential oil biosynthesis. Full article

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

N⁶-methyladenosine (m⁶A) is an important epigenetic modification of eukaryotic RNA, playing a significant role in various biological processes. Metasequoia glyptostroboides (M. glyptostroboides) is an ancient tree species in China, with a long history and excellent genetic characteristics. In this study, we identified six MgYTH genes in the genome of M. glyptostroboides, elucidating their phylogenetic relationships, conserved domains, gene structures, conserved motifs, chromosome locations, and prediction of LLPS. The analysis of the cis-regulatory elements in the promoter region suggested that MgYTH genes are associated with drought and the ABA-responsive expression patterns signaling pathway, which was further supported by expression pattern analysis. In addition, to directly evaluate the m⁶A binding ability of MgYTH proteins, we selected MgYTH5 as the representative for homology modeling analysis and electrophoretic mobility shift assay (EMSA). The results demonstrated that MgYTH5 has the ability to bind m⁶A in vitro, thereby providing biochemical evidence that MgYTH5 can bind m⁶A-modified RNA in vitro mRNAs. The subcellular localization results showed that MgYTH5 is located in the cytoplasm. These findings provide new insights into the epigenetic regulation mechanisms in gymnosperms and provide a resource for future functional studies in this species. Full article

Salt stress affects the growth, quality, and secondary metabolism of medicinal plants, but its effects on essential oil biosynthesis in Schizonepeta tenuifolia remain unclear. In this study, a salt stress model was established for Schizonepeta tenuifolia (Benth.) Briq. to investigate changes in growth, monoterpenoid accumulation, non-targeted metabolism, and transcriptional profiles. To further clarify the regulatory mechanism of monoterpenoids biosynthesis, the MYB family members were identified at the genome-wide level, and candidate regulators were screened based on the expression patterns and promoter features of StL3OH (limonene -3-hydroxylase). Among them, StMYB71 and StMYB8774 were identified as candidate regulators of monoterpene biosynthesis. Functional analysis indicated that both transcription factors negatively regulated StL3OH expression by binding to the MYBHv1 cis-element in its promoter. These findings improve our understanding of the salt stress response and transcriptional regulation of monoterpene biosynthesis in S. tenuifolia and provide a basis for the future improvement of Schizonepetae Herba quality and salt tolerance. Full article

Histone methyltransferases of the Trithorax-related (ATXR) family act as critical epigenetic regulators in plants. However, systematic characterization of this gene family remains limited in the economically important oilseed crop Brassica napus. In this study, we performed a pan-genomic analysis of the BnaATXR family genes using 11 genetically diverse rapeseed accessions and identified a total of 185 BnaATXR family members, among which BnaATXR5 was categorized as a dispensable gene. Pan-genomic and phylogenetic analyses grouped these genes into five distinct subfamilies and uncovered strong sequence conservation and pervasive purifying selection across the family. Whole-genome duplication (WGD) was identified as the major evolutionary force driving BnaATXR genes expansion. Cis-acting regulatory element analysis further revealed significant enrichment of stress- and phytohormone-responsive motifs in the promoter regions of BnaATXR genes. BnaATXR members exhibited divergent tissue expression profiles: subfamilies B and C displayed constitutive and broad expression across multiple tissues, whereas subfamilies A and E exhibited pronounced tissue-specific expression, with preferential enrichment in reproductive organs. Notably, CRISPR/Cas9-mediated knockout of BnaATXR6 led to delayed flowering time, shortened siliques, and decreased seed size, thereby demonstrating a key functional role of this gene in the modulation of yield-associated agronomic traits. Collectively, our findings present a genome-wide systematic characterization of the ATXR gene family and highlight their critical functional relevance to agronomically important traits in rapeseed. Full article

The Polyomaviridae family contains members known for achieving high seroprevalence within their target species despite a limited genomic economy. Minimalism, by definition, allows for the clarification and streamlining of purpose via the removal of unnecessary or distracting components. Among viruses, Simian Vacuolating Virus 40 (SV40) and other polyomaviruses are master minimalists, achieving efficient replication and persistence with compact genomes of approximately 5 kb in length. This review examines how polyomaviruses employ limited genetic material and simple structure to participate in complex functions and interactions, highlighting minimalism as both an evolutionary and functional advantage. Polyomaviruses make the most of their compact genomes in each stage of the viral lifecycle through the production of multifunctional early proteins and cis-regulatory elements, utilization of alternative splicing and host infrastructure, and organization of compact structural proteins. This allows for the successful replication and proliferation of virions while also reducing evolutionary pressure and promoting host immune evasion. Examination of the implications of polyomaviral minimalism illustrates that genome economy is not a constraint, but rather a driver of biological sophistication. Full article

Ammonium transporters (AMTs) represent a class of proteins within the ammonium transporter domain, which play an important role in mediating the transmembrane transport of NH₄⁺ in plants. However, research on AMT genes in foxtail millet remains limited. In this study, members of the AMT gene family in foxtail millet were identified at the whole genome level through bioinformatic analysis. The gene structure, evolutionary relationships, chromosomal localization, interspecies collinearity, cis-acting elements, and expression patterns of SiAMT members were systematically analyzed. The results revealed that there were nine SiAMT family members in foxtail millet, with molecular weights ranging from 49.5 to 53.8 kDa. Phylogenetic analysis classified them into three groups, which were unevenly distributed across chromosomes. The analysis of promoter cis-acting elements identified multiple regulatory elements, including light-, anaerobic-, and hormone-responsive elements. Collinearity analysis showed that the divergence time of AMT family members in foxtail millet and rice was more recent compared to Arabidopsis thaliana. The expression levels of SiAMT members varied across different tissues of foxtail millet, with most SiAMT family members showing high expression in roots, while SiAMT7 was significantly expressed in leaves. qRT-PCR analysis showed that SiAMT1 was significantly down-regulated in roots, stems, and leaves under salt stress. This study provides a theoretical foundation for further investigation into the functions of the AMT gene family. Full article

Banana productivity is severely limited by drought, yet the molecular basis of drought adaptation and endophyte-mediated stress alleviation remains poorly understood. Here, we performed a genome-wide analysis of the SQUAMOSA promoter-binding protein-like (SPL) transcription factor family in Musa acuminata and examined their transcriptional responses to drought stress and Serendipita indica inoculation. We identified 38 MaSPL genes, all encoding proteins with the conserved SBP domain and predicted nuclear localization. Phylogenetic, motif, gene structure, and collinearity analyses indicated that MaSPL genes are evolutionarily conserved, unevenly distributed across chromosomes, and expanded primarily through segmental duplication under purifying selection. Promoter analysis showed several cis-acting elements and transcription factor binding sites related to light, phytohormone, and stress signaling. Ten MaSPL genes were predicted as putative targets of miR156. qRT-PCR analysis showed that drought stress markedly downregulated the tested MaSPL genes, whereas miR156a expression increased, supporting an inverse regulatory relationship. Under drought, S. indica inoculation enhanced expression of most tested MaSPLs, restoring transcript accumulation while reducing miR156a to near-basal levels. Notable responses were observed in members of the MaSPL2, MaSPL9, and MaSPL13, respectively. S. indica improves drought tolerance by enhancing antioxidant defenses, reducing oxidative stress, and preserving photosynthetic and osmotic stability. Taken together, our results demonstrate that S. indica confers drought resilience in banana by counteracting drought-induced repression of MaSPL genes via the miR156–SPL module and by strengthening key physiological defense mechanisms. Full article