Xiaoli Hu

Citrus reticulata ‘Chachi’ (CRC) has long been recognized for its nutritional benefits, health-promoting properties, and pharmacological potential. Despite its importance, the bioactive components of CRC and their biosynthetic pathways have remained largely unexplored. In this study, we introduce a gap-free genome assembly for CRC, which has a size of 312.97 Mb and a contig N50 size of 32.18 Mb. We identified key structural genes, transcription factors, and metabolites crucial to flavonoid biosynthesis through genomic, transcriptomic, and metabolomic analyses. Our analyses reveal that 409 flavonoid metabolites, accounting for 83.30% of the total identified, are highly concentrated in the early stage of fruit development. This concentration decreases as the fruit develops, with a notable decline in compounds such as hesperetin, naringin, and most polymethoxyflavones observed in later fruit development stages. Additionally, we have examined the expression of 21 structural genes within the flavonoid biosynthetic pathway, and found a significant reduction in the expression levels of key genes including 4CL, CHS, CHI, FLS, F3H, and 4′OMT during fruit development, aligning with the trend of flavonoid metabolite accumulation. In conclusion, this study offers deep insights into the genomic evolution, biosynthesis processes, and the nutritional and medicinal properties of CRC, which lay a solid foundation for further gene function studies and germplasm improvement in citrus.

Due to the protracted transgenic timeline and low efficiency in stable genetic transformation of woody plants, there has been limited exploration of real-time organelle imaging within stable transgenic woody plant cells. Here, we established an efficient in vivo genetic transformation system for woody plants using an Agrobacterium rhizogenes-mediated approach. This system was successfully validated in multiple perennial woody species. Using citrus as a model, we introduced organelle-targeted fluorescent reporters via genetic transformation and investigated their subcellular localization and dynamics using advanced imaging techniques, such as confocal microscopy and live-cell imaging. Moreover, we subjected transgenic MT-GFP-labeled mitochondria in root cells to stress conditions simulating agricultural adversities faced by fruit crops. The stress-induced experiments revealed notable alterations in mitochondrial morphology. Our study contributes novel insights into membrane trafficking processes, protein localization dynamics, and cellular physiology in woody plants, while also providing stable and efficient genetic transformation methods for perennial woody species.

The ever-increasing food requirement with globally growing population demands advanced agricultural practices to improve grain yield, to gain crop resilience under unpredictable extreme weather, and to reduce production loss caused by insects and pathogens. To fulfill such requests, genome engineering technology has been applied to various plant species. To date, several generations of genome engineering methods have been developed. Among these methods, the new mainstream technology is clustered regularly interspaced short palindromic repeats (CRISPR) with nucleases. One of the most important processes in genome engineering is to deliver gene cassettes into plant cells. Conventionally used systems have several shortcomings, such as being labor- and time-consuming procedures, potential tissue damage, and low transformation efficiency. Taking advantage of nanotechnology, the nanoparticle-mediated gene delivery method presents technical superiority over conventional approaches due to its high efficiency and adaptability in different plant species. In this review, we summarize the evolution of plant biomolecular delivery methods and discussed their characteristics as well as limitations. We focused on the cutting-edge nanotechnology-based delivery system, and reviewed different types of nanoparticles, preparation of nanomaterials, mechanism of nanoparticle transport, and advanced application in plant genome engineering. On the basis of established methods, we concluded that the combination of genome editing, nanoparticle-mediated gene transformation and de novo regeneration technologies can accelerate crop improvement efficiently in the future.

Pecan (Carya illinoinensis) is an economically important nut tree that is greatly affected by drought, limiting its production and distribution. Although the complete genome of the pecan was published several years ago, the molecular basis of the pecan’s response to drought remains unclear. In this study, we analyzed the high-throughput transcriptome data for pecans under 3, 6, 9, 12, and 15 days of drought stress compared with the controls. A total of 12,893 differentially expressed genes (DEGs) were identified under drought stress, with 11,684 of them showing significant changes after 15 d of drought treatment. Among these, 4448 genes were up-regulated while 7226 were down-regulated. The trend analysis revealed that DEGs could be classified into 20 clusters. Surprisingly, the majority of genes (6148) showed a gradual down-regulation, and 3683 genes showed a gradual up-regulation in response to drought. Gene ontology enrichment analysis showed that the DEGs were mainly enriched in biological processes. The KEGG pathway enrichment results indicated that the DEGs were mainly enriched in several pathways, including metabolic pathways, the biosynthesis of secondary metabolites, and plant hormone signal transduction processes. Among the DEGs, 457 protein kinase and 734 transcription factor genes were shown to be drought-responsive and may play key roles in the response to drought, and the expression patterns of selected candidate genes were further validated using quantitative real-time PCR. Collectively, these findings highlighted the multiple processes in pecans under drought stress and provided valuable insights into the further investigation of the functions of drought stress-responsive genes and the molecular basis of the pecan drought stress response.