Pangenome of water caltrop reveals structural variations and asymmetric subgenome divergence after allopolyploidization.

Water caltrop (Trapa spp., Lythraceae) is a traditional but currently underutilized non-cereal crop. Here, we generated chromosome-level genome assemblies for the two diploid progenitors of allotetraploid Trapa. natans (4x, AABB), i.e., diploid T. natans (2x, AA) and Trapa incisa (2x, BB). In conjunction with four published (sub)genomes of Trapa, we used gene-based and graph-based pangenomic approaches and a pangenomic transposable element (TE) library to develop Trapa genomic resources. The pangenome displayed substantial gene-content variation with dispensable and private gene clusters occupying a large proportion (51.95%) of the total cluster sets in the six (sub)genomes. Genotyping of presence-absence variation (PAVs) identified 40 453 PAVs associated with 2570 genes specific to A- or B-lineages, of which 1428 were differentially expressed, and were enriched in organ development process, organic substance metabolic process and response to stimulus. Comparative genome analyses showed that the allotetraploid T. natans underwent asymmetric subgenome divergence, with the B-subgenome being more dominant than the A-subgenome. Multiple factors, including PAVs, asymmetrical amplification of TEs, homeologous exchanges (HEs), and homeolog expression divergence, together affected genome evolution after polyploidization. Overall, this study sheds lights on the genome architecture and evolution of Trapa, and facilitates its functional genomic studies and breeding program.

The Difference in Diversity between Endophytic Microorganisms in White and Grey Zizania latifolia.

The Zizania latifolia is usually infected by the obligate parasitic fungus Ustilago esculenta to form an edible fleshy stem which is an aquatic vegetable called Jiaobai in China. The infection by the teliospore (T) strain of U. esculenta induces Z. latifolia forming gray fleshy stems, while the mycelia-teliospore (MT) strain of U. esculenta induces white fleshy stems which are more suitable for edibility than gray fleshy stems. The mechanism of this phenomenon is still largely unknown. One of the possible causes is the diversity of endophytic microbial communities between these two fleshy stems. Therefore, we utilized fungal ITS1 and bacterial 16S rDNA amplicon sequencing to investigate the diversity of endophytic microbial communities in the two different fleshy stems of Z. latifolia. The results revealed that the α diversity and richness of endophytic fungi in white Z. latifolia were significantly greater than in gray Z. latifolia. The dominant fungal genus in both fleshy stems was U. esculenta, which accounted for over 90% of the endophytic fungi. The community composition of endophytic fungi in gray and white Z. latifolia was different except for U. esculenta, and a negative correlation was observed between U. esculenta and other endophytic fungi. In addition, the dominant bacterial genus in gray Z. latifolia was Alcaligenaceae which is also negatively correlated with other bacterium communities. Additionally, the co-occurrence network of white Z. latifolia was found to have a stronger scale, connectivity, and complexity compared to that of gray Z. latifolia. And the detected beneficial bacteria and pathogens in the stems of Z. latifolia potentially compete for resources. Furthermore, the function of endophytic bacteria is more abundant than endophytic fungi in Z. latifolia. This research investigated the correlation between the development of Z. latifolia fleshy stems and endophytic microbial communities. Our findings indicate that the composition of endophytic microbial communities is closely related to the type of Z. latifolia fleshy stems. This research also suggests the potential utilization of specific microbial communities to enhance the growth and development of Z. latifolia, thereby contributing to the breeding of Z. latifolia.

The Impact of Photosynthetic Characteristics and Metabolomics on the Fatty Acid Biosynthesis in Tea Seeds.

The synthesis of tea fatty acids plays a crucial role in determining the oil content of tea seeds and selecting tea tree varieties suitable for harvesting both leaves and fruits. However, there is limited research on fatty acid synthesis in tea trees, and the precise mechanisms influencing tea seed oil content remain elusive. To reveal the fatty acid biosynthesis mechanism, we conducted a photosynthetic characteristic and targeted metabolomics analysis in comparison between Jincha 2 and Wuniuzao cultivars. Our findings revealed that Jincha 2 exhibited significantly higher net photosynthetic rates (Pn), stomatal conductance (Gs), and transpiration rate (Tr) compared with Wuniuzao, indicating the superior photosynthetic capabilities of Jincha 2. Totally, we identified 94 metabolites with significant changes, including key hormone regulators such as gibberellin A1 (GA1) and indole 3-acetic acid (IAA). Additionally, linolenic acid, methyl dihydrojasmonate, and methylthiobutyric acid, precursors required for fatty acid synthesis, were significantly more abundant in Jincha 2 compared with Wuniuzao. In summary, our research suggests that photosynthetic rates and metabolites contribute to the increased yield, fatty acid synthesis, and oil content observed in Jincha 2 when compared with Wuniuzao.

Anti-Candida albicans Effects and Mechanisms of Theasaponin E1 and Assamsaponin A.

Candida albicans is an opportunistic human fungal pathogen, and its drug resistance is becoming a serious problem. Camellia sinensis seed saponins showed inhibitory effects on resistant Candida albicans strains, but the active components and mechanisms are unclear. In this study, the effects and mechanisms of two Camellia sinensis seed saponin monomers, theasaponin E1 (TE1) and assamsaponin A (ASA), on a resistant Candida albicans strain (ATCC 10231) were explored. The minimum inhibitory concentration and minimum fungicidal concentration of TE1 and ASA were equivalent. The time-kill curves showed that the fungicidal efficiency of ASA was higher than that of TE1. TE1 and ASA significantly increased the cell membrane permeability and disrupted the cell membrane integrity of C. albicans cells, probably by interacting with membrane-bound sterols. Moreover, TE1 and ASA induced the accumulation of intracellular ROS and decreased the mitochondrial membrane potential. Transcriptome and qRT-PCR analyses revealed that the differentially expressed genes were concentrated in the cell wall, plasma membrane, glycolysis, and ergosterol synthesis pathways. In conclusion, the antifungal mechanisms of TE1 and ASA included the interference with the biosynthesis of ergosterol in fungal cell membranes, damage to the mitochondria, and the regulation of energy metabolism and lipid metabolism. Tea seed saponins have the potential to be novel anti-Candida albicans agents.

First Report of Leaf Sheath Disease, Caused by Microdochium seminicola, on Zizania latifolia in China.

Zizania latifolia, which belongs to the tribe Oryzea, has been widely grown over thousands of years as an aquatic vegetable in China. In the autumn of 2019, the disease harmful to the leaf sheaths of Z. latifolia was found in Jinhua City and Lishui City, Zhejiang Province. The disease caused brown oval-shaped spots (3~5 cm long, 0.5~1 cm wide) on leaf sheaths (Figure 1A). The infected plants produced non-commercial Jiaobai. The surface of the Jiaobai was pale yellow instead of white, and the length of the Jiaobai was 25% shorter than the uninfected plants. To 2022, the disease has been found in most planting areas of Z. latifolia in Zhejiang, Jiangsu, Fujian, Jiangxi and Anhui provinces in China. About 20%~50% incidence of the disease in these main production areas has seriously threatened the yield and quality of Jiaobai. To identify the causal agent, diseased leaf sheaths were collected. Symptomatic leaf sheath tissue was sterilized with 75% alcohol for 30 sec, and then washed three times with sterile distilled water for 1 min. A total of 37 strains were isolated on potato dextrose agar (PDA). We selected 10 strains for further morphological identification. An abundant mass of aerial mycelia was formed in 8 days (Figure 1B). The mycelium is transparent, septate and smooth. Conidia is fusiform, straight or curved, 0~3 septa, hyaline, tapering and rounding at the apex (Figure 1C and 1D). Strain XYQ3 was obtained through multi-generation culture. To further identify the pathogen of this fungus, genomic DNA was extracted and internal transcribed spacer (ITS), large subunit rDNA (LSU), ß-tubulin (BTUB) and DNA-directed RNA polymerase II subunit (RPB2) of strain XYQ3 were amplified. These sequences were obtained and submitted to GenBank (accession numbers MT605000, OP585914, MZ619085, MZ619084, respectively). After alignment analysis of sequencing data, we found that the ITS sequence indicated 100% identity with M. seminicola (GenBank acc no. KP859007). The LSU sequence showed 100% identity with M. seminicola (GenBank acc no. KP858943). The BTUB sequence showed 99.47% identity with M. seminicola (GenBank acc no. KP859070). The RPB2 sequence has higher identity with M. seminicola, reaching 99.76% with 4 sequences (GenBank acc nos. KP859140, KP859116, KP859134 and KP859130). Strain XYQ3 and a total of 16 other Microdochium isolates were selected for phylogenetic analysis using the ITS, LSU, BTUB and RPB2 sequences (Figure 2). Phylogenetic tree analysis revealed that strain XYQ3 was clustered with the M. seminicola clade, including M. seminicola strains MFG 60131, MFG 60132, CBS 122706 and KAS 1527. Therefore, this fungus was identified as M. seminicola based on morphological observation, multiple sequences alignment analysis and phylogenetic analysis. Strain XYQ3 was used in pathogenicity tests. According to Koch's postulates, 10 fresh leaf sheaths and leaves of host plants were inoculated by spraying conidial suspension at the concentration of 1×106 conidia/mL. Sterile water was sprayed as negative control. Inoculated plants were cultured under 25℃ light for 10 h, darkness for 14 h, covered with plastic film to maintain high humidity above 65%, and observed daily for disease development. After 6 d, symptoms similar to those observed in the field (Figure 1E and 1F). The pathogen of this fungus was re-isolated from the symptomatic inoculated leaf sheath and re-identified as strain XYQ3. Many Microdochium species are important pathogens of Poaceae (Liang et al., 2019). M. seminicola is classified as a new species in the Xylariales family by the report of Hernández-Restrepo (Hernandez-Restrepo et al., 2016) and was only found in wheat, oats and barley so far (Gagkaeva et al., 2020; Gavrilova et al., 2020). To the best of our knowledge, this fungus is the first report in the disease of Z. latifolia. As this disease is prevalent in main planting areas of Z. latifolia and has seriously threatened the production of Jiaobai, it is very important to isolate and identify the pathogen for the subsequent drug screening and control.

Genome sequencing and transcriptome analyses provide insights into the origin and domestication of water caltrop (Trapa spp., Lythraceae).

Humans have domesticated diverse species from across the plant kingdom; however, our current understanding of plant domestication is largely founded on major cereal crops. Here, we examine the evolutionary processes and genetic basis underlying the domestication of water caltrop (Trapa spp., Lythraceae), a traditional, yet presently underutilized non-cereal crop that sustained early Chinese agriculturalists. We generated a chromosome-level genome assembly of tetraploid T. natans, and then divided the allotetraploid genome into two subgenomes. Based on resequencing data from 57 accessions, representing cultivated diploid T. natans, wild T. natans (2x and 4x) and diploid T. incisa, we showed that water caltrop was likely first domesticated in the Yangtze River Valley as early as 6300 yr BP, and experienced a second improvement c. 800 years ago. We also provided strong support for an allotetraploid origin of T. natans within the past 230 000-310 000 years. By integrating selective sweep and transcriptome profiling analyses, we identified a number of genes potentially selected and/or differentially expressed during domestication, some of which likely contributed not only to larger fruit sizes but also to a more vigorous root system, facilitating nutrient uptake, environmental stress response and underwater photosynthesis. Our results shed light on the evolutionary and domestication history of water caltrop, one of the earliest domesticated crops in China. This study has implications for genomic-assisted breeding of this presently underutilized aquatic plant, and improves our general understanding of plant domestication.

A novel starch: Characterizations of starches separated from tea (Camellia sinensis (L.) O. Ktze) seed.

The physicochemical, thermal and crystal properties of starches isolated from 3 different tea (Camellia sinensis (L.) O. Ktze) seeds were analyzed in this study. The shape of tea starch granules were flat spherical or oval shape, showed unimodal or bimodal distribution with average size of around 9 µm. Tea starch was typical A-type starch. Apparent amylose contents of three tea seed starches ranged from 27.06% to 33.17%. The chains having degree of polymerization (DP) 13-24 were over 50% of the total detectable chains for tea amylopectin. Peak gelatinization temperature of tea starch ranged from 65 to 77 °C and the water solubility reached up to 9.70%. The peak viscosity of tea starches were as high as 5300 cP and final viscosity ranged from 4000 to 6700 cP. The results indicated that tea seed starch had potential as gel reagents and provide some guides for comprehensive utilization of tea starch in food and non-food applications.

[Physiological characteristics of nitrogen nutrition and stress-resistance of film-mulched rice in various ecological regions of Zhejiang Province].

The study showed that different ecological environment and cultivation system in various ecological regions of Zhejiang Province resulted in some different physiological characteristics of nitrogen nutrition and stress-resistance, especially in the aspect of NO3(-)-N and NH4+-N concentrations, between film-mulched and conventional flooded rice. Owing to the heat stress in Hangjiahu plain, the NO3(-)-N concentration of film-mulched rice decreased to some extent, but NH4+-N concentration increased markedly at tillering, jointing and booting stages, compared to conventional flooded rice. In Jinqu basin, the NO3(-)-N concentration of film-mulched rice at booting stage was higher, while the NH4+-N concentration in its roots was notably lower than those of conventional flooded rice, with NH4+-N concentration in its basal stems and leaves somewhat increased. Generally, the glutamine synthetase (GS) and nitrate reductase (NR) activities in film-mulched rice leaves were enhanced at booting stage, while malondiadehyde (MDA), soluble sugar (SS) and proline (Pro) concentrations had little changes. In conclusion, film-mulched cultivation was beneficial to the rice growth and its high yielding.