Chromosome-level genome assembly of Zizania latifolia provides insights into its seed shattering and phytocassane biosynthesis

Chinese wild rice (Zizania latifolia; family: Gramineae) is a valuable medicinal homologous grain in East and Southeast Asia. Here, using Nanopore sequencing and Hi-C scaffolding, we generated a 547.38 Mb chromosome-level genome assembly comprising 332 contigs and 164 scaffolds (contig N50 = 4.48 Mb; scaffold N50 = 32.79 Mb). The genome harbors 38,852 genes, with 52.89% of the genome comprising repetitive sequences. Phylogenetic analyses revealed close relation of Z. latifolia to Leersia perrieri and Oryza species, with a divergence time of 19.7–31.0 million years. Collinearity and transcriptome analyses revealed candidate genes related to seed shattering, providing basic information on abscission layer formation and degradation in Z. latifolia. Moreover, two genomic blocks in the Z. latifolia genome showed good synteny with the rice phytocassane biosynthetic gene cluster. The updated genome will support future studies on the genetic improvement of Chinese wild rice and comparative analyses between Z. latifolia and other plants.

Transcriptomics and Metabolomics Reveal the Possible Mechanism by which 1-MCP Regulates the Postharvest Senescence of Zizania latifolia

To understand the mechanism governing the postharvest senescence of Zizania latifolia, and the regulatory mechanism induced by 1-methylcyclopropene (1-MCP) during storage at 25°C, physiobiochemical and conjoint analyses of the transcriptome and metabolome were performed. The results indicated that 1-MCP treatment engendered changes in the expression of genes and metabolites during the postharvest storage of Z. latifolia. The 1-MCP treatment maintained a good visual appearance, preserved the cell structure, and membrane integrity of Z. latifolia by keeping the expression of membranes-related lipolytic enzymes (and related genes) low and the amount of phosphatidylethanolamine high. Compared to the control group, 1-MCP treatment enhanced the activities of antioxidant enzymes, resulting in a decrease of reactive oxygen species (ROS) and malondialdehyde (MDA) contents, and thus inhibition of oxidative damage and loss of membrane integrity. In addition, 1-MCP treatment retarded the senescence of Z. latifolia by down-regulating the expression of ethylene biosynthesis-related genes and promoting up-regulation of brassinosteroid insensitive 1 (BRI1) kinase inhibitor 1, calmodulin (CaM), glutathione reductase, jasmonate amino acid synthase, and mitogen-activated protein kinase (MAPK)-related genes. Moreover, 1-MCP retarded Z. latifolia senescence by inducing the activity of ATP-biosynthesis related genes and metabolites. Our findings should facilitate future research on the postharvest storage of Z. latifolia, and could help delay senescence and prolong the storage time for commercial applications.

Mixed Transcriptome Analysis Revealed the Possible Interaction Mechanisms between Zizania latifolia and Ustilago esculenta Inducing Jiaobai Stem-Gall Formation

The smut fungus Ustilago esculenta infects Zizania latifolia and induces stem expansion to form a unique vegetable named Jiaobai. Although previous studies have demonstrated that hormonal control is essential for triggering stem swelling, the role of hormones synthesized by Z. latifolia and U. esculenta and the underlying molecular mechanism are not yet clear. To study the mechanism that triggers swollen stem formation, we analyzed the gene expression pattern of both interacting organisms during the initial trigger of culm gall formation, at which time the infective hyphae also propagated extensively and penetrated host stem cells. Transcriptional analysis indicated that abundant genes involving fungal pathogenicity and plant resistance were reprogrammed to maintain the subtle balance between the parasite and host. In addition, the expression of genes involved in auxin biosynthesis of U. esculenta obviously decreased during stem swelling, while a large number of genes related to the synthesis, metabolism and signal transduction of hormones of the host plant were stimulated and showed specific expression patterns, particularly, the expression of ZlYUCCA9 (a flavin monooxygenase, the key enzyme in indole-3-acetic acid (IAA) biosynthesis pathway) increased significantly. Simultaneously, the content of IAA increased significantly, while the contents of cytokinin and gibberellin showed the opposite trend. We speculated that auxin produced by the host plant, rather than the fungus, triggers stem swelling. Furthermore, from the differently expressed genes, two candidate Cys2-His2 (C2H2) zinc finger proteins, GME3058_g and GME5963_g, were identified from U. esculenta, which may conduct fungus growth and infection at the initial stage of stem-gall formation.

Identification and First Report of Fusarium andiyazi Causing Sheath Rot of Zizania latifolia in China

Zizania latifolia is a perennial plant native to East Asia. The swollen culm of Z. latifolia is a popular vegetable and traditional herbal medicine consumed in China and some other Asian countries. From 2019 to 2021, a sheath rot disease was found in Zhejiang Province of China. Symptoms mainly occurred in the leaf sheath showing as brown necrotic lesions surrounded by yellow halos. The pathogen fungal isolates were isolated from the affected sheaths. Ten representative isolates were selected for morphological and molecular identification by phylogenetic analyses of the translation elongation factor 1-α (TEF1) and the RNA polymerase II subunit beta (RPB2) gene regions. Based on the combined datasets, the fungal isolates were identified as Fusarium andiyazi. Koch’s postulates were confirmed by pathogenicity test, re-isolation and re-identification of the fungal isolates. To the best of our knowledge, this is the first report of sheath rot caused by F. andiyazi in Z. latifolia in China.

Flora and Vegetation Characteristics of the Natural Habitat of the Endangered Plant Pterygopleurum neurophyllum

This study analyzed the flora, life form, and vegetation of the Nakdong River wetland. Vegetation analysis was performed on 37 plots using the phytosociological method of the Zürich-Montpellier School. PCA analysis was conducted by using the vegetation data (ground cover of class; 1~9) of 37 plots surveyed by phytosociological method. PCA (Principal Component Analysis) was used to statistically analyze the objectivity of the community classification and the character species. The traditional classification and mathematical statistic methods were used. A total of 82 taxa belonging to 28 families, 65 genera, 72 species, 2 subspecies, and 8 varieties were present in the vegetation of the survey area. The life form was analyzed to be the Th-R5-D4-e type. The communities were classified into seven communities: Miscanthus sacchariflorus community, Phragmites communis community, Phragmites communis–Carex dispalata community, Ulmus parvifolia community, Zizania latifolia community, Setaria viridis community, and Salix koriyanagi–Salix chaenomeloides community. As a result of PCA analysis, it was classified into seven communities. Seven communities were analyzed, where the most dominant species (M. sacchariflorus, P. communis, C. dispalata, U. parvifolia, Z. latifolia, S. viridis, S. koriyanagi, S. chaenomeloides) of each community were examined as character species. Another species is analyzed as Salix koreensis. Of the sixteen M. sacchariflorus communities, Pterygopleurum neurophyllum was present in six plots (A-2 group) but not in ten plots (A-1 group). These two groups showed differences in coverage and the number of occurring species. As for the relative net contribution degree (r-NCD) in the A-2 group, most species showed low r-NCD except for M. sacchariflorus, which showed an r-NCD of 100. The r-NCDs in the A-1 group were as follows: Miscanthus sacchariflorus (100), P. neurophyllum (21.74), and Persicaria perfoliata (10.14). Therefore, P. neurophyllum is difficult to grow in the A-1 group. As a result, it is thought that the high density of M. sacchariflorus affects the growth and distribution of P. neurophyllum. In order to expand and maintain P. neurophyllum, the habitat environment needs to be altered by adjusting the density of M. sacchariflorus.

Development of Biochars Derived from Water Bamboo (Zizania latifolia) Shoot Husks Using Pyrolysis and Ultrasound-Assisted Pyrolysis for the Treatment of Reactive Black 5 (RB5) in Wastewater

Adsorbent made by carbonization of biomass under oxygen-limited conditions has become a promising material for wastewater treatment owing to its cost-effective, simple, and eco-friendly processing method. Ultrasound is considered a green technique to modify carbon materials because it uses water as the solvent. In this study, a comparison of Reactive Black 5 (RB5) adsorption capacity between biochar (BC) generated by pyrolysis of water bamboo (Zizania latifolia) husks at 600 °C and ultrasound-assisted biochar (UBC) produced by pyrolysis at 600 °C assisted by ultrasonic irradiation was performed. UBC showed a greater reaction rate and reached about 80% removal efficiency after 4 h, while it took 24 h for BC to reach that level. Scanning electron microscope (SEM) images indicated that the UBC morphology surface was more porous, with the structure of the combination of denser mesopores enhancing physiochemical properties of UBC. By Brunauer, Emmett, and Teller (BET), the specific surface areas of adsorbent materials were analyzed, and the surface areas of BC and UBC were 56.296 m2/g and 141.213 m2/g, respectively. Moreover, the pore volume of UBC was 0.039 cm3/g, which was higher than that of BC at 0.013 cm3/g. The adsorption isotherms and kinetics revealed the better fits of reactions to Langmuir isotherm and pseudo-second-order kinetic model, indicating the inclination towards monolayer adsorption and chemisorption of RB5 on water bamboo husk-based UBC.