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High-quality genome assembly of Huazhan and Tianfeng,the parents of an elite rice hybrid Tian-you-hua-zhan

Science China(Life Sciences) 2022年第2期65卷 398-411页

作者： Hui Zhang Yuexing Wang Ce Deng Sheng Zhao Peng Zhang Jie Feng Wei Huang Shujing Kang Qian Qian Guosheng Xiong yuxiao chang Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources College of Life SciencesSouth China Agricultural UniversityGuangzhou 510642China State Key Laboratory of Rice Biology China National Rice Research InstituteHangzhou 310006China National Key Laboratory of Wheat and Maize Crop Science College of AgronomyHenan Agricultural UniversityZhengzhou 450002China College of Life Science and Technology Guangxi UniversityNanning 530004China Plant Phenomics Research Center Nanjing Agricultural UniversityNanjing 210095China

High-quality rice reference genomes have accelerated the comprehensive identification of genome-wide variations and research on functional genomics and breeding.Tian-you-hua-zhan has been a leading hybrid in China over the past decade.Here,de novo genome assembly strategy optimization for the rice indica lines Huazhan(HZ)and Tianfeng(TF),including sequencing platforms,assembly pipelines and sequence depth,was carried out.The PacBio and Nanopore platforms for long-read se-quencing were utilized,with the Canu,wtdbg2,SMARTdenovo,Flye,Canu-wtdbg2,Canu-SMARTdenovo and Canu-Flye assemblers.The combination of PacBio and Canu was optimal,considering the contig N50 length,contig number,assembled genome size and polishing process.The assembled contigs were scaffolded with Hi-C data,resulting in two“golden quality”rice reference genomes,and evaluated using the scaffold N50,BUSCO,and LTR assembly index.Furthermore,42,625 and 41,815 non-transposable element genes were annotated for HZ and TF,respectively.Based on our assembly of HZ and TF,as well as Zhenshan97,Minghui63,Shuhui498 and 9311,comprehensive variations were identified using Nipponbare as a reference.The de novo assembly strategy for rice we optimized and the“golden quality”rice genomes we produced for HZ and TF will benefit rice genomics and breeding research,especially with respect to uncovering the genomic basis of the elite traits of HZ and TF.

关键词： de novo genome assembly high-quality PacBio Nanopore variation rice

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Effort and Contribution of T-DNA Insertion Mutant Library for Rice Functional Genomics Research in China:Review and Perspective

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Journal of Integrative Plant Biology 2012年第12期54卷 953-966页

作者： yuxiao chang Tuan Long changyin Wu National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research(Wuhan) Huazhong Agricultural University

With the completion of the rice （Oryza sativa L.） genome-sequencing project, the rice research community proposed to characterize the func- tion of every predicted gene in rice by 2020. One of the most effective and high-throughput strategies for studying gene function is to employ genetic mutations induced by insertion elements such as T-DNA or transposons. Since 1999, with support from the Ministry of Science and Technology of China for Rice Functional Genomics Programs, large-scale T-DNA insertion mutant populations have been generated in Huazhong Agricultural University, the Chinese Academy of Sciences and the Chinese Academy of Agricultural Sciences. Currently, a total of 372,346 mutant lines have been generated, and 58,226 T-DNA or Tos17 flanking sequence tags have been isolated. Using these mutant resources, more than 40 genes with potential applications in rice breeding have already been identified. These include genes involved in biotic or abiotic stress responses, nutrient metabolism, pollen development, and plant architecture. The functional analysis of these genes will not only deepen our understanding of the fundamental biological questions in rice, but will also offer valuable gene resources for developing Green Super Rice that is high-yielding with few inputs even under the poor growth conditions of many regions of Africa and Asia.

关键词： Flanking sequence tags functional genomics insertion site rice T-DNA insertion mutant library.

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Genetic and Functional Differences of Escherichia coli Strains from Colorectal Cancer Mucosal Tissues

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Engineering 2022年第9期16卷 210-219页

作者： yuxiao chang Xiang Li Lei Ding Chao Yang Zhiyuan Pan Ni Han Yujun Cui Fachao Zhi Ruifu Yang Hong Gao Yujing Bi State Key Laboratory of Pathogen and Biosecurity Beijing Institute of Microbiology and EpidemiologyBeijing 100071China Beijing Shijitan Hospital Capital Medical UniversityBeijing 100038China Guangdong Provincial Key Laboratory of Gastroenterology Institute of Gastroenterology of Guangdong Province&Department of GastroenterologyNanfang HospitalSouthern Medical UniversityGuangzhou 510515China Shenzhen Center for Disease Control and Prevention Shenzhen 518055China

Colorectal cancer(CRC)is the third leading cancer globally.Metagenomics has been widely used to analyze the association between the gut microbiota and CRC based on bacterial genus-or species-level comparisons,providing evidence of dysbiosis in CRC development.However,this kind of analysis is unable to provide strain-level information for understanding the individual role of a species in CRC.Here,we used culturomics to isolate CRC mucosal samples and selected 158 Escherichia coli strains to reveal their differences in both genomics and functions by means of phylogenetic analysis and inflammatory induction based on cell and animal experiments.Through genomic comparison,these strains were divided into five phylogroups.The representative strains of each phylogroup significantly induced different levels of cytokine secretion by human leukemic monocyte(THP-1 cell)-based Transwell and animal experiments.Further bioinformatic analysis revealed different profiles of single-nucleotide polymorphisms,genes,and metabolic pathways in the different phylogroups,which can improve the current understanding of the phenotypic differences between these strains.The strain differences revealed in both genomics and functions indicate that the microbiota’s function at the strain level should be investigated in order to understand the interacting mechanisms between hosts and gut bacteria.

关键词： Colorectal cancer Gut microbiota Culturomics Escherichia coli Strain level

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A prolific and robust whole-genome genotyping method using PCR amplification via primer-template mismatched annealing

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Journal of Integrative Plant Biology 2023年第3期65卷 633-645页

作者： Sheng Zhao Cuicui Zhang Liqun Wang Minxuan Luo Peng Zhang Yue Wang Waqar Afzal Malik Yue Wang Peng Chen Xianjin Qiu Chongrong Wang Hong Lu Yong Xiang Yuwen Liu Jue Ruan Qian Qian Haijian Zhi yuxiao chang National Key Laboratory for Crop Genetics and Germplasm Enhancement National Center for Soybean ImprovementNanjing Agricultural UniversityNanjing 210095China Guangdong Laboratory of Lingnan Modern Agriculture Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China College of Agriculture Yangtze UniversityJingzhou 434023China Guangdong Provincial Key Laboratory of New Technology in Rice Breeding Rice Research InstituteGuangdong Academy of Agricultural SciencesGuangzhou 510640China

Whole-genome genotyping methods are important for breeding.However,it has been challenging to develop a robust method for simultaneous foreground and background genotyping that can easily be adapted to different genes and species.In our study,we accidently discovered that in adapter ligation-mediated PCR,the amplification by primertemplate mismatched annealing(PTMA)along the genome could generate thousands of stable PCR products.Based on this observation,we consequently developed a novel method for simultaneous foreground and background integrated genotyping by sequencing(FBI-seq)using one specific primer,in which foreground genotyping is performed by primer-template perfect annealing(PTPA),while background genotyping employs PTMA.Unlike DNA arrays,multiple PCR,or genome target enrichments,FBI-seq requires little preliminary work for primer design and synthesis,and it is easily adaptable to different foreground genes and species.FBI-seq therefore provides a prolific,robust,and accurate method for simultaneous foreground and background genotyping to facilitate breeding in the postgenomics era.

关键词： background selection foreground genotyping primer-template mismatched annealing marker-assisted breeding whole-genome genotyping

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泛素化修饰和SUMO化修饰在电离辐射诱导的DNA损伤修复中的作用机制

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国际放射医学核医学杂志 2024年第2期48卷 130-136页

作者：张焕腾孙毓筱徐畅中国医学科学院北京协和医学院放射医学研究所天津市放射医学与分子核医学重点实验室天津300192

泛素和小泛素样修饰物(SUMO)以共价键形式连接到特定的蛋白底物上,进行泛素化修饰或SUMO化修饰,通过调控蛋白质的稳定性、活性、定位或相互作用来影响多种细胞活动,其中包括DNA损伤修复、细胞周期、细胞凋亡和免疫应答等。当细胞受到DN... 详细信息

泛素和小泛素样修饰物(SUMO)以共价键形式连接到特定的蛋白底物上,进行泛素化修饰或SUMO化修饰,通过调控蛋白质的稳定性、活性、定位或相互作用来影响多种细胞活动,其中包括DNA损伤修复、细胞周期、细胞凋亡和免疫应答等。当细胞受到DNA损伤时,泛素化修饰和SUMO化修饰能够调控相关蛋白质的功能和相互作用,参与到DNA损伤修复和信号传导的过程中。这些修饰作用对于维持基因组的完整性至关重要。近年来,研究发现泛素化修饰和SUMO化修饰在DNA损伤修复中都发挥着重要作用。笔者对这些作用机制进行综述,为深入了解电离辐射诱导的DNA损伤修复机制提供参考。

关键词：泛素小泛素相关修饰蛋白质类辐射电离 DNA损伤 DNA修复

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患者报告结局在淋巴瘤临床研究中的应用进展

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中国综合临床 2024年第2期40卷 133-138页

作者：赵婉越钱思宇宋云飞常宇笑张旭东郑州大学第一附属医院肿瘤科郑州450052

随着生物-心理-社会医学模式备受重视,患者报告结局取得了重大进展。现通过综合分析和总结领域内的文献,探讨患者报告结局在淋巴瘤临床研究中的应用进展,旨在为未来的相关研究提供有益参考。

关键词：淋巴瘤患者报告结局健康相关生命质量

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A pillared-layer metal-organic framework for efficient separation of C_(3)H_(8)/C_(2)H_(6)/CH_(4) in natural gas

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Chinese Journal of Chemical Engineering 2022年第2期35卷 10-16页

作者： Pengtao Guo Miao chang Tongan Yan yuxiao Li Dahuan Liu State Key Laboratory of Organic-Inorganic Composites Beijing University of Chemical TechnologyBeijing 100029China

Metal-organic frameworks(MOFs)have great potentials as adsorbents for natural gas purification.However,the trade-off between selectivity and adsorption capacity remains a challenge.Herein,we report a pillared-layer metal-organic framework Ni(HBTC)(bipy)for efficiently separating the C_(3)H_(8)/C_(2)H_(6)/CH_(4) mixture.The experimental results show that the adsorption capacity of C_(3)H_(8) and C_(2)H_(6) on Ni(HBTC)(bipy)are as high as 6.18 and 5.85 mmol·g^(-1),while only 0.93 mmol·g^(-1) for CH_(4) at 298 K and 100 kPa.Especially,the adsorption capacity of C_(3)H_(8) at 5 kPa can reach an unprecedented 4.52 mmol·g^(-1) and for C_(2)H_(6) it is 1.48 mmol·g^(-1) at 10 kPa.The ideal adsorbed solution theory predicted C_(3)H_(8)/CH_(4) selectivity is as high as 1857.0,superior to most of the reported materials.Breakthrough experiment results indicated that material could completely separate the C_(3)H_(8)/C_(2)H_(6)/CH_(4) mixture.Therefore,Ni(HBTC)(bipy)is a promising material for separation of natural gas.

关键词： Adsorption Light hydrocarbons Metal-organic framework Natural gas Selectivity Separation

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The RppC-AvrRppC NLR-effector interaction mediates the resistance to southern corn rust in maize

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Molecular Plant 2022年第5期15卷 904-912页

作者： Ce Deng April Leonard James Cahill Meng Lv Yurong Li Shawn Thatcher Xueying Li Xiaodi Zhao Wenjie Du Zheng Li Huimin Li Victor Llaca Kevin Fengler Lisa Marshall Charlotte Harris Girma Tabor Zhimin Li Zhiqiang Tian Qinghua Yang Yanhui Chen Jihua Tang Xintao Wang Junjie Hao Jianbing Yan Zhibing Lai Xiaohong Fei Weibin Song Jinsheng Lai Xuecai Zhang Guoping Shu Yibo Wang yuxiao chang Weiling Zhu Wei Xiong Juan Sun Bailin Li Junqiang Ding College of Agronomy Henan Agricultural UniversityZhengzhou 450046China The State Key Laboratory of Wheat and Maize Crop Science and Center for Crop Genome Engineering Henan Agricultural UniversityZhengzhou 450046China Corteva Agriscience JohnstonIA 50131USA Institute of Plant Protection Henan Academy of Agricultural SciencesZhengzhou 450002China National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070China State Key Laboratory of Plant Physiology and Biochemistry National Maize Improvement CenterCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijing 100193China International Maize and Wheat Improvement Center(CIMMYT) El Batan56237 TexcocoMexico Center of Biotechnology Beijing Lantron SeedZhengzhou 450001China Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China Henan Dingyou Agricultural Science and Technology Co. LtdZhengzhou 450001China

Southern corn rust(SCR),caused by the fungal pathogen Puccinia polysora,is a major threat to maize pro-duction worldwide.Efficient breeding and deployment of resistant hybrids are key to achieving durable control of SCR.Here,we report the molecular cloning and characterization of RppC,which encodes an NLR-type immune receptor and is responsible for a major SCR resistance quantitative trait locus.Further-more,we identified the corresponding avirulence effector,AvrRppC,which is secreted by P.polysora and triggers RppC-mediated resistance.Allelic variation of AvrRppC directly determines the effectiveness of RppC-mediated resistance,indicating that monitoring of AvrRppC variants in the field can guide the rational deployment of RppC-containing hybrids in maize production.Currently,RppC is the most frequently deployed SCR resistance gene in China,and a better understanding of its mode of action is crit-ical for extending its durability.

关键词： maize Zea mays RppC AvrRpp Csouthern corn rust SCR

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The First High-quality Reference Genome of Sika Deer Provides Insights into High-tannin Adaptation

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Genomics, Proteomics & Bioinformatics 2023年第1期21卷 203-215页

作者： Xiumei Xing Cheng Ai Tianjiao Wang Yang Li Huitao Liu Pengfei Hu Guiwu Wang Huamiao Liu Hongliang Wang Ranran Zhang Junjun Zheng Xiaobo Wang Lei Wang yuxiao chang Qian Qian Jinghua Yu Lixin Tang Shigang Wu Xiujuan Shao Alun Li Peng Cui Wei Zhan Sheng Zhao Zhichao Wu Xiqun Shao Yimeng Dong Min Rong Yihong Tan Xuezhe Cui Shuzhuo chang Xingchao Song Tongao Yang Limin Sun Yan Ju Pei Zhao Huanhuan Fan Ying Liu Xinhui Wang Wanyun Yang Min Yang Tao Wei Shanshan Song Jiaping Xu Zhigang Yue Qiqi Liang Chunyi Li Jue Ruan Fuhe Yang Key Laboratory of Genetics Breeding and Reproduction of Special Economic AnimalsMinistry of Agriculture and Rural AffairsInstitute of Special Animal and Plant SciencesChinese Academy of Agricultural SciencesChangchun 130112China Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China CAS Key Laboratory of Forest Ecology and Management Institute of Applied EcologyChinese Academy of SciencesShenyang 110016China Annoroad Gene Technology(Beijing)Co. LtdBeijing 100176China Novogene Bioinformatics Institute Beijing 100083China

Sika deer are known to prefer oak leaves,which are rich in tannins and toxic to most mammals;however,the genetic mechanisms underlying their unique ability to adapt to living in the jungle are still unclear.In identifying the mechanism responsible for the tolerance of a highly toxic diet,we have made a major advancement by explaining the genome of sika deer.We generated the first high-quality,chromosome-level genome assembly of sika deer and measured the correlation between tannin intake and RNA expression in 15 tissues through 180 experiments.Comparative genome analyses showed that the UGT and CYP gene families are functionally involved in the adaptation of sika deer to high-tannin food,especially the expansion of the UGT family 2 subfamily B of UGT genes.The first chromosome-level assembly and genetic characterization of the tolerance to a highly toxic diet suggest that the sika deer genome may serve as an essential resource for understanding evolutionary events and tannin adaptation.Our study provides a paradigm of comparative expressive genomics that can be applied to the study of unique biological features in non-model animals.

关键词： Sika deer Whole-genome sequencing Chromosome-scale assembly Oak leaf Tannin tolerance

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常克教授运用“开郁顺气”治疗小儿肺系疾病举隅

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成都中医药大学学报 2024年第3期47卷 23-26页

作者：车昭杨钰潇罗慧张静祎常克成都中医药大学临床医学院四川成都610075 成都中医药大学附属医院四川成都610032

本文旨在介绍常克教授治疗小儿肺系疾病的经验。常克教授认为“肺气郁闭”是小儿肺系疾病的常见病机,病邪在少阳经脉,与肺、脾、肝三脏关系密切,与小儿生理病理特点相关。治疗当以“开郁顺气”为总原则,促使人体气机运行快速恢复正常,... 详细信息

本文旨在介绍常克教授治疗小儿肺系疾病的经验。常克教授认为“肺气郁闭”是小儿肺系疾病的常见病机,病邪在少阳经脉,与肺、脾、肝三脏关系密切,与小儿生理病理特点相关。治疗当以“开郁顺气”为总原则,促使人体气机运行快速恢复正常,教授临床上还注重辨病与辨证相结合,常用自拟柴府汤加减,调气开郁,祛火通腑,复肺脾肝之气机,临床反应良好。

关键词：开郁顺气肺系疾病儿科医家经验

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