Background: CCCH-type zinc finger proteins play important roles in plant development and biotic/abiotic stress responses. Wintersweet (Chimonanthus praecox) is a popular ornamental plant with strong resistance to various stresses, which is a good material for exploring gene resource for stress response. In this study, we isolated a CCCH type zinc finger protein gene CpC3H3 (MZ964860) from flower of wintersweet and performed functional analysis with a purpose of identifying gene resource for floral transition and stress tolerance. Results: CpC3H3 was predicted a CCCH type zinc finger protein gene encoding a protein containing 446 amino acids with five conserved C-X₈-C-X₅-C-X₃-H motifs. CpC3H3 was localized in the cell membrane but with a nuclear export signal at the N-terminal. Transcripts of CpC3H3 were significantly accumulated in flower buds at floral meristem formation stage, and were induced by polyethylene glycol. Overexpression of CpC3H3 promoted flowering, and enhanced drought tolerance in transgenic A. thaliana. CpC3H3 overexpression affects the expression level of genes involved in flower inducement and stress responses. Further comparative studies on physiological indices showed the contents of proline and soluble sugar, activity of peroxidase and the rates of electrolyte leakage were significantly increased and the content of malondialdehyde and osmotic potential was significantly reduced in transgenic A. thaliana under PEG stress. Conclusion: Overall, CpC3H3 plays a role in flowering inducement and drought tolerance in transgenic A. thaliana. The CpC3H3 gene has the potential to be used to promote flowering and enhance drought tolerance in plants.

Leaf morphology plays a crucial role in forecasting the productivity and environmental adaptability of economically important trees. Plants with larger leaves usually have higher photosynthesis efficiency and can accumulate more nutrients, thereby increasing yield. In the natural population of Z. armatum, due to long-term selection, the leaves size and shape show rich diversity in different latitude regions. This diversity is the result of plants’ adaptation to different environments. However, to date, no studies have systematically revealed the genetic mechanism of Z. armatum leaf variation. In higher plants, lateral organ boundaries domain (LBD) proteins comprise a unique family of transcription factors that play pivotal roles in the establishment of plant leaf polarity and morphogenesis. However, little is currently known regarding the LBD gene family in Z. armatum. In this study, we identified 97 members of the LBD gene family within the genome of Z. armatum, which were unevenly distributed among the 33 chromosomes of this species. Physicochemical analysis revealed that these ZaLBDs are hydrophilic proteins with nuclear subcellular localization, whereas phylogenetic analysis of 234 LBD protein from different species indicated that these can be divided into five subfamilies (Ia, Ib, Ic, Id, and II). Furthermore, and analysis of cis-acting regulatory elements revealed that ZaLBDs may play important roles in responses to abiotic stress, hormone signal transduction, and plant growth and development. Transcriptomic data were used to compare the expression of these genes in leaves with differing morphologies collected from Z. armatum plants originating from sites at three different latitudes within the distribution range of this species. These data revealed differences in the expression of 14 genes among Z. armatum populations with different latitudinal distributions, with difference in the expression of the ZaLBD45 gene being the most pronounced, the expression trend of ZaLBD19 was consistent with the trend of leaf size. Moreover, qRT-PCR analysis verified that the relative expression of these genes was highly consistent with the transcriptomic data. In this study, we comprehensively analyzed the functional characteristics and expression patterns of genes in the LBD family within the heterophyllous plant Z. armatum distributed at different latitudes. By mediating the regulation of leaf morphology, these genes may play important roles in the response to abiotic stress and adaptation to ecological changes. Our findings will not only enhance our understanding of the genetic mechanisms underlying the adaptive variation in Z. armatum but also provide valuable resources for the genetic improvement of this plant.

Background: Zanthoxylum L., an important genus in the Rutaceae family, has great edible and medical values. However, the high degree of morphological similarity among Zanthoxylum species and the lack of sufficient chloroplast (cp) genomic resources have greatly impeded germplasm identification and phylogenetic analyses of Zanthoxylum.Methods: Here we assembled cp genomes of five widespread species (Zanthoxylum bungeanum, Z. armatum, Z. nitidum, Z. ailanthoides and Z. piasezkii) in China as a case study, comparative analysis of these assembled cp genomes.Results: Each of them, ranging from 157,231 to 158,728 bp, has a quadripartite structure. Except for one extra gene in Z. piasezkii, 132 genes were identified in each species, including 87 encode protein genes, 37 transfer ribose nucleic acid (tRNA) genes, and eight ribosomal RNA (rRNA) genes. Substantial variation was observed among these five cp genome sequences in the IR/SC boundary regions. Variation in insertions and deletions were observed in the cp genomes of the five species over three different intervals, and a large number of single-nucleotide polymorphism variants were detected in the rps3-rpl22-rps19 region. Phylogenetic analysis of complete cp genome sequences revealed the evolutionary relationships among 23 Zanthoxylum species (29 samples).Conclusion: Comparative analysis revealed that rps3-rpl22-rps19 is a highly variable divergent region in Zanthoxylum that could be developed as candidate markers for phylogenetic studies and species identification. This study identified a pair of molecular markers from hypervariable regions that can be used to distinguish between the five Zanthoxylum species and validated their utility. Overall, the results of this study provide new insights into the genetic breeding, germplasm exploration, and phylogeny of Zanthoxylum species.

Introduction: The basic helix-loop-helix (bHLH) proteins are a large family of transcription factors that are essential to physiology, metabolism, and development. However, the available information is limited about the bHLH gene family in Chimonobambusa utilis, which is widely cultivated in China because of its high-quality and economic value. C. utilis cultivars exhibit five natural color variations in their shoot sheaths, but the molecular mechanism behind this color diversity remains unclear.Methods: De novo assembly was employed to obtain gene sequences. To identify pathways related to color formation, GO enrichment analysis was performed on the 44,255 functionally annotated unigenes.Results: The transcriptomic analysis of C. utilis yielded a total of 195,977 transcripts and 75,137 unigenes after removing redundancy. The enrichment results revealed that four pathways were most strongly associated with color formation. Phylogenetic, conserved motif, and protein–protein interaction analyses, along with qRT–PCR validation, confirmed CubHLH17's role in red sheath color.Discussion: This research not only deepens insights into the functional roles of CubHLH genes but also lays the foundation for genetic improvement of bamboo species. We suggest that these findings will contribute to both scientific research and commercial bamboo cultivation through gene editing technology in the future.

Auxin response factors (ARFs) are a class of significant transcription factors that play crucial roles in the regulation of plant growth and development. Although ARF genes have been extensively characterized in various plants, their functions in perennial woody crops, particularly their involvement in regulating starch accumulation—a key determinant of yield and quality in Castanea mollissima—remain largely unexplored. To address this knowledge gap, we conducted a comprehensive study of the ARF gene family in the C. mollissima. In this study, 18 CmARF members, exhibiting diverse physicochemical properties, were identified within the C. mollissima genome. These CmARFs were categorized into four groups. Dispersed duplication emerged as the primary mechanism driving the expansion of the CmARF gene family. As C. mollissima seed kernels developed, notable changes were observed in starch content and the activity of enzymes related to starch biosynthesis, particularly a significant decrease in GBSS activity, which corresponded with an increase in seed kernel size and starch content. Transcriptome analysis delineated the expression patterns of CmARF genes during the development of C. mollissima seed kernels. A key novel finding of our research is that CmARF5a and CmARF18 are hypothesized to act as pivotal repressors of starch accumulation. This hypothesis is based on their expression profiles, strong negative correlations with physiological indicators, and WGCNA. Notably, the lack of correlation between these CmARFs and the expression of core starch biosynthetic genes suggests a potential indirect regulatory mechanism, offering a new perspective on ARF function in storage organ development. This study not only provides the first comprehensive characterization of the CmARF family but also offers a theoretical framework and candidate genes for future functional research on C. mollissima seed kernel development and starch biosynthesis.