Comprehensive identification, characterization, and expression analysis of the MORF gene family in Brassica napus.

BACKGROUND: RNA editing in chloroplast and mitochondrion transcripts of plants is an important type of post-transcriptional RNA modification in which members of the multiple organellar RNA editing factor gene family (MORF) play a crucial role. However, a systematic identification and characterization of MORF members in Brassica napus is still lacking. RESULTS: In this study, a total of 43 MORF genes were identified from the genome of the Brassica napus cultivar "Zhongshuang 11". The Brassica napus MORF (BnMORF) family members were divided into three groups through phylogenetic analysis. BnMORF genes distributed on 14 chromosomes and expanded due to segmental duplication and whole genome duplication repetitions. The majority of BnMORF proteins were predicted to be localized to mitochondria and chloroplasts. The promoter cis-regulatory element analysis, spatial-temporal expression profiling, and co-expression network of BnMORF genes indicated the involvement of BnMORF genes in stress and phytohormone responses, as well as growth and development. CONCLUSION: This study provides a comprehensive analysis of BnMORF genes and lays a foundation for further exploring their physiological functions in Brassica napus.

The ATP Synthase γ Subunit ATPC1 Regulates RNA Editing in Chloroplasts.

RNA editing is the process of modifying RNA molecules by inserting, deleting, or substituting nucleotides. In flowering plants, RNA editing occurs predominantly in RNAs encoded by the organellar genomes of mitochondria and chloroplasts, and the main type of editing involves the substitution of cytidine with uridine at specific sites. Abnormal RNA editing in plants can affect gene expression, organelle function, plant growth, and reproduction. In this study, we report that ATPC1, the gamma subunit of ATP synthase in Arabidopsis chloroplasts, has an unexpected role in the regulation of editing at multiple sites of plastid RNAs. The loss of function of ATPC1 severely arrests chloroplast development, causing a pale-green phenotype and early seedling lethality. Disruption of ATPC1 increases the editing of matK-640, rps12-i-58, atpH-3'UTR-13210, and ycf2-as-91535 sites while decreasing the editing of rpl23-89, rpoA-200, rpoC1-488, and ndhD-2 sites. We further show that ATPC1 participates in RNA editing by interacting with known multiple-site chloroplast RNA editing factors, including MORFs, ORRM1, and OZ1. The transcriptome in the atpc1 mutant is profoundly affected, with a pattern of defective expression of chloroplast development-related genes. These results reveal that the ATP synthase γ subunit ATPC1 is involved in multiple-site RNA editing in Arabidopsis chloroplasts.

Regulation mechanisms of flavonoids biosynthesis of Hancheng Dahongpao peels (Zanthoxylum bungeanum Maxim) at different development stages by integrated metabolomics and transcriptomics analysis.

BACKGROUND: Flavonoids have strong free radical scavenging and antioxidant capacity. The high abundance of flavonoids in Chinese prickly ash peels have many benefits to human health. In this study, 'Hancheng Dahongpao', a main cultivar, was taken as materials to investigate the flavonoids biosynthesis mechanism of Zanthoxylum bungeanum Maxim at three key development stages by integration of metabolomics and transcriptomics analysis. RESULTS: A total of 19 differentially accumulated metabolites were identified, the key flavonoids compounds were kaempferol, quercetin and their glycoside derivatives, and two major anthocyanins (peonidin O-hexoside and peonidin 3-O-glucoside). 5 gene networks/modules including 15 important candidate genes were identified, which was highly correlated with flavonoids. Among these genes, ZM-163828 and ZM-184209 were strongly correlated with kaempferol and quercetin, and ZM-125833 and ZM-97481 were controlled the anthocyanins biosynthesis. Moreover, it was shown that MYB-ZM1, MYB-ZM3, MYB-ZM5, MYB-ZM6 and MYB-ZM7 coordinately controlled flavonoids accumulation through regulating the structural genes. CONCLUSIONS: Generally, this study systematically revealed the flavonoids metabolic pathways and candidate genes involved in flavonoids biosynthesis and laid a foundation for the potential targets for the breeding of new valuable Chinese prickly ash cultivars.

Quality Evaluation of Wild Germplasm of Chinese Prickly Ash (Zanthoxylum bungeanum Maxim) from Qinling Mountains at Different Elevations Based on HPLC-Fingerprint.

Wild Chinese prickly ash resources provide a valuable genetic resource for Zanthoxylum bungeanum Maxim improvement and breeding. The Qinling Mountains was an abundant source for wild Chinese prickly ash. In this study, the phenolic and flavonoid compounds of wild germplasm resources from different altitudes and six cultivated varieties were analyzed by high performance liquid chromatography (HPLC). The chromatograms of them were essentially consistent, although their chemical composition contents were greatly different. The thirty samples were divided into three categories through the hierarchical clustering analysis. Catechin, hyperoside and quercitrin were considered to be key compounds for the quality evaluation, and by contrast, the wild samples with an altitude of 2300±50 m (Group IV) had the highest content of key compounds, and presented stronger antioxidant activity and antibacterial ability, indicating that these wild samples could be identified as the excellent breeding resources. This is the first time to evaluate the quality of wild Chinese prickly ash at different altitudes in Qinling Mountains. These excellent wild germplasm resources provided substantial potential accessions for use directly in Chinese prickly ash breeding programs.

Combined morphological and multi-omics analyses to reveal the developmental mechanism of Zanthoxylum bungeanum prickles.

Zanthoxylum bungeanum Maxim. as an important economic forest, its epidermis bears prickles which complicate the harvesting process and increase the labor costs. To explore the developmental mechanism of prickles, three varieties of Zanthoxylum bungeanum (PZB, SZB, GSZB) were selected for morphological and multi-omics analyses. The absorption spectra of prickles and stems were detected using Fourier-transform infrared spectroscopy (FTIR), and they were found different at 1617, 1110, 3319, and 1999 cm-1. The morphology of prickles and stems were observed using light microscopy and transmission electron microscopy (TEM). The growth direction of cells on the prickle side and stem side were perpendicular to each other, and there was a resembling abscission zone (RAZ) between them. The vacuolar deposits of prickle cells were much more than stem cells, indicating that the lignification degree of prickles was higher than stems. In addition, 9 candidate genes (ZbYABBY2, ZbYABBY1, ZbYABBY5, ZbWRKY, ZbLOG5, ZbAZG2, ZbGh16, ZbIAA33, and ZbGh16X1) were screened out and validated base on transcriptome and qRT-PCA. As well as, 30 key metabolites were found related to prickle development base on metabolome analysis. Among them, 4-hydroxy-2-oxopentanoate, trans-2-hydroxy-cinnamate, trans-cinnamate, polyhydroxy-fatty acid, 10,16-dihydroxypalmitate, cinnamic acid were related to the biosynthesis of cutin, suberine and wax. Indole-3-acetate, tryptamine, anthranilate, fromylanthranilate, N6-(delta2-isopentenyl)-adenine were related to plant hormone signal transduction. Generally, this is the first study to reveal the developmental mechanism of prickles. The results of this study lay the foundation for the breeding of non-prickle Zanthoxylum bungeanum.

Chemotaxonomic variation in volatile component contents and their correlation between climate factors in Chinese prickly ash peels (Zanthoxylum bungeanum Maxim.).

In this study, we analyzed the characteristics of volatile compounds of Chinese prickly ash peels with different climate conditions and their correlation. The data revealed that the contents of limonene and linalool in peels from southwest and northwest regions were higher, and the aroma was stronger, while the contents of ß-myrcene and (E)-ocimene in them from north, east and central China were higher, and the spicy flavor was heavier. Hierarchical cluster analysis demonstrated that the classification had geographical continuity. Through the correlation analysis and path analysis, it was found that the contents of volatile compounds were closely related to the climatic factors. The influence of wind speed and annual average temperature on volatile substances was greater than that of annual average precipitation and annual sunshine duration. This enriched the effect of climatic factors on the accumulation of volatile substances, and promoted the agriculture practices in area having similar climate conditions.

Transcriptome and metabolome analyses reveal the regulation of peel coloration in green, red Chinese prickly ash (Zanthoxylum L.).

Peel colour is an important external economic characteristic of Chinese prickly ash cultivars (Zanthoxylum bungeanum Maxim.). To gain insight into their coloration mechanisms, we performed an integrated analysis of green and red peels using combined metabolomic and transcriptomic analyses. Pelargonin-O-hexoside-O-rhamnoside-O-hexoside, pelargonidin 3,5-diglucoside, peonidin O-hexoside, cyanidin O-syringic acid and peonidin 3-O-glucoside were found to be the key anthocyanins. Transcriptome data indicated that the anthocyanidin synthase genes and UDP-glucose flavonoid 3-O-glucosytransferase genes were significantly increased to promote the redness of the peels. In addition, we discussed the role of R2R3-MYB transcription factors in coloration, of which the c80935 and c226097 genes may be the key regulatory factors for anthocyanin biosynthesis. Generally, this is the first study to identify and reveal the main anthocyanins in Chinese prickly ash peels during different developmental periods. The results of this research lay the foundation for understanding the regulation of coloration in Chinese prickly ash peels.