Search

Abstract Bacterial blight of rice is a devastating disease caused by the gram-negative bacteria Xanthomonas oryzae pv. oryzae (Xoo). Chinese Xoo strain pathotypes IV, V, and IX are the major virulent Xoo strain types in South China sequentially from the 1990s to the present. Here, we report the isolation of GD0201 and GD0202, which belong to pathotypes IV and IX, respectively, and the complete genome sequence and transcriptomic analysis of GD0201 (IV), GD1358 (V), and GD0202 (IX). We found that resistance genes xa5, Xa23, and Xa27 confer strong resistance to all three Xoo strains, indicating that they are currently good choices for resistance rice breeding. The genome analysis reveals fewer TAL and non-TAL effector coding genes in GD0202 than in the other two strains, potentially contributing to its strong virulence. Transcriptomic analysis of ZH11 inoculated with the three Xoo strains strongly suggests that three Xoo strains for better infection repress the ethylene response factor (ERF) gene family members. Furthermore, weighted gene co-expression network analysis (WGCNA) and protein-protein interaction (PPI) analysis revealed 14 hub genes potentially associated with rice response to the three Xoo strains. The expression of several hub genes was validated to be induced by all three Xoo strains, suggesting its role in bacterial blight disease response to Xoo strains. Genomic analysis of the Xoo strains belonging to pathotypes IV, V, and IX, identification of effectors and genes related to Xoo virulence in rice plants will provide insights into understanding the molecular mechanism underlying rice-Xoo interaction and the gene expression pattern in response to Xoo infection.

Abstract Upon Xanthomonas oryzae pv. oryzae (Xoo) infection of rice leaves, the invasion induces systematic expression changes for both the coding genes and the non-coding genes, allowing the plant to make corresponding responses. However, the roles of circular RNAs (circRNAs) in rice defending against Xoo remain largely unknown. To address this question, we conducted a whole-transcriptomic analysis to systematically screen the differentially expressed (DE) mRNAs and non-coding RNAs (ncRNAs) in rice responding to Xoo infection. Our results revealed a total of 4076 DE mRNAs, 89 DE long non-coding RNAs (lncRNAs), 82 DE microRNAs (miRNAs), and 14 DE circRNAs identified from Xoo-infected rice plants at 48 h post inoculation. Three circRNAs (ciR52, ciR298, and ciR133) were found to be able to form circular RNAs, and their expression was induced by Xoo infection. ciR133 was found to repress the expression of its parental gene OsARAB (putative arabinofuranosidase gene) during Xoo infection. Overexpression of ciR133 and mutation of OsARAB enhanced rice resistance against Xoo, without compromising main agronomic traits. Our data suggest that circRNAs are associated with rice response to Xoo infection, providing a potential strategy for breeding Xoo-resistant rice plants by manipulating ciR133 and OsARAB.

This review presents a systematic analysis of the studies on volatiles in Dendrobium. Among the various components, aromatic terpenes are a crucial component in the development of the aromatic characteristics of Dendrobium and other plants. Recent advancements in detection and sequencing technology have resulted in a considerable rise in research on the biosynthetic processes of aromatic terpenes in Dendrobium and other flowering plants. Nevertheless, the inquiry into the precise means by which plants regulate the proportion of diverse aromatic terpenes in their floral scent, thereby preserving their olfactory traits, requires further investigation. A conjecture on the botanical perfumer mechanism, which condensed the findings of earlier studies, was put forward to address this area of interest. Specific transcription factors likely govern the coordinated expression of multiple key terpene synthase (TPS) genes during the flowering stage of plants, thereby regulating the proportional biosynthesis of diverse aromatic terpenes and sustaining the distinctive aromatic properties of individual plants. This review serves as a significant theoretical reference for further investigations into aromatic volatile compounds in Dendrobium.

Long non-coding RNAs (lncRNAs) regulate gene expression in eukaryotic organisms. Research suggests that lncRNAs may be involved in the regulation of nitrogen use efficiency in plants. In this study, we identified 1628 lncRNAs based on the transcriptomic sequencing of rice roots under low-nitrogen (LN) treatment through the implementation of an integrated bioinformatics pipeline. After 4 h of LN treatment, 50 lncRNAs and 373 mRNAs were significantly upregulated, and 17 lncRNAs and 578 mRNAs were significantly downregulated. After 48 h LN treatment, 43 lncRNAs and 536 mRNAs were significantly upregulated, and 42 lncRNAs and 947 mRNAs were significantly downregulated. Moreover, the interaction network among the identified lncRNAs and mRNAs was investigated and one of the LN-induced lncRNAs (lncRNA24320.6) was further characterized. lncRNA24320.6 was demonstrated to positively regulate the expression of a flavonoid 3′-hydroxylase 5 gene (OsF3′H5). The overexpression of lncRNA24320.6 was shown to improve nitrogen absorption and promote growth in rice seedlings under LN conditions. Our results provide valuable insights into the roles of lncRNAs in the rice response to nitrogen starvation.

Dendrobium chrysotoxum is considered as an important ornamental dendrobium because of its strong and long-lasting floral scent. Nevertheless, few information is known about the dynamic changes and related formation mechanism of dendrobium floral scent at different flowering stages. In this study, the characteristics and biosynthetic mechanism of floral scent in D. chrysotoxum during flowering was revealed by using widely-targeted volatilomics (WTV) combined with transcriptome analysis. Over 500 kinds of volatile organic compounds (VOCs) were detected in the floral scents of D. chrysotoxum, which improved the knowledge about floral scent components of dendrobium. A total of 153 differential VOCs and 4,487 differentially expressed genes (DEGs) were identified between flowers of different flowering stages, respectively. The results for both volatilomics and transcriptomics data indicated that terpenes and related genes played an important role in the formation of floral characteristics of D. chrysotoxum. But in general, the expression of genes showed an opposite trend to the accumulation of metabolites during flowering, suggesting that the regulation of floral scent biosynthesis might have started at the budding stage in D. chrysotoxum. Additionally, a transcriptional metabolic regulatory network consisting of terpenes, terpene synthases and candidate transcription factors was established. This research is the first systematic and comprehensive exploration of floral characteristics and related mechanisms during flowering in D. chrysotoxum. It provides basis for exploration of mechanisms on the floral scents and the breeding of aromatic dendrobium.

Flower fragrance is one of the traits that holds important economical values in flowering plants. Extensive attention has converged on fragrance preservation in flower cultivation and breeding. Dendrobium loddigesii is an important species for cultivating aromatic Dendrobium orchid varieties for the long term due to its fragrance. Few studies focus on exploring related genes responsible for the aroma components in D. loddigesii. We analyzed flowers from two aromatic D. loddigesii varieties using high-throughput RNA sequencing and gas chromatography-mass spectrometry (GC-MS). The metabolomics results showed that the main volatile compounds responsible for the aroma formation of D. loddigesii were terpenes, especially monoterpenes. The de novo transcriptome assembly comprised 175,089 unigenes, and 24,570 unigenes of the genes were identified as differential expressed genes (DEGs) between the two varieties. Among these DEGs, 525 genes were mapped into seven pathways that related to the floral scent synthesis. Seventeen key genes were significantly correlated with volatile aroma metabolites, including geraniol, α-pinene, eugenol, and (Z)-3-hexenal. These results provide references for understanding the aroma biosynthesis and perfume formulations of D. loddigesii.

Photosynthesis affects crop growth and yield. The roles of microRNAs (miRNAs) in photosynthesis are little known. In the present study, the role of the OsNF-YB7–OsMIR5810–OsMRLP6 regulatory module in photosynthesis was investigated. The malectin-like protein gene OsMRLP6 was identified as a target gene of osa-miR5810 (miR5810). Overexpression in rice of miR5810 or down-expression of OsMRLP6 resulted in reduced expression of genes involved in chloroplast development and photosynthesis and decreased net photosynthetic rate, finally leading to lower shoot biomass and grain yield. Down-expression of miR5810 and overexpression of OsMRLP6 showed the opposite effect. Overexpression of transcription factor OsNF-YB7 elevated expression of OsMIR5810 in rice seedlings by binding to its promoter. The OsNFYB7–OsMIR5810–OsMRLP6 regulatory module affects photosynthesis to mediate growth and grain yield. [ABSTRACT FROM AUTHOR]