Transcriptomic Analysis for the Identification of Metabolic Pathway Genes Related to Toluene Response in Ardisia pusilla.

Toluene is an industrial raw material and solvent that can be found abundantly in our daily life products. The amount of toluene vapor is one of the most important measurements for evaluating air quality. The evaluation of toluene scavenging ability of different plants has been reported, but the mechanism of plant response to toluene is only partially understood. In this study, we performed RNA sequencing (RNA-seq) analysis to detect differential gene expression in toluene-treated and untreated leaves of Ardisiapusilla. A total of 88,444 unigenes were identified by RNA-seq analysis, of which 49,623 were successfully annotated and 4101 were differentially expressed. Gene ontology analysis revealed several subcategories of genes related to toluene response, including cell part, cellular process, organelle, and metabolic processes. We mapped the main metabolic pathways of genes related to toluene response and found that the differentially expressed genes were mainly involved in glycolysis/gluconeogenesis, starch and sucrose metabolism, glycerophospholipid metabolism, carotenoid biosynthesis, phenylpropanoid biosynthesis, and flavonoid biosynthesis. In addition, 53 transcription factors belonging to 13 transcription factor families were identified. We verified 10 differentially expressed genes related to metabolic pathways using quantitative real-time PCR and found that the results of RNA-seq were positively correlated with them, indicating that the transcriptome data were reliable. This study provides insights into the metabolic pathways involved in toluene response in plants.

Progress and Challenges in the Improvement of Ornamental Plants by Genome Editing.

Biotechnological approaches have been used to modify the floral color, size, and fragrance of ornamental plants, as well as to increase disease resistance and vase life. Together with the advancement of whole genome sequencing technologies, new plant breeding techniques have rapidly emerged in recent years. Compared to the early versions of gene editing tools, such as meganucleases (MNs), zinc fingers (ZFNs), and transcription activator-like effector nucleases (TALENs), clustered regularly interspaced short palindromic repeat (CRISPR) is capable of altering a genome more efficiently and with higher accuracy. Most recently, new CRISPR systems, including base editors and prime editors, confer reduced off-target activity with improved DNA specificity and an expanded targeting scope. However, there are still controversial issues worldwide for the recognition of genome-edited plants, including whether genome-edited plants are genetically modified organisms and require a safety evaluation process. In the current review, we briefly summarize the current progress in gene editing systems and also introduce successful/representative cases of the CRISPR system application for the improvement of ornamental plants with desirable traits. Furthermore, potential challenges and future prospects in the use of genome-editing tools for ornamental plants are also discussed.

Volatile Organic Compounds from Orchids: From Synthesis and Function to Gene Regulation.

Orchids are one of the most significant plants that have ecologically adapted to every habitat on earth. Orchids show a high level of variation in their floral morphologies, which makes them popular as ornamental plants in the global market. Floral scent and color are key traits for many floricultural crops. Volatile organic compounds (VOCs) play vital roles in pollinator attraction, defense, and interaction with the environment. Recent progress in omics technology has led to the isolation of genes encoding candidate enzymes responsible for the biosynthesis and regulatory circuits of plant VOCs. Uncovering the biosynthetic pathways and regulatory mechanisms underlying the production of floral scents is necessary not only for a better understanding of the function of relevant genes but also for the generation of new cultivars with desirable traits through molecular breeding approaches. However, little is known about the pathways responsible for floral scents in orchids because of their long life cycle as well as the complex and large genome; only partial terpenoid pathways have been reported in orchids. Here, we review the biosynthesis and regulation of floral volatile compounds in orchids. In particular, we focused on the genes responsible for volatile compounds in various tissues and developmental stages in Cymbidium orchids. We also described the emission of orchid floral volatiles and their function in pollination ecology. Taken together, this review will provide a broad scope for the study of orchid floral scents.

RNA sequencing analysis of Cymbidium goeringii identifies floral scent biosynthesis related genes.

BACKGROUND: Cymbidium goeringii belongs to the Orchidaceae, which is one of the most abundant angiosperm families. Cymbidium goeringii consist with high economic value and characteristics include fragrance and multiple flower colors. Floral scent is one of the important strategies for ensuring fertilization. However, limited genetic data is available in this non-model plant, and little known about the molecular mechanism responsible for floral scent in this orchid. Transcriptome and expression profiling data are needed to identify genes and better understand the biological mechanisms of floral scents in this species. Present transcriptomic data provides basic information on the genes and enzymes related to and pathways involved in flower secondary metabolism in this plant. RESULTS: In this study, RNA sequencing analyses were performed to identify changes in gene expression and biological pathways related scent metabolism. Three cDNA libraries were obtained from three developmental floral stages: closed bud, half flowering stage and full flowering stage. Using Illumina technique 159,616,374 clean reads were obtained and were assembled into 85,868 final unigenes (average length 1194 nt), 33.85% of which were annotated in the NCBI non redundant protein database. Among this unigenes 36,082 were assigned to gene ontology and 23,164 were combined with COG groups. Total 33,417 unigenes were assigned in 127 pathways according to the Kyoto Encyclopedia of Genes and Genomes pathway database. According these transcriptomic data we identified number of candidates genes which differentially expressed in different developmental stages of flower related to fragrance biosynthesis. In q-RT-PCR most of the fragrance related genes highly expressed in half flowering stage. CONCLUSIONS: RNA-seq and DEG data provided comprehensive gene expression information at the transcriptional level that could be facilitate the molecular mechanisms of floral biosynthesis pathways in three developmental phase's flowers in Cymbidium goeringii, moreover providing useful information for further analysis on C. goeringii, and other plants of genus Cymbidium.

Volatiles Profile of the Floral Organs of a New Hybrid Cymbidium, 'Sunny Bell' Using Headspace Solid-Phase Microextraction Gas Chromatography-Mass Spectrometry Analysis.

Cymbidium is one of the most important genera of flowering plants in the Orchidaceae family, and comprises a wide variety of beautiful and colorful species. Among these, only a few species possess floral scents and flavors. In order to increase the availability of a new Cymbidum hybrid, "Sunny Bell", this study investigated the volatile floral scents. Volatiles of the floral organs of the new Cymbidium hybrid, "Sunny Bell", at the full-flowering stage were characterized with headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS) analysis. A divinylbenzene-carboxen-polydimethylsiloxane (DVB-CAR-PDMS) fiber gave the best extraction for volatile components. Twenty-three components were identified as the main volatiles for the floral organs of the new Cymbidium hybrid, "Sunny Bell" at the full-flowering stage; twelve compounds in the column, sixteen compounds in the labellum, eleven compounds in the sepals, and nine compounds in the petals were identified. Terpenes are the major source of floral scents in this plant. As a result of GC-MS analysis, the most abundant compound was linalool (69-80%) followed by α-pinene (3-27%), 4,8-dimethyl-1,3,7-nonatriene (5-18%), eucalyptol (6-16%), and 2,6-dimethylnonane (2-16%). The main components were identified as monoterpenes in the petals and sepals, and as monoterpenes and aliphatics in the column and labellum. The results of this study provide a basis for breeding Cymbidium cultivars which exhibit desirable floral scents.