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BjuIR:A multi-omics database with various tools for accelerating functional genomics research in Brassica juncea

Plant Communications 2024年第8期5卷 96-99页

作者： Linna Zhang Jinyuan Xiao Congyuan Liang Yifan Chen Changchun Yu Xinle Zhao Jiawei Li Mingli Yan Qian Yang Hao Chen Zhongsong Liu Zhengjie Wan Zhiquan Yang Qing-Yong Yang National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops College of InformaticsHuazhong Agricultural UniversityWuhan 430070China Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data College of InformaticsHuazhong Agricultural UniversityWuhan 430070China National Key Laboratory of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China Yazhouwan National Laboratory Sanya 572025China National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhan 430070China Crop Research Institute Hunan Academy of Agricultural SciencesChangsha 410125China College of Agronomy Hunan Agricultural UniversityChangsha 410128China

Dear Editor,Advances in high-throughput omics technologies,along with methodologies for integrating multi-omics datasets,have substantially enhanced the efficiency of identifying candidate genes in breeding(Gusev et al.,2018;Gupta et al.,2019).However,this process is often complex and *** address this challenge,databases that integrate extensive data and enable convenient and efficient functional genomics studies are being developed(Ma et al.,2021;Yang et al.,2023).

关键词： functional integrating convenient

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Insights into the Superrosids phylogeny and flavonoid synthesis from the telomere-to-telomere gap-free genome assembly of Penthorum chinense Pursh

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园艺研究（英文） 2024年第2期11卷 75-85页

作者： Zhoutao Wang Junmei Zhou Junjie Pan Wei Cheng Jie Fang Qundan Lv Xiaodan Lin Wenliang Cheng Liangsheng Zhang Kejun Cheng Genomics and Genetic Engineering Laboratory of Ornamental Plants College of Agriculture and BiotechnologyZhejiang UniversityHangzhou 311300China Chemical Biology Center Lishui Institute of Agriculture and Forestry SciencesLishui 323000China Postdoctoral Research Enter Zhejiang Kangning Pharmaceutical Co.LtdLishui 323000China Chemical Biology Center Lishui Institute of Agriculture and Forestry SciencesLishui 323000China Genomics and Genetic Engineering Laboratory of Ornamental Plants College of Agriculture and BiotechnologyZhejiang UniversityHangzhou 311300China Chemical Biology Center Lishui Institute of Agriculture and Forestry SciencesLishui 323000China Product Development Department Zhejiang Shaowei Yuanzhi Science and Technology Development Co.LtdLishui 323000China Genomics and Genetic Engineering Laboratory of Ornamental Plants College of Agriculture and BiotechnologyZhejiang UniversityHangzhou 311300China Chemical Biology Center Lishui Institute of Agriculture and Forestry SciencesLishui 323000China Postdoctoral Research Enter Zhejiang Kangning Pharmaceutical Co.LtdLishui 323000China Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine Zhejiang A&F UniversityHangzhou311300China

The completion of the first telomere-to-telomere(T2T)genome assembly of Penthorum chinense Pursh(PC),a prominent medicinal plant in China,represents a significant *** assembly spans a length of 257.5 Mb and consists of nine ***'s notably smaller genome size in Saxifragales,compared to that of Paeonia ostii,can be attributed to the low abundance of transposable *** utilizing single-copy genes from 30 species,including 28 other Superrosids species,we successfully resolved a previously debated Superrosids *** findings unveiled Saxifragales as the sister group to the core rosids,with both being the sister group to *** previously characterized cytochrome P450(CYP)genes,we predicted the compound classes that most CYP genes of PC are involved in synthesizing,providing insight into PC's potential metabolic *** and transcriptomic data revealed that the richest sources of the three most noteworthy medicinal components in PC are young leaves and *** also observed higher activity of upstream genes in the flavonoid synthesis pathway in these plant ***,through weighted gene co-expression network analysis,we identified gene regulatory networks associated with the three medicinal ***,these findings deepen our understanding of PC,opening new avenues for further research and exploration.

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PbrRALF2-elicited reactive oxygen species signaling is mediated by the PbrCrRLK1L13-PbrMPK18 module in pear pollen tubes

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Horticulture research 2021年第1期8卷 3042-3054页

作者： Xiaobing Kou Jiangmei Sun Peng Wang Danqi Wang Peng Cao Jing Lin Youhong Chang Shaoling Zhang Juyou Wu Center of Pear Engineering Technology Research State Key Laboratory of Crop Genetics and Germplasm EnhancementCollege of HorticultureNanjing Agricultural University210095 NanjingChina Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement 210014 NanjingChina

Rapid alkalinization factors(RALFs)are cysteine-rich peptides that play important roles in a variety of biological processes,such as cell elongation and immune *** studies in Arabidopsis have shown that RALFs regulate pollen tube growth via plasma membrane receptor-like kinases(RLKs).However,the downstream signal transduction mechanisms of RLKs in pollen tubes are ***,we identified PbrRALF2,a pear(Pyrus bretschneideri)pollen RALF peptide that inhibits pollen tube *** found that PbrRALF2 interacts with a malectin-like domain-containing RLK,*** relative affinity between PbrRALF2 and PbrCrRLK1L13 was at the submicromolar level,which is consistent with the values of ligand–receptor kinase pairs and the physiological concentration for PbrRALF2-mediated inhibition of pollen tube *** binding to its extracellular domain,PbrRALF2 activated the phosphorylation of PbrCrRLK1L13 in a dose-dependent *** further showed that the MAP kinase PbrMPK18 is a downstream target of PbrCrRLK1L13 that mediates PbrRALF2-elicited reactive oxygen species(ROS)*** excessive accumulation of ROS inhibits pollen tube *** show that MPK acts as a mediator for CrRLK1L to stimulate ROS production,which might represent a general mechanism by which RALF and CrRLK1L function in signaling pathways.

关键词： RALF reactive alkali

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Transferrin Is Up-Regulated by Microbes and Acts as a Negative Regulator of Immunity to Induce Intestinal Immunotolerance

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research 2024年第3期7卷 761-774页

作者： Xiaopeng Tang Mingqian Fang Ruomei Cheng Junkun Niu Xiaoshan Huang Kuanhong Xu Gan Wang Yang Sun Zhiyi Liao Zhiye Zhang James Mwangi Qiumin Lu Aili Wang Longbao Lv Chao Liu Yinglei Miao Ren Lai Engineering Laboratory of Peptides of Chinese Academy of Sciences Key Laboratory of Bioactive Peptides of Yunnan ProvinceKIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common DiseasesNational Resource Center for Non-Human PrimatesNational Research Facility for Phenotypic&Genetic Analysis of Model Animals(Primate Facility)and Sino-African Joint Research CenterNew Cornerstone Science InstituteKunming Institute of Zoologythe Chinese Academy of SciencesNo.17 Longxin RoadKunmingYunnan650201China School of Basic Medicine Qingdao UniversityQingdao 266071ShandongChina. Department of Gastroenterology First Affiliated Hospital of Kunming Medical UniversityYunnan Institute of Digestive DiseaseKunming 650032YunnanChina Yunnan Province Clinical Research Center for Digestive Diseases Kunming 650032YunnanChina Kunming College of Life Science University of Chinese Academy of SciencesKunming 650204YunnanChina Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences University of Science and Technology of ChinaHefei 230027AnhuiChina Center for Evolution and Conservation Biology Southern Marine Science and Engineering Guangdong LaboratoryGuangzhou 511458GuangdongChina.

Cross-talks (e.g., host-driven iron withdrawal and microbial iron uptake between host gastrointestinal tract and commensal microbes) regulate immunotolerance and intestinal homeostasis. However, underlying mechanisms that regulate the cross-talks remain poorly understood. Here, we show that bacterial products up-regulate iron-transporter transferrin and transferrin acts as an immunosuppressor by interacting with cluster of differentiation 14 (CD14) to inhibit pattern recognition receptor (PRR) signaling and induce host immunotolerance. Decreased intestinal transferrin is found in germ-free mice and human patients with ulcerative colitis, which are characterized by impaired intestinal immunotolerance. Intestinal transferrin and host immunotolerance are returned to normal when germ-free mice get normal microbial commensalism, suggesting an association between microbial commensalism, transferrin, and host immunotolerance. Mouse colitis models show that transferrin shortage impairs host’s tolerogenic responses, while its supplementation promotes immunotolerance. Designed peptide blocking transferrin–CD14 interaction inhibits immunosuppressive effects of transferrin. In monkeys with idiopathic chronic diarrhea, transferrin shows comparable or even better therapeutic effects than hydrocortisone. Our findings reveal that by up-regulating host transferrin to silence PRR signaling, commensal bacteria counteract immune activation induced by themselves to shape host immunity and contribute for intestinal tolerance.

关键词： impaired immunity tolerance

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Genomic variation reveals demographic history and biological adaptation of the ancient relictual,lotus(Nelumbo Adans.)

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园艺研究（英文） 2022年第1期9卷 1545-1558页

作者： Xingwen Zheng Tao Wang Teng Cheng Lingling Zhao Xingfei Zheng Fenglin Zhu Chen Dong Jinxing Xu Keqiang Xie Zhongli Hu Liangbo Yang Ying Diao State Key Laboratory of Hybrid Rice Lotus Engineering Research Center of Hubei ProvinceCollege of Life SciencesWuhan UniversityWuhan 430072China Guangchang White Lotus Research Institute Guangchang 344900China State Key Laboratory of Hybrid Rice Lotus Engineering Research Center of Hubei ProvinceCollege of Life SciencesWuhan UniversityWuhan 430072China College of Biological Engineering Henan University of TechnologyZhengzhouHenan 450001China Guangchang White Lotus Research Institute Guangchang 344900China

Lotus(Nelumbo Adans.),a relict plant,is testimony to long-term sustained ecological success,but the underlying genetic changes related to its survival strategy remain ***,we assembled the high-quality lotus genome,investigated genome variation of lotus mutation accumulation(MA)lines and reconstructed the demographic history of wild Asian *** identified and validated 43 base substitutions fixed in MA lines,implying a spontaneous mutation rate of 1.4×10-9 bases/generation in lotus shoot stem *** past history of the lotus revealed that the ancestors of the lotus in eastern and southern Asia could be traced back to～20 million years ago and twice experienced significant bottlenecks and population *** further identified selected genes among three lotus groups in different habitats,suggesting that 453 differed genes between the tropical and temperate group and 410 differed genes between two subgroups from Northeastern China and the Yangtze River-Yellow River Basin might play important roles in natural selection in the lotus's adaptation and *** findings not only improve understanding of the evolutionary history of the lotus and the genetic basis of its survival advantages,but also provide valuable data for addressing various questions in evolution and protection for relict plants.

关键词： biological adaptation de novo assembly demographic history lotus (Nelumbo) mutation rate relict plant

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Comparative genomics reveals the diversification of triterpenoid biosynthesis and origin of ocotilloltype triterpenes in Panax

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Plant Communications 2023年第4期4卷 271-285页

作者： Zijiang Yang Xiaobo Li Ling Yang Sufang Peng Wanling Song Yuan Lin Guisheng Xiang Ying Li Shuang Ye Chunhua Ma Jianhua Miao Guanghui Zhang Wei Chen Shengchao Yang Yang Dong National&Local Joint Engineering Research Center on Germplasm Innovation&Utilization of Chinese Medicinal Materials in Southwest China Yunnan Agricultural UniversityKunmingChina The Key Laboratory of Medicinal Plant Biology of Yunnan Province Yunnan Agricultural UniversityKunmingChina College of Food Science and Technology Yunnan Agricultural UniversityKunmingChina Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement Guangxi Botanical Garden of Medicinal PlantsNanningChina Yunnan Plateau Characteristic Agriculture Industry Research Institute KunmingChina

gene duplication is assumed to be the major force driving the evolution of metabolite biosynthesis in *** from functional burdens,duplicated genes can mutate toward novelties until fixed due to selective ***,the extent to which this mechanism has driven the diversification of metabolite biosynthesis remains to be *** we performed comparative genomics analysis and functional characterization to evaluate the impact of gene duplication on the evolution of triterpenoid biosynthesis using Panax species as *** that whole-genome duplications(WGDs)occurred independently in Araliaceae and Apiaceae *** genomics revealed the evolutionary trajectories of triterpenoid biosynthesis in plants,which was mainly promoted by WGDs and tandem *** synthase(LAS)was likely derived from a tandemduplicate of cycloartenol synthase that predated the emergence of *** episodic diversifying selection,the LAS gene duplicates produced by g whole-genome triplication have given rise to triterpene biosynthesis in core eudicots through ***,functional characterization revealed that oxidosqualene cyclases(OSCs)responsible for synthesizing dammarane-type triterpenes in Panax species were also capable of producing ocotilloltype *** and biochemical evidence suggested that Panax genes encoding the above OSCs originated from the specialization of one OSC gene duplicate produced from a recent WGD shared by Araliaceae(Pg-b).Our results reveal the crucial role of gene duplication in diversification of triterpenoid biosynthesis in plants and provide insight into the origin of ocotillol-type triterpenes in Panax species.

关键词： gene duplication Panax genomes whole-genome duplications triterpenoid biosynthesis ocotilloltype triterpenes specialization

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Blockade of NMT1 enzymatic activity inhibits N-myristoylation of VILIP3 protein and suppresses liver cancer progression

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Signal Transduction and Targeted Therapy 2023年第2期8卷 716-729页

作者： Xiang-Peng Tan Yan He Jing Yang Xian Wei You-Long Fan Guo-Geng Zhang Yi-Dong Zhu Zheng-Qiu Li Hua-Xin Liao Da-Jiang Qin Xin-Yuan Guan Bin Li The First Affiliated Hospital of Jinan University Jinan UniversityGuangzhouChina Key Laboratory of Biological Targeting Diagnosis Therapy and Rehabilitation of Guangdong Higher Education Institutes and Key Laboratory of Protein Modification and DegradationThe Fifth Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina MOE Key Laboratory of Tumor Molecular Biology and National Engineering Research Center of Genetic Medicine College of Life Science and TechnologyJinan UniversityGuangzhouChina School of Pharmacy Jinan UniversityGuangzhouChina Department of Clinical Oncology The University of Hong KongHong KongChina

Hepatocellular carcinoma(HCC)is one of the most common malignant *** of the underlying mechanism of HCC progression and exploration of new therapeutic drugs are urgently ***,a compound library consisting of 419 FDA-approved drugs was taken to screen potential anticancer drugs.A series of functional assays showed that desloratadine,an antiallergic drug,can repress proliferation in HCC cell lines,cell-derived xenograft(CDX),patient-derived organoid(PDO)and patient-derived xenograft(PDX)models.N-myristoyl transferase 1(NMT1)was identified as a target protein of desloratadine by drug affinity responsive target stability(DARTS)and surface plasmon resonance(SPR)*** of NMT1 expression enhanced but NMT1 knockdown suppressed tumor growth in vitro and in *** labeling and mass spectrometry analyses revealed that Visinin-like protein 3(VILIP3)was a new substrate of NMT1 in protein N-myristoylation modification,and high NMT1 or VILIP3 expression was associated with advanced stages and poor survival in ***,desloratadine binds to Asn-246 in NMT1 and inhibits its enzymatic activity,disrupting the NMT1-mediated myristoylation of the VILIP3 protein and subsequent NFκB/Bcl-2 ***,this study demonstrates that desloratadine may be a novel anticancer drug and that NMT1-mediated myristoylation contributes to HCC progression and is a potential biomarker and therapeutic target in HCC.

关键词： drugs VILI allergic

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A 48-bp deletion upstream of LIGULELESS 1 alters rice panicle architecture

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The Crop Journal 2024年第2期12卷 354-363页

作者： Linhua Wu Min Hu Shuwei Lyu Wenfeng Chen Hang Yu Qing Liu Wei He Chen Li Zuofeng Zhu Rice Research Institute Guangdong Academy of Agricultural SciencesGuangzhou 510640GuangdongChina National Center for Evaluation of Agricultural Wild Plants(Rice) Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing 100193China State Key Laboratory for Rice Biology and Breeding China National Rice Research InstituteHangzhou 310006ZhejiangChina Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China(Co-construction by Ministry and Province) Ministry of Agriculture and Rural AffairsGuangzhou 510640GuangdongChina Guangdong Key Laboratory of New Technology in Rice Breeding Guangzhou 510640GuangdongChina Guangdong Rice Engineering Laboratory Guangzhou 510640GuangdongChina

Panicle architecture is an agronomic determinant of crop yield and a target for cereal crop *** investigate its molecular mechanisms in rice,we performed map-based cloning and characterization of OPEN PANICLE 1(OP1),a gain-of-function allele of LIGULELESS 1(LG1),controlling the spread-panicle *** allele results from a 48-bp deletion in the LG1 upstream region and promotes pulvinus development at the base of the primary *** OP1 expression and altered panicle phenotype in chimeric transgenic plants and upstream-region knockout mutants indicated that the deletion regulates spread-panicle architecture in the mutant spread panicle 1(sp1).Knocking out BRASSINOSTEROID UPREGULATED1(BU1)gene in the background of OP1 complementary plants resulted in compact panicles,suggesting OP1 may regulate inflorescence architecture via the brassinosteroid signaling *** regard that manipulating the upstream regulatory region of OP1 or genes involved in BR signal pathway could be an efficient way to improve rice inflorescence architecture.

关键词： Upstream region Panicle architecture gene expression BR Rice

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GLUL stabilizes N-Cadherin by antagonizing β-Catenin to inhibit the progresses of gastric cancer

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Acta Pharmaceutica Sinica B 2024年第2期14卷 698-711页

作者： Qiwei Jiang Yong Li Songwang Cai Xingyuan Shi Yang Yang Zihao Xing Zhenjie He Shengte Wang Yubin Su Meiwan Chen Zhesheng Chen Zhi Shi Department of Cell Biology&Institute of Biomedicine National Engineering Research Center of Genetic MedicineState Key Laboratory of Bioactive Molecules and Druggability AssessmentMOE Key Laboratory of Tumor Molecular BiologyGuangdong Provincial Key Laboratory of Bioengineering MedicineCollege of Life Science and TechnologyJinan UniversityGuangzhou 510632China Department of Gastrointestinal Surgery&General Surgery the Guangdong Provincial People’s HospitalGuangdong Academy of Medical SciencesGuangzhou 510080China Department of Thoracic Surgery The First Affiliated Hospital of Jinan UniversityGuangzhou 510632China Department of Radiation Oncology The Fifth Hospital of Guangzhou Medical UniversityGuangzhou 510150China State Key Laboratory of Quality Research in Chinese Medicine Institute of Chinese Medical SciencesUniversity of MacaoMacao 519000China Department of Pharmaceutical Sciences College of Pharmacy and Health SciencesSt.John’s UniversityQueensNY 11439USA

Glutamate-ammonia ligase(GLUL, also known as glutamine synthetase) is a crucial enzyme that catalyzes ammonium and glutamate into glutamine in the ATP-dependent condensation. Although GLUL plays a critical role in multiple cancers, the expression and function of GLUL in gastric cancer remain unclear. In the present study, we have found that the expression level of GLUL was significantly lower in gastric cancer tissues compared with adjacent normal tissues, and correlated with N stage and TNM stage, and low GLUL expression predicted poor survival for gastric cancer patients. Knockdown of GLUL promoted the growth, migration, invasion and metastasis of gastric cancer cells in vitro and in vivo, and vice versa, which was independent of its enzyme activity. Mechanistically, GLUL competed with β-Catenin to bind to N-Cadherin, increased the stability of N-Cadherin and decreased the stability of β-Catenin by alerting their ubiquitination. Furthermore, there were lower N-Cadherin and higher β-Catenin expression levels in gastric cancer tissues compared with adjacent normal tissues. GLUL protein expression was correlated with that of N-Cadherin, and could be the independent prognostic factor in gastric cancer. Our findings reveal that GLUL stabilizes N-Cadherin by antagonizing β-Catenin to inhibit the progress of gastric cancer.

关键词： Gastric cancer GLUL N-Cadherin β-Catenin Enzyme

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Development of a molecular marker for cherry crinkle leaf disease

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Molecular Horticulture 2023年第1期3卷 124-126页

作者： Jing Wang Xiaoming Zhang Guohua Yan Yu Zhou Xuwei Duan Chuanbao Wu Xin Zhang Kaichun Zhang Institute of Forestry and Pomology Beijing Academy of Agriculture and Forestry SciencesBeijing 100093P.R.China Cherry Engineering and Technical Research Center of the State Forestry and Grassland Administration Beijing 100093P.R.China Key Laboratory of Biology and Genetic Improvement of Horticultural Crops(North China) Ministry of Agriculture and Rural AffairsBeijingChina Beijing Engineering Research Center for Deciduous Fruit Trees BeijingChina

Sweet cherry(Prunus avium L.)is an economic fruit tree of the Prunus genus in the Roaceae family(Vignati et al.2022).It is popular with consumers because of its early ripening in open-field,bright color,and rich *** the 80’s,sweet cherry industry in our country has developed *** present,the production,planting area and import of sweet cherry are ranked first in the world,which is known as‘gold planting industry’(Zhang et al.2020).

关键词： ranked planting cherry

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