Chromosome-level genome assembly and characterization of Sophora Japonica

Sophora japonica is a medium-size deciduous tree belonging to Leguminosae family and famous for its high ecological, economic and medicinal value. Here, we reveal a draft genome of S. japonica, which was ∼511.49 Mb long (contig N50 size of 17.34 Mb) based on Illumina, Nanopore and Hi-C data. We reliably assembled 110 contigs into 14 chromosomes, representing 91.62% of the total genome, with an improved N50 size of 31.32 Mb based on Hi-C data. Further investigation identified 271.76 Mb (53.13%) of repetitive sequences and 31,000 protein-coding genes, of which 30,721 (99.1%) were functionally annotated. Phylogenetic analysis indicates that S. japonica separated from Arabidopsis thaliana and Glycine max ∼107.53 and 61.24 million years ago, respectively. We detected evidence of species-specific and common-legume whole-genome duplication events in S. japonica. We further found that multiple TF families (e.g. BBX and PAL) have expanded in S. japonica, which might have led to its enhanced tolerance to abiotic stress. In addition, S. japonica harbours more genes involved in the lignin and cellulose biosynthesis pathways than the other two species. Finally, population genomic analyses revealed no obvious differentiation among geographical groups and the effective population size continuously declined since 2 Ma. Our genomic data provide a powerful comparative framework to study the adaptation, evolution and active ingredients biosynthesis in S. japonica. More importantly, our high-quality S. japonica genome is important for elucidating the biosynthesis of its main bioactive components, and improving its production and/or processing.     

TEB/POLQ plays dual roles in protecting Arabidopsis from NO-induced DNA damage

Nitric oxide (NO) is a key player in numerous physiological processes. Excessive NO induces DNA damage, but how plants respond to this damage remains unclear. We screened and identified an Arabidopsis NO hypersensitive mutant and found it to be allelic to TEBICHI/POLQ, encoding DNA polymerase θ. The teb mutant plants were preferentially sensitive to NO- and its derivative peroxynitrite-induced DNA damage and subsequent double-strand breaks (DSBs). Inactivation of TEB caused the accumulation of spontaneous DSBs largely attributed to endogenous NO and was synergistic to DSB repair pathway mutations with respect to growth. These effects were manifested in the presence of NO-inducing agents and relieved by NO scavengers. NO induced G2/M cell cycle arrest in the teb mutant, indicative of stalled replication forks. Genetic analyses indicate that Polθ is required for translesion DNA synthesis across NO-induced lesions, but not oxidation-induced lesions. Whole-genome sequencing revealed that Polθ bypasses NO-induced base adducts in an error-free manner and generates mutations characteristic of Polθ-mediated end joining. Our experimental data collectively suggests that Polθ plays dual roles in protecting plants from NO-induced DNA damage. Since Polθ is conserved in higher eukaryotes, mammalian Polθ may also be required for balancing NO physiological signaling and genotoxicity.     

Rapid improvement of rice eating and cooking quality through gene editing toward glutelin as target

Rice eating and cooking quality(ECQ) is a major concern of breeders and consumers, determining market competitiveness worldwide. Rice grain protein content(GPC) is negatively related to ECQ,making it possible to improve ECQ by manipulating GPC. However, GPC is genetically complex and sensitive to environmental conditions; therefore, little progress has been made in traditional breeding for ECQ. Here, we report that CRISPR/Cas9-mediated knockout of genes encoding the grain storage protein gluteli...     

异质水分环境下野牛草相连分株间光合同化物的生理整合及其调控

异质环境下,克隆植物通过生理整合机制使资源在分株间实现共享,提高了其对异质性环境的适应能力,具有重要的生态进化意义,研究生理整合机制及其调控机理可为进一步发掘克隆植物应用潜力提供理论依据。以野牛草3个相连分株为材料,对其中一个分株用30%聚乙二醇6000(PEG-6000)模拟水分胁迫,通过Hoagland营养液培养试验,研究了异质水分环境下光合同化物在野牛草相连分株间的生理整合及分株叶片与根系内源激素ABA与IAA含量的变化规律。结果表明,14C-光合同化物在克隆片断内存在双向运输,但以向顶运输为主,异质水分环境下,受胁迫分株光合同化物的输出率明显降低,而与其相邻分株合成的光合同化物向受胁迫分株方向运输率明显增加;异质水分环境下,各分株ABA含量均明显增加,但以受胁迫的分株叶片及根系ABA的含量增加幅度最大,各分株IAA含量较对照均显著下降(P0.05),且以受胁迫分株IAA含量下降幅度最大;各分株叶片与根系ABA/IAA均显著提高(P0.05),相邻分株ABA/IAA增加幅度低于受胁迫分株。异质水分环境影响野牛草克隆分株间光合同化物的生理整合,且ABA与IAA在分株间光合同化物运输与分配过程中具有重要的调节作用。     

城镇化背景下深圳典型流域鱼类群落特征及驱动因子

理解城镇的快速发展对河流鱼类群落结构的影响,是城镇河流科学管理和生物多样性保护的关键基础。本研究于2019年丰水期（8月）和枯水期（11月）,选取我国城镇化典型城市-深圳域内两个处于不同城镇化程度的代表性流域,应用多重统计方法比较分析了流域间鱼类群落结构的差异,并探讨了驱动鱼类群落变异的关键环境要素。结果发现,城镇化程度高的观澜河流域其鱼类种类组成、优势类群、生物多样性指数与城镇化程度低的坪山河流域有明显差别。 具体表现为：城镇化程度高的流域土著敏感种类如异鱲、吸鳅等几近消失,优势类群为外来入侵耐受种类,其物种多样性显著低于城镇化程度低的流域（P<0.05）。同时,外来鱼类在城镇河段其数量占比平均达92.5%,广泛分布于深圳城镇河流中。在环境因素方面,城镇化程度高的观澜河流域水体理化指标总氮、总磷、氨氮、化学需氧量、生化需氧量、高锰酸盐指数均显著性高于城镇化程度低的坪山河流域（P<0.05）。基于Bray-Curtis距离的冗余分析显示：城镇用地占比和总氮是影响观澜河和坪山河流域鱼类群落差异的主要因素。城镇化进程中河流生境的改变已影响到土著鱼类的生物多样性。因此,推动以恢复土著鱼类生物多样性的河流生态治理与保护是今后水生态目标管理的重要方向。     

Comparing Protein Expression in Erwinia amylovora Strain TS3128 Cultured under Three Sets of Environmental Conditions

Erwinia amylovora, the causal agent of fire-blight disease in apple and pear trees, was first isolated in South Korea in 2015. Although numerous studies, including omics analyses, have been conducted on other strains of E. amylovora, studies on South Korean isolates remain limited. In this study, we conducted a comparative proteomic analysis of the strain TS3128, cultured in three media representing different growth conditions. Proteins related to virulence, type III secretion system, and amylovoran production, were more abundant under minimal conditions than in rich conditions. Additionally, various proteins associated with energy production, carbohydrate metabolism, cell wall/membrane/envelope biogenesis, and ion uptake were identified under minimal conditions. The strain TS3128 expresses these proteins to survive in harsh environments. These findings contribute to understanding the cellular mechanisms driving its adaptations to different environmental conditions and provide proteome profiles as reference for future studies on the virulence and adaptation mechanisms of South Korean strains.