Chloroplast Genomes of Vitis flexuosa and Vitis amurensis: Molecular Structure, Phylogenetic, and Comparative Analyses for Wild Plant Conservation.

The chloroplast genome plays a crucial role in elucidating genetic diversity and phylogenetic relationships. Vitis vinifera L. (grapevine) is an economically important species, prompting exploration of wild genetic resources to enhance stress resilience. We meticulously assembled the chloroplast genomes of two Korean Vitis L. species, V. flexuosa Thunb. and V. amurensis Rupr., contributing valuable data to the Korea Crop Wild Relatives inventory. Through exhaustive specimen collection spanning diverse ecological niches across South Korea, we ensured comprehensive representation of genetic diversity. Our analysis, which included rigorous codon usage bias assessment and repeat analysis, provides valuable insights into amino acid preferences and facilitates the identification of potential molecular markers. The assembled chloroplast genomes were subjected to meticulous annotation, revealing divergence hotspots enriched with nucleotide diversity, thereby presenting promising candidates for DNA barcodes. Additionally, phylogenetic analysis reaffirmed intra-genus relationships and identified related crops, shedding light on evolutionary patterns within the genus. Comparative examination with chloroplast genomes of other crops uncovered conserved sequences and variable regions, offering critical insights into genetic evolution and adaptation. Our study advances the understanding of chloroplast genomes, genetic diversity, and phylogenetic relationships within Vitis species, thereby laying a foundation for enhancing grapevine genetic diversity and resilience to environmental challenges.

Methods for Improving the Germination of Rhodotypos scandens (Thunb.) Makino Seeds through Endocarp Removal.

Rhodotypos scandens (Thunb.) Makino is known to have a seed dispersal that is thick and stony (endocarp + seeds) and has potential as a landscaping tree seed. In several Rosaceae species, seeds are covered with a hard endocarp, making the internal seeds water-impermeable and germination difficult. Here, we analyzed the morphoanatomical traits and germination properties of R. scandens seeds. To identify ideal seed propagation conditions, we immersed R. scandens seeds in sulfuric acid for varying durations and subjected them to phytohormone (gibberellic acid A3 and fluridone) and a cold stratification (CS) (5 °C) treatment after endocarp removal (ER). The R. scandens stony seeds did not increase in mass by ≥25.0%. Following ER, the seed mass increased by ≥50.0% with water absorption when compared to the initial dry mass. Seed surfaces showed damage and cracks through scarification after 1 h of immersion in sulfuric acid, failing to germinate. A combination of ER, phytohormone treatment, and CS improved seed germination compared to ER alone (26.0 ± 5.3%). Overall, R. scandens seeds showed a dispersal with a hard endocarp from the parent plant, and a pre-treatment with ER, phytohormones, and CS was required for effective seed propagation.

Dormancy-release and germination improvement of Korean bellflower (Campanula takesimana Nakai), a rare and endemic plant native to the Korean peninsula.

Korean bellflower (Campanula takesimana Nakai) is a rare and perennial herb with medicinal and ornamental values, is endemic to the Ulleung Island of Korea. In this study, we investigated the dormancy-release and germination characteristics of C. takesimana (Campanulaceae) seeds by subjecting them to varying temperatures (5, 10, 15, 20, and 25°C and diurnal/nocturnal temperatures of 15/6, 20/10, and 25/15°C), cold stratification periods (0, 4, 8, or 12 weeks at 5°C), and gibberellic acid (GA3) concentrations (0, 10, 100, or 1,000 mg·L-1 at 15/6°C and 25/15°C) to identify the ideal seed propagation conditions. The seeds were stimulated to germinate (at 25°C, 12-h photoperiod with fluorescent lamps at 40 ± 10 µmol∙m-2∙s-1) after cold stratification. To examine the germination characteristics, the seeds were tested for water imbibition and found to readily absorb water. The seeds exhibited underdeveloped embryos during dispersal, showed final germination of 37.00% ± 4.43 at 25°C and were not influenced by temperature. The seeds subjected to 0, 4, 8, or 12 weeks of cold stratification germinated at a success rate of 22.00% ± 4.76, 87.00% ± 6.80, 79.00% ± 2.52, and 77.00% ± 1.91, respectively. Additionally, the germination characteristics, which were based on final germination, mean germination time, and germination velocity (Timson index), were significantly greater in the seeds pretreated with 1,000 mg·L-1 GA3 at 25/15°C than in seeds pretreated with 0 mg·L-1 GA3. Overall, the seeds broke dormancy with GA3 and short-term cold stratification. Therefore, we concluded that C. takesimana seeds have non-deep, simple, morphophysiological dormancy, and pretreatment with cold stratification and GA3 is required for effective seed propagation.

The complete chloroplast genomes of Allium sacculiferum, A. thunbergii, and A. taquetii (Amaryllidaceae) from Korea.

The genus Allium comprises some of the most commonly consumed food crops worldwide. The chloroplast genomes of A. sacculiferum, A. thunbergii, and A. taquetii are 152,444, 153,459, and 154,056 bp circular molecular genomes, respectively. The annotation results revealed the presence of 132 (89 protein-coding, 35 tRNA, and eight rRNA), 132 (86 protein-coding, 38 tRNA, and eight rRNA), and 132 (86 protein-coding, 38 tRNA, and eight rRNA) genes with 36.78%, 36.83%, and 36.88% total GC content in each genome, respectively. The chloroplast genome of each Allium species contains an 81,254, 82,473, and 83,068 bp LSC region, an 18,176, 18,006, and 17,958 bp SSC region, and a pair of 26,507, 26,490, and 26,515 bp IR regions, respectively. Phylogenetic analysis based on the 21 complete chloroplast genomes indicates that A. sacculiferum is closely related to A. koreanum; A. thunbergii and A taquetii are closely related to A. hookeri. This study shows that the three Allium species are Korean crop wild relatives that may be used to develop new Allium varieties in the future.

Assessing the Potential Distribution of Oxalis latifolia, a Rapidly Spreading Weed, in East Asia under Global Climate Change.

Oxalis latifolia, a perennial herbaceous weed, is a highly invasive species that poses a threat to agricultural lands worldwide. East Asia is under a high risk of invasion of O. latifolia under global climate change. To evaluate this risk, we employed maximum entropy modeling considering two shared socio-economic pathways (SSP2-4.5 and SSP5-8.5). Currently, a small portion (8.02%) of East Asia is within the O. latifolia distribution, with the highest coverages in Chinese Taipei, China, and Japan (95.09%, 9.8%, and 0.24%, respectively). However, our projections indicated that this invasive weed will likely be introduced to South Korea and North Korea between 2041 and 2060 and 2081 and 2100, respectively. The species is expected to cover approximately 9.79% and 23.68% (SSP2-4.5) and 11.60% and 27.41% (SSP5-8.5) of the total land surface in East Asia by these time points, respectively. South Korea and Japan will be particularly susceptible, with O. latifolia potentially invading up to 80.73% of their territory by 2081-2100. Mongolia is projected to remain unaffected. This study underscores the urgent need for effective management strategies and careful planning to prevent the introduction and limit the expansion of O. latifolia in East Asian countries.

Microbial Diversity Analysis of Bupleurum latissimum Nakai from Ulleung-Do of South Korea Using Next-Generation Sequencing.

Bupleurum latissimum Nakai is a rare endemic species native to Ulleung-do in South Korea. This study aimed to report on the rhizosphere soil microbial diversity of B. latissimum. Proteobacteria, Actinobacteria, and Verrucomicrobia were identified in relative abundances of 27.77%, 21.70%, and 15.27%, respectively.

Does oxygen affect ageing mechanisms of Pinus densiflora seeds? A matter of cytoplasmic physical state.

During desiccation, the cytoplasm of orthodox seeds solidifies into an intracellular glass with highly restricted diffusion and molecular mobility. Temperature and water content govern seed ageing rates, while oxygen (O2) can promote deteriorative reactions. However, whether the cytoplasmic physical state affects involvement of O2 in seed ageing remains unresolved. We aged Pinus densiflora seeds by controlled deterioration (CD) at 45 °C and distinct relative humidity (RH), resulting in cells with a glassy (11% and 30% RH) or fluid (60% and 80% RH) cytoplasm. Hypoxic conditions (0.4% O2) during CD delayed seed deterioration, lipid peroxidation, and decline of antioxidants (glutathione, α-tocopherol, and γ-tocopherol), but only when the cytoplasm was glassy. In contrast, when the cytoplasm was fluid, seeds deteriorated at the same rate regardless of O2 availability, while being associated with limited lipid peroxidation, detoxification of lipid peroxide products, substantial loss of glutathione, and resumption of glutathione synthesis. Changes in metabolite profiles provided evidence of other O2-independent enzymatic reactions in a fluid cytoplasm, including aldo-keto reductase and glutamate decarboxylase activities. Biochemical profiles of seeds stored under seed bank conditions resembled those obtained after CD regimes that maintained a glassy cytoplasm. Overall, O2 contributed more to seed ageing when the cytoplasm was glassy, rather than fluid.

Improved production of deglucosylated platycodin D from saponins from balloon flower leaf by a food-grade enzyme using high hydrostatic pressure.

Platycosides, saponins contained in balloon flower, which have been used as food health supplements for respiratory diseases, have diverse pharmacological effects. Platycosides exhibit better pharmacological activity by hydrolyzing their own sugars. However, to date, there have been no studies on the production of deglucosylated platycodin D suitable for food applications. In this study, Pluszyme 2000P, which was derived from Aspergillus niger, a food-grade microorganism, was used to completely convert platycoside E into deglucosylated platycodin D. For an efficient and economical production of deglucosylated platycodin D, the productivity was improved approximately 2.4 times by application of high hydrostatic pressure and the discarded balloon flower leaf was used as a substrate. As a result, deglucosylated platycodin D was produced with the highest concentration (3.49 mg/mL) and productivity (581.7 mg/L/h) reported so far. Our results contribute to functional saponin production and the related food industries.

Non-Deep Simple Morphophysiological Dormancy and Germination Characteristics of Gentiana triflora var. japonica (Kusn.) H. Hara (Gentianaceae), a Rare Perennial Herb in Korea.

This study investigated the kind of seed dormancy and seed germination of Gentiana triflora var. japonica (Kusn.) H. Hara for developing a seed propagation method. The seeds were collected in October 2020 from plants at Mt. Sobaeksan, Korea. In a water imbibition experiment, seed weights increased by >101.9% of their initial masses over 12 h. Effects of incubation temperature (5, 15, 20, 25, 15/6, or 25/15 °C), cold stratification period (5 °C; 0, 4, 8, or 12 weeks), and gibberellic acid (GA3; 0, 10, 100, or 1000 mg∙L-1) and potassium nitrate treatment (KNO3; 0, 1000, 2000, or 4000 mg∙L-1) on seed germination were investigated to characterize seed dormancy. These seeds exhibited underdeveloped embryos during seed dispersal. The seeds failed to reach the final germination of 15.0% after treatment at 5, 15, 20, 25, 15/6, or 25/15 °C. After cold stratification for 8 weeks, the germination increased dramatically by >90.0% compared to that at 0 weeks. After the GA3 treatment, the germination reached >80.0% within 5 days. The final germination was 90.0% in the 100 mg∙L-1 GA3 treatment group. However, the KNO3 treatment had no effect on seed germination. Therefore, the G. triflora var. japonica seeds exhibited non-deep simple morphophysiological dormancy.

Features of Bacterial Microbiota in the Wild Habitat of Pulsatilla tongkangensis, the Endangered "Long-Sepal Donggang Pasque-Flower Plant," Endemic to Karst Topography of Korea.

Microbes associated with plants significantly influence the development and health of the plants. The diversity and function of microbiomes associated with the long-sepal Donggang pasque-flower (DPF) plant, an endemic and endangered species in karst ecosystems, remain unexplored. In this study, we investigated the features of bacterial communities associated with the rhizosphere and roots of DPF plants and their functions in plant growth promotion. The DPF plants were collected from natural and cultivated habitats, and their 16S rDNA was sequenced to assess the bacterial community structures. The bacterial microbiota was more diverse in wild than in cultivated plants. The core bacterial microbiota commonly functioned as endophytes in both wild and cultivated DPF plants, although there were some differences. The identified bacterial strains benefited plants through nitrogen fixation, phosphate solubilization, or phytohormone production, inducing measurable growth differences in Arabidopsis thaliana. To the best of our knowledge, this study is the first to report the bacterial community structures associated with the rhizosphere soil and roots of DPF plants in karst ecosystems. The bacterial strains isolated in this study could be used to aid sustainable growth and restoration of rare plants in karst ecosystems. Our systematic research on the microbiomes associated with these endangered plants will contribute to their conservation as well as development of better cultivation.

Discrimination of Transgenic Canola (Brassica napus L.) and their Hybrids with B. rapa using Vis-NIR Spectroscopy and Machine Learning Methods.

In recent years, the rapid development of genetically modified (GM) technology has raised concerns about the safety of GM crops and foods for human health and the ecological environment. Gene flow from GM crops to other crops, especially in the Brassicaceae family, might pose a threat to the environment due to their weediness. Hence, finding reliable, quick, and low-cost methods to detect and monitor the presence of GM crops and crop products is important. In this study, we used visible near-infrared (Vis-NIR) spectroscopy for the effective discrimination of GM and non-GM Brassica napus, B. rapa, and F1 hybrids (B. rapa X GM B. napus). Initially, Vis-NIR spectra were collected from the plants, and the spectra were preprocessed. A combination of different preprocessing methods (four methods) and various modeling approaches (eight methods) was used for effective discrimination. Among the different combinations, the Savitzky-Golay and Support Vector Machine combination was found to be an optimal model in the discrimination of GM, non-GM, and hybrid plants with the highest accuracy rate (100%). The use of a Convolutional Neural Network with Normalization resulted in 98.9%. The same higher accuracy was found in the use of Gradient Boosted Trees and Fast Large Margin approaches. Later, phenolic acid concentration among the different plants was assessed using GC-MS analysis. Partial least squares regression analysis of Vis-NIR spectra and biochemical characteristics showed significant correlations in their respective changes. The results showed that handheld Vis-NIR spectroscopy combined with chemometric analyses could be used for the effective discrimination of GM and non-GM B. napus, B. rapa, and F1 hybrids. Biochemical composition analysis can also be combined with the Vis-NIR spectra for efficient discrimination.

The non-photochemical quenching protein LHCSR3 prevents oxygen-dependent photoinhibition in Chlamydomonas reinhardtii.

Non-photochemical quenching (NPQ) helps dissipate surplus light energy, preventing formation of reactive oxygen species (ROS). In Chlamydomonas reinhardtii, the thylakoid membrane protein LHCSR3 is involved in pH-dependent (qE-type) NPQ, lacking in the npq4 mutant. Preventing PSII repair revealed that npq4 lost PSII activity faster than the wild type (WT) in elevated O2, while no difference between strains was observed in O2-depleted conditions. Low Fv/Fm values remained 1.5 h after moving cells out of high light, and this qH-type quenching was independent of LHCSR3 and not accompanied by losses of maximum PSII activity. Culturing cells in historic O2 atmospheres (30-35%) increased the qE of cells, due to increased LHCSR1 and PsbS levels, and LHCSR3 in the WT, showing that atmospheric O2 tensions regulate qE capacity. Colony growth of npq4 was severely restricted at elevated O2, and npq4 accumulated more reactive electrophile species (RES) than the WT, which could damage PSI. Levels of PsaA (PSI) were lower in npq4 grown at 35% O2, while PsbA (PSII) levels remained stable. We conclude that even at high O2 concentrations, the PSII repair cycle is sufficient to maintain net levels of PSII. However, LHCSR3 has an important function in protecting PSI against O2-mediated damage, such as via RES.

LHCSR3 affects de-coupling and re-coupling of LHCII to PSII during state transitions in Chlamydomonas reinhardtii.

Photosynthetic organisms have to tolerate rapid changes in light intensity, which is facilitated by non-photochemical quenching (NPQ) and involves modification of energy transfer from light-harvesting complexes (LHC) to the photosystem reaction centres. NPQ includes dissipating excess light energy to heat (qE) and the reversible coupling of LHCII to photosystems (state transitions/qT), which are considered separate NPQ mechanisms. In the model alga Chlamydomonas reinhardtii the LHCSR3 protein has a well characterised role in qE. Here, it is shown in the npq4 mutant, deficient in LHCSR3, that energy coupling to photosystem II (PSII) more akin to qT is also disrupted, but no major differences in LHC phosphorylation or LHC compositions were found in comparison to wild-type cells. The qT of wild-type cells possessed two kinetically distinguishable phases, with LHCSR3 participating in the more rapid (<2 min) phase. This LHCSR3-mediated qT was sensitive to physiological levels of H2O2, which accelerated qE induction, revealing a way that may help C. reinhardtii tolerate a sudden increase in light intensity. Overall, a clear mechanistic overlap between qE and qT is shown.

High light-induced hydrogen peroxide production in Chlamydomonas reinhardtii is increased by high CO2 availability.

The production of reactive oxygen species (ROS) is an unavoidable part of photosynthesis. Stress that accompanies high light levels and low CO2 availability putatively includes enhanced ROS production in the so-called Mehler reaction. Such conditions are thought to encourage O2 to become an electron acceptor at photosystem I, producing the ROS superoxide anion radical (O2·-) and hydrogen peroxide (H2 O2 ). In contrast, here it is shown in Chlamydomonas reinhardtii that CO2 depletion under high light levels lowered cellular H2 O2 production, and that elevated CO2 levels increased H2 O2 production. Using various photosynthetic and mitochondrial mutants of C. reinhardtii, the chloroplast was identified as the main source of elevated H2 O2 production under high CO2 availability. High light levels under low CO2 availability induced photoprotective mechanisms called non-photochemical quenching, or NPQ, including state transitions (qT) and high energy state quenching (qE). The qE-deficient mutant npq4 produced more H2 O2 than wild-type cells under high light levels, although less so under high CO2 availability, whereas it demonstrated equal or greater enzymatic H2 O2 -degrading capacity. The qT-deficient mutant stt7-9 produced the same H2 O2 as wild-type cells under high CO2 availability. Physiological levels of H2 O2 were able to hinder qT and the induction of state 2, providing an explanation for why under high light levels and high CO2 availability wild-type cells behaved like stt7-9 cells stuck in state 1.

Neuroprotective effects of constituents of Eragrostis ferruginea against Aß-induced toxicity in PC12 cells.

A new flavonoid, 7-demethylageconyflavone A (1), and five known compounds, tricin (2), ageconyflavone A (3), corylin (4), nectandrin B (5), and 4-ketopinoresinol (6) were isolated from the aerial parts of Eragrostis ferruginea. Their structures were determined using spectroscopic techniques, including 1D- and 2D-NMR. All compounds were tested for the neuroprotective effects against amyloid beta peptide (Abeta) using PC12 cells, a major cause of the pathology of Alzheimer's disease. Tricin (2) was found to have a neuroprotective effect with an ED(50) value of 20.3 microM against Abeta-induced toxicity in PC12 cells. Ageconyflavone A (3), nectandrin B (5) and 4-ketopinoresinol (6) demonstrated moderate neuroprotective effects with ED(50) values of 58.7, 44.1, and 54.8 microM, respectively.