Plant Communications最新文献_第3页

GhATL68b regulates cotton fiber cell development by ubiquitinating the enzyme required for β-oxidation of polyunsaturated fatty acids. GhATL68b通过泛素化多不饱和脂肪酸β-氧化所需的酶来调控棉纤维细胞的发育。

IF 9.4 1区生物学

Plant Communications Pub Date : 2024-10-14 Epub Date: 2024-06-13 DOI: 10.1016/j.xplc.2024.101003

Xin Li, Gai Huang, Yifan Zhou, Kun Wang, Yuxian Zhu

{"title":"GhATL68b regulates cotton fiber cell development by ubiquitinating the enzyme required for β-oxidation of polyunsaturated fatty acids.","authors":"Xin Li, Gai Huang, Yifan Zhou, Kun Wang, Yuxian Zhu","doi":"10.1016/j.xplc.2024.101003","DOIUrl":"10.1016/j.xplc.2024.101003","url":null,"abstract":"E3 ligases are key enzymes required for protein degradation. Here, we identified a C3H2C3 RING domain-containing E3 ubiquitin ligase gene named GhATL68b. It is preferentially and highly expressed in developing cotton fiber cells and shows greater conservation in plants than in animals or archaea. The four orthologous copies of this gene in various diploid cottons and eight in the allotetraploid G. hirsutum were found to have originated from a single common ancestor that can be traced back to Chlamydomonas reinhardtii at about 992 million years ago. Structural variations in the GhATL68b promoter regions of G. hirsutum, G. herbaceum, G. arboreum, and G. raimondii are correlated with significantly different methylation patterns. Homozygous CRISPR-Cas9 knockout cotton lines exhibit significant reductions in fiber quality traits, including upper-half mean length, elongation at break, uniformity, and mature fiber weight. In vitro ubiquitination and cell-free protein degradation assays revealed that GhATL68b modulates the homeostasis of 2,4-dienoyl-CoA reductase, a rate-limiting enzyme for the β-oxidation of polyunsaturated fatty acids (PUFAs), via the ubiquitin proteasome pathway. Fiber cells harvested from these knockout mutants contain significantly lower levels of PUFAs important for production of glycerophospholipids and regulation of plasma membrane fluidity. The fiber growth defects of the mutant can be fully rescued by the addition of linolenic acid (C18:3), the most abundant type of PUFA, to the ovule culture medium. This experimentally characterized C3H2C3 type E3 ubiquitin ligase involved in regulating fiber cell elongation may provide us with a new genetic target for improved cotton lint production.","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141322000","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

TWAS facilitates gene-scale trait genetic dissection through gene expression, structural variations, and alternative splicing in soybean. TWAS 通过大豆的基因表达、结构变异和替代剪接，促进了基因规模的性状遗传分析。

IF 9.4 1区生物学

Plant Communications Pub Date : 2024-10-14 Epub Date: 2024-06-25 DOI: 10.1016/j.xplc.2024.101010

Delin Li, Qi Wang, Yu Tian, Xiangguang Lyv, Hao Zhang, Huilong Hong, Huawei Gao, Yan-Fei Li, Chaosen Zhao, Jiajun Wang, Ruizhen Wang, Jinliang Yang, Bin Liu, Patrick S Schnable, James C Schnable, Ying-Hui Li, Li-Juan Qiu

{"title":"TWAS facilitates gene-scale trait genetic dissection through gene expression, structural variations, and alternative splicing in soybean.","authors":"Delin Li, Qi Wang, Yu Tian, Xiangguang Lyv, Hao Zhang, Huilong Hong, Huawei Gao, Yan-Fei Li, Chaosen Zhao, Jiajun Wang, Ruizhen Wang, Jinliang Yang, Bin Liu, Patrick S Schnable, James C Schnable, Ying-Hui Li, Li-Juan Qiu","doi":"10.1016/j.xplc.2024.101010","DOIUrl":"10.1016/j.xplc.2024.101010","url":null,"abstract":"A genome-wide association study (GWAS) identifies trait-associated loci, but identifying the causal genes can be a bottleneck, due in part to slow decay of linkage disequilibrium (LD). A transcriptome-wide association study (TWAS) addresses this issue by identifying gene expression-phenotype associations or integrating gene expression quantitative trait loci with GWAS results. Here, we used self-pollinated soybean (Glycine max [L.] Merr.) as a model to evaluate the application of TWAS to the genetic dissection of traits in plant species with slow LD decay. We generated RNA sequencing data for a soybean diversity panel and identified the genetic expression regulation of 29 286 soybean genes. Different TWAS solutions were less affected by LD and were robust to the source of expression, identifing known genes related to traits from different tissues and developmental stages. The novel pod-color gene L2 was identified via TWAS and functionally validated by genome editing. By introducing a new exon proportion feature, we significantly improved the detection of expression variations that resulted from structural variations and alternative splicing. As a result, the genes identified through our TWAS approach exhibited a diverse range of causal variations, including SNPs, insertions or deletions, gene fusion, copy number variations, and alternative splicing. Using this approach, we identified genes associated with flowering time, including both previously known genes and novel genes that had not previously been linked to this trait, providing insights complementary to those from GWAS. In summary, this study supports the application of TWAS for candidate gene identification in species with low rates of LD decay.","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141452109","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

PCMD: A multilevel comparison database of intra- and cross-species metabolic profiling in 530 plant species. PCMD：530 个植物物种的种内和跨物种代谢图谱的多层次比较数据库。

IF 9.4 1区生物学

Plant Communications Pub Date : 2024-10-14 Epub Date: 2024-07-11 DOI: 10.1016/j.xplc.2024.101038

Yue Hu, Yao Ruan, Xin-Le Zhao, Feng Jiang, Dongxu Liu, Qiang Zhu, Qing-Ye Zhang, Qing-Yong Yang

{"title":"PCMD: A multilevel comparison database of intra- and cross-species metabolic profiling in 530 plant species.","authors":"Yue Hu, Yao Ruan, Xin-Le Zhao, Feng Jiang, Dongxu Liu, Qiang Zhu, Qing-Ye Zhang, Qing-Yong Yang","doi":"10.1016/j.xplc.2024.101038","DOIUrl":"10.1016/j.xplc.2024.101038","url":null,"abstract":"Comparative metabolomics plays a crucial role in investigating gene function, exploring metabolite evolution, and accelerating crop genetic improvement. However, a systematic platform for intra- and cross-species comparison of metabolites is currently lacking. Here, we report the Plant Comparative Metabolome Database (PCMD; http://yanglab.hzau.edu.cn/PCMD), a multilevel comparison database based on predicted metabolic profiles of 530 plant species. The PCMD serves as a platform for comparing metabolite characteristics at various levels, including species, metabolites, pathways, and biological taxonomy. The database also provides a number of user-friendly online tools, such as species comparison, metabolite enrichment, and ID conversion, enabling users to perform comparisons and enrichment analyses of metabolites across different species. In addition, the PCMD establishes a unified system based on existing metabolite-related databases by standardizing metabolite numbering. The PCMD is the most species-rich comparative plant metabolomics database currently available, and a case study demonstrates its ability to provide new insights into plant metabolic diversity.","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141592129","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A near-complete assembly of the Houttuynia cordata genome provides insights into the regulatory mechanism of flavonoid biosynthesis in Yuxingcao. 蕺菜基因组为了解玉星草中黄酮类化合物生物合成的调控机制提供了启示。

IF 9.4 1区生物学

Plant Communications Pub Date : 2024-10-14 Epub Date: 2024-09-02 DOI: 10.1016/j.xplc.2024.101075

Zhengting Yang, Fayin He, Yingxiao Mai, Sixian Fan, Yin An, Kun Li, Fengqi Wu, Ming Tang, Hui Yu, Jian-Xiang Liu, Rui Xia

{"title":"A near-complete assembly of the Houttuynia cordata genome provides insights into the regulatory mechanism of flavonoid biosynthesis in Yuxingcao.","authors":"Zhengting Yang, Fayin He, Yingxiao Mai, Sixian Fan, Yin An, Kun Li, Fengqi Wu, Ming Tang, Hui Yu, Jian-Xiang Liu, Rui Xia","doi":"10.1016/j.xplc.2024.101075","DOIUrl":"10.1016/j.xplc.2024.101075","url":null,"abstract":"Houttuynia cordata, also known as Yuxingcao in Chinese, is a perennial herb in the Saururaceae family. It is highly regarded for its medicinal properties, particularly in treating respiratory infections and inflammatory conditions, as well as boosting the human immune system. However, a lack of genomic information has hindered research on the functional genomics and potential improvements of H. cordata. In this study, we present a near-complete assembly of H. cordata genome and investigate the biosynthetic pathway of flavonoids, specifically quercetin, using genomics, transcriptomics, and metabolomics analyses. The genome of H. cordata diverged from that of Saururus chinensis around 33.4 million years ago; it consists of 2.24 Gb with 76 chromosomes (4n = 76) and has undergone three whole-genome duplication (WGD) events. These WGDs played a crucial role in shaping the H. cordata genome and influencing the gene families associated with its medicinal properties. Through metabolomics and transcriptomics analyses, we identified key genes involved in the β-oxidation process for biosynthesis of houttuynin, one of the volatile oils responsible for the plant's fishy smell. In addition, using the reference genome, we identified genes involved in flavonoid biosynthesis, particularly quercetin metabolism, in H. cordata. This discovery has important implications for understanding the regulatory mechanisms that underlie production of active pharmaceutical ingredients in traditional Chinese medicine. Overall, the high-quality genome assembly of H. cordata serves as a valuable resource for future functional genomics research and provides a solid foundation for genetic improvement of H. cordata for the benefit of human health.","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142127206","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

lcQTH: Rapid quantitative trait mapping by tracing parental haplotypes with ultra-low-coverage sequencing. lcQTH：通过超低覆盖率测序追踪亲本单倍型，快速绘制数量性状图。

IF 9.4 1区生物学

Plant Communications Pub Date : 2024-10-14 Epub Date: 2024-06-24 DOI: 10.1016/j.xplc.2024.101008

Wenxi Wang, Zhe Chen, Zhengzhao Yang, Zihao Wang, Jilu Liu, Jie Liu, Huiru Peng, Zhenqi Su, Zhongfu Ni, Qixin Sun, Weilong Guo

引用次数: 0

The biosynthesis of asiaticoside and madecassoside reveals tandem duplication-directed evolution of glycoside glycosyltransferases in the Apiales. 芦荟苷和马黛茶苷的生物合成揭示了芹属植物苷糖基转移酶的串联复制定向进化。

IF 9.4 1区生物学

Plant Communications Pub Date : 2024-10-14 Epub Date: 2024-06-19 DOI: 10.1016/j.xplc.2024.101005

Xiaoyang Han, Jingyi Zhao, Hong Zhou, Xuan Zhou, Zixin Deng, Zhenhua Liu, Yi Yu

{"title":"The biosynthesis of asiaticoside and madecassoside reveals tandem duplication-directed evolution of glycoside glycosyltransferases in the Apiales.","authors":"Xiaoyang Han, Jingyi Zhao, Hong Zhou, Xuan Zhou, Zixin Deng, Zhenhua Liu, Yi Yu","doi":"10.1016/j.xplc.2024.101005","DOIUrl":"10.1016/j.xplc.2024.101005","url":null,"abstract":"Certain plant species within the Apiales order accumulate triterpenoid saponins that feature a distinctive glucose-glucose-rhamnose (G-G-R) sugar chain attached at the C-28 position of the pentacyclic triterpene skeleton. Until recently, the genomic basis underlying the biosynthesis and evolution of this sugar chain has remained elusive. In this study, we identified two novel glycoside glycosyltransferases (GGTs) that can sequentially install the sugar chain's second D-glucose and third L-rhamnose during the biosynthesis of asiaticoside and madecassoside, two representative G-G-R sugar chain-containing triterpenoid saponins produced by Centella asiatica. Enzymatic assays revealed the remarkable substrate promiscuity of the two GGTs and the key residues crucial for sugar-donor selectivity of the glucosyltransferase and rhamnosyltransferase. We further identified syntenic tandem gene duplicates of the two GGTs in the Apiaceae and Araliaceae families, suggesting a well-conserved genomic basis underlying sugar chain assembly that likely has evolved in the early ancestors of the Apiales order. Moreover, expression patterns of the two GGTs in pierced leaves of C. asiatica were found to be correlated with the production of asiaticoside and madecassoside, implying their involvement in host defense against herbivores and pathogens. Our work sheds light on the biosynthesis and evolution of complex saponin sugars, paving the way for future engineering of diverse bioactive triterpenoids with unique glycoforms.","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141433341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Breeding herbicide-resistant rice (Oryza sativa) using CRISPR/Cas gene editing and other technologies. 利用 CRISPR/Cas 基因编辑和其他技术培育抗除草剂水稻（Oryza sativa）。

IF 9.4 1区生物学

Plant Communications Pub Date : 2024-10-12 DOI: 10.1016/j.xplc.2024.101172

Qiyu Luo, Yao-Guang Liu

引用次数: 0

Developing an FBP-based bioluminescence reporter system for studying transcriptional regulation in plants. 开发基于 FBP 的生物发光报告系统，用于研究植物的转录调控。

IF 9.4 1区生物学

Plant Communications Pub Date : 2024-10-09 DOI: 10.1016/j.xplc.2024.101143

Siyuan Sun, Qiye Ni, Daren Luo, Xiao Hong, Wei Li, Tiange Wang, Xuye Lang, Hao Du

引用次数: 0

UV-B increases active phytochrome B to suppress thermomorphogenesis and enhance UV-B stress tolerance at high temperatures. 紫外线-B能提高植物色素B的活性，从而抑制高温下的热形态发生，增强对紫外线-B胁迫的耐受性。

IF 9.4 1区生物学

Plant Communications Pub Date : 2024-10-09 DOI: 10.1016/j.xplc.2024.101142

Geonhee Hwang, Taedong Lee, Jeonghyang Park, Inyup Paik, Nayoung Lee, Yun Ju Kim, Young Hun Song, Woe-Yeon Kim, Eunkyoo Oh

{"title":"UV-B increases active phytochrome B to suppress thermomorphogenesis and enhance UV-B stress tolerance at high temperatures.","authors":"Geonhee Hwang, Taedong Lee, Jeonghyang Park, Inyup Paik, Nayoung Lee, Yun Ju Kim, Young Hun Song, Woe-Yeon Kim, Eunkyoo Oh","doi":"10.1016/j.xplc.2024.101142","DOIUrl":"https://doi.org/10.1016/j.xplc.2024.101142","url":null,"abstract":"Plants respond to small increases in ambient temperature by changing their architecture, a response collectively termed thermomorphogenesis. Thermomorphogenesis is considered to attenuate the damage caused by potentially harmful high-temperature conditions, and multiple environmental factors can modulate this process. Among these factors, ultraviolet-B (UV-B) light has been shown to strongly suppress this response. However, the molecular mechanisms through which it regulates thermomorphogenesis and the physiological roles of the UV-B-mediated suppression of thermomorphogenesis remain poorly understood. Here, we show that UV-B inhibits thermomorphogenesis through the UVR8-COP1-phyB/HFR1 signaling module. We found that cop1 mutants maintain high levels of active phyB at high temperatures. Extensive genetic analyses revealed that the increased phyB, HFR1, and CRY1 in cop1 mutants redundantly reduce both the level and activity of a key positive regulator in thermomorphogenesis, PIF4, thereby repressing this growth response. Additionally, we found that UV-B light increases phyB stability and its photobody number through the inactivation of COP1. The UV-B-stabilized active phyB, together with HFR1, inhibits thermomorphogenesis by interfering with PIF4. We further show that the increased active phyB enhances UV-B tolerance by activating flavonoid biosynthesis and inhibiting thermomorphogenic growth. Taken together, our study demonstrates that UV-B increases the levels of active phyB and HFR1 by inhibiting COP1 to suppress PIF4-mediated growth responses, which is essential for plant tolerance to UV-B stress at high temperatures.","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142401931","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A PHR-dependent reciprocal antagonistic interplay between UV response and P-deficiency adaptation in plants. 植物紫外线反应与缺钾性适应之间相互依赖的拮抗相互作用

IF 9.4 1区生物学

Plant Communications Pub Date : 2024-10-03 DOI: 10.1016/j.xplc.2024.101140

Jianhao Ren, Tianjie Li, Meina Guo, Qianqian Zhang, Suna Ren, Long Wang, Qingyu Wu, Shihui Niu, Keke Yi, Wenyuan Ruan

{"title":"A PHR-dependent reciprocal antagonistic interplay between UV response and P-deficiency adaptation in plants.","authors":"Jianhao Ren, Tianjie Li, Meina Guo, Qianqian Zhang, Suna Ren, Long Wang, Qingyu Wu, Shihui Niu, Keke Yi, Wenyuan Ruan","doi":"10.1016/j.xplc.2024.101140","DOIUrl":"https://doi.org/10.1016/j.xplc.2024.101140","url":null,"abstract":"Plants are often simultaneously stressed by both UV radiation and phosphorus (P) deficiency in agricultural ecosystems. Coordinated responses and adaptations to these stressors are critical for plant growth, development, and survival. However, the underlying molecular response and adaptation mechanisms in plants remain elusive. Here, we show that plants use a reciprocal antagonistic strategy in response to UV radiation and P deficiency. UV radiation inhibited P-starvation response (PSR) processes and disrupted phosphate (Pi) homeostasis by suppressing the function of PHOSPHATE STARVATION RESPONSE PROTEINS (PHRs), the Pi central regulators. Conversely, P availability modulated the plant UV tolerance and the expression level of UV radiation response (URR) genes in a PHR-dependent manner. Therefore, reducing P supply or increasing PHRs activities can improve the tolerance to UV stress in rice. Moreover, this antagonistic interaction is conserved across various plant species. Furthermore, our meta-analysis showed that the increase in global UV radiation over the last forty years may reduce crop P-utilization efficiency worldwide. Our findings provide insights for optimizing P fertilizer management and breeding smart crops resilient to fluctuations in UV radiation and soil P levels.","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142376225","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0