TL;DR
This work sets a starting point for furthur investigation into cotton GolS genes and provides novel resources for breeding programmes aimed at enhancing abiotic stress tolerance in cotton.
GDSL esterases/lipases constitute a large and functionally versatile gene family in plants, yet their systematic characterization in bamboo—perennial woody grasses with exceptionally rapid shoot elongation—remains scarce. Here, we performed a genome-wide identification of the GDSL family in allohexaploid Dendrocalamus farinosus and characterized the function of a candidate gene in secondary wall synthesis. A total of 265 DfGDSL genes were identified and classified into nine clades; rice xylan deacetylases BS1 and DARX1 fell within Clade VIII, which harbors 75 members. Chromosomal distribution, exon–intron organization, conserved motifs, and collinearity analyses indicated that whole-genome and tandem duplications drove family expansion, with purifying selection as the predominant evolutionary force. Expression profiling across tissues and shoot developmental stages pinpointed DfGDSL58 as the sole highly expressed OsDARX1 homolog in D. farinosus, showing specific upregulation during rapid elongation (50–400 cm). Its promoter contains auxin-responsive elements, and exogenous NAA treatment significantly induced its expression, with a peak at 6 h. Heterologous overexpression of DfGDSL58 (designated DfDACX1) in tobacco increased plant height and basal diameter while reducing lignin and hemicellulose deposition, xylem width, and transcript levels of xylan synthase (NtIRX9) and lignin biosynthetic genes (NtC4H, NtCOMT, NtCAD), whereas cellulose content and cellulose synthase genes (NtCESA4, NtCESA7) remained largely unchanged. Collectively, these findings demonstrate that DfDACX1 negatively regulates secondary wall thickening and promotes longitudinal growth, likely via modulating xylan deacetylation and downstream lignin biosynthesis. This study presents the first systematic characterization of the GDSL family in D. farinosus and identifies DfDACX1 as a key modulator of the trade-off between cell wall deposition and rapid shoot elongation, offering mechanistic insights into bamboo’s extraordinary growth and a potential target for engineering plant architecture.
Auxin is a central phytohormone involved in regulating plant growth, development, and stress responses, with the Aux/IAA gene family functioning as an essential component of the auxin signaling pathway. To elucidate the genomic features and potential functions of the Aux/IAA gene family in pumpkin ( Cucurbita moschata ), we performed a genome-wide identification and systematic characterization. A total of 72 CmIAA genes were identified, encoding proteins ranging from 158 to 1275 amino acids with predicted isoelectric points of 4.57–9.81. These genes were unevenly distributed across 20 chromosomes, with Chr17 harboring the highest number, while no CmIAA genes were detected on Chr3. Phylogenetic analysis classified the genes into nine subgroups (Groups Ⅰ–Ⅸ), with Groups Ⅰ, Ⅵ, and Ⅸ exhibiting relative expansion. Gene structure and conserved motif analyses revealed subgroup-specific motif compositions, with motif 1 representing the core conserved domain. Intraspecific collinearity analysis identified 54 segmentally duplicated gene pairs but no tandem duplication events, whereas interspecific synteny revealed extensive orthologous relationships between pumpkin and Cucurbita pepo and Cucurbita maxima . Promoter analysis showed that CmIAA genes contain multiple cis-elements associated with hormone responses and abiotic stress responses, including ABRE, MBS, and DRE. Tissue expression analysis demonstrated that many CmIAA genes exhibited tissue-preferential expression patterns. Under abiotic stress conditions, CmIAA 69 showed a salt-specific expression pattern, whereas CmIAA 39 and CmIAA 58 responded to both salt and drought treatments, indicating that these CmIAA genes play distinct roles in pumpkin responses to different abiotic stresses. This study systematically characterized the Aux/IAA gene family in pumpkin, highlighting its evolutionary diversity, structural conservation, and distinct regulatory features. These findings provide valuable genetic resources for further functional studies and inform the potential roles of CmIAA genes in abiotic stress responses.
The monosaccharide transporter (MST) family mediates soluble sugar transport and distribution, playing critical roles in plant growth, development, and fruit sugar accumulation. Citrus is a globally important fruit crop whose organoleptic quality depends heavily on sugar content. However, a systematic genome-wide analysis of MST genes in citrus is lacking. In this study, we identified 68 MST genes in the Citrus sinensis genome and classified them into seven subfamilies based on phylogenetic analysis. Chromosomal localization revealed uneven distribution across all nine chromosomes. Conserved motif, domain, and gene structure analyses further supported the evolutionary conservation and functional divergence. Syntenic analysis identified segmental duplication as the main driver for family expansion, and interspecific comparisons with Arabidopsis thaliana, Solanum lycopersicum, and Malus domestica provided evolutionary insights. Promoter cis-regulatory element analysis indicated that CsMSTs may respond to light, phytohormones, and stress signals, with several members carrying sugar-responsive elements potentially involved in sugar–acid metabolism. Moreover, by integrating soluble sugar content and transcriptome data across three fruit developmental stages, we performed a correlation analysis and identified 6 CsMST members showing high correlation with sucrose, glucose, and fructose simultaneously based on the Mantel test. qRT-PCR validation and linear correlation analysis confirmed that three of these members were significantly negatively correlated with sugar levels, whereas one was significantly positively correlated. This work provides a comprehensive characterization of the MST family in citrus and highlights candidate genes for future functional dissection of sugar transport and fruit quality improvement.
Respiratory burst oxidase homologs (RBOHs) are key enzymes on the plant plasma membrane that mediate stress-induced extracellular reactive oxygen species (ROS) bursts, playing important roles in plant growth, development, and stress responses. Previous studies on the RBOH gene family have largely focused on identification and functional analysis in single species, and systematic phylogenetic analyses across a broad range of Brassicaceae species remain lacking. In this study, based on genomic data from 22 Brassicaceae species, we systematically identified the RBOH gene family and obtained a total of 314 RBOH genes. Phylogenetic analysis classified these 314 RBOH genes into five conserved groups. Whole genome duplication (WGD) was the major driving force for gene family expansion, contributing 58.6% of the genes (184 genes). Synteny analysis revealed the evolutionary and retention patterns of RBOH genes between Brassica napus and its diploid progenitors Brassica rapa and Brassica oleracea. Promoter analysis revealed abundant stress-responsive and hormone-responsive cis-elements, with the abscisic acid-responsive element ABRE and the hormone cross-regulatory element as-1 being the most enriched. Expression analysis showed that BnRBOH genes exhibited differential response patterns under abiotic stresses such as drought and salt stress, with significantly more responses in root tissues than in leaf tissues. Transcription factor regulatory network analysis identified 244 transcription factors regulating 18 BnRBOH genes, with stress-responsive core transcription factor families such as ERF, NAC, and WRKY being dominant. This study fills the gap in large-scale phylogenetic research on the RBOH gene family in Brassicaceae and provides priority candidate targets — root-specific, stress-inducible BnRBOH genes — for stress tolerance improvement in rapeseed.
Phoebe bournei is an economically and ecologically important woody species native to China. As a core component of colchicine-triggered polyploid breeding, the tubulin genes (TUA and TUB) have been identified and functionally analyzed in many plants, but not yet in P. bournei. Here, tubulin family members in P. bournei were identified through sequence alignment and subsequently characterized using comprehensive bioinformatic analyses. In particular, a total of six PbTUA and ten PbTUB members were identified and grouped into two and five subfamilies, respectively, according to phylogenetic relationships. Most tubulin proteins were small (414–522 aa) with predicted stability. Furthermore, 36 collinear gene pairs were identified, suggesting a possible contribution to the evolutionary expansion of this family. For different tissues, the expression levels of most tubulin genes were generally lower in leaves but higher in roots. Besides, treatment with 1.0% colchicine inhibited the expression of all 15 tubulin genes except PbTUB6. These results provide preliminary insights into tubulin genes associated with polyploid induction and supply candidate genes for future functional studies toward polyploid germplasm creation of P. bournei.
Chalcone synthase (CHS) is a key enzyme in flavonoid biosynthesis, and its activity strongly influences the efficiency of flavonoid production in plants. By controlling the biosynthesis of secondary metabolites, CHS contributes to plant adaptation to diverse environmental stresses. Here, we identified CHS members across the Phoebe zhennan genome and systematically examined their gene structures, phylogenetic relationships, and potential roles in golden-thread wood color formation and drought response. Genome-wide screening resolved 11 putatively functional PzCHSs, which were unevenly distributed across six chromosomes. Physicochemical analyses indicated that most PzCHS proteins were hydrophilic. Phylogenetic reconstruction divided the PzCHS family into three groups, whose members generally shared similar gene structures. One tandem duplication event and five segmental duplication events were detected. Synteny analysis revealed extensive collinearity between the CHS families of P. zhennan, Phoebe bournei and Cinnamomum camphora, consistent with their close evolutionary relationships. Promoter regions of PzCHS genes were enriched for phytohormone-responsive and growth-related cis-elements, suggesting roles in development and hormonal regulation. Transcriptome profiling showed that PzCHS6 was upregulated in the transition zone of wood and under drought stress, suggesting that this gene may be associated with both golden-thread wood color formation and drought response. These results provide a framework for functional dissection of the CHS members and offer candidate genes for golden-thread wood color improvement and drought response breeding.