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Genomics, Proteomics & Bioinformatics 2022年第3期20卷 524-535页

作者： qichao lian Yamao Chen Fang Chang Ying Fu Ji Qi State Key Laboratory of Genetic Engineering Institute of Plant BiologySchool of Life SciencesFudan UniversityShanghai 200433China

Accurately identifying DNA polymorphisms can bridge the gap between phenotypes and genotypes and is essential for molecular marker assisted genetic studies.Genome complexities,including large-scale structural variations,bring great challenges to bioinformatic analysis for obtaining high-confidence genomic variants,as sequence differences between non-allelic loci of two or more genomes can be misinterpreted as polymorphisms.It is important to correctly filter out artificial variants to avoid false genotyping or estimation of allele frequencies.Here,we present an efficient and effective framework,inGAP-family,to discover,filter,and visualize DNA polymorphisms and structural variants(SVs)from alignment of short reads.Applying this method to polymorphism detection on real datasets shows that elimination of artificial variants greatly facilitates the precise identification of meiotic recombination points as well as causal mutations in mutant genomes or quantitative trait loci.In addition,inGAP-family provides a user-friendly graphical interface for detecting polymorphisms and SVs,further evaluating predicted variants and identifying mutations related to genotypes.It is accessible at https://***/projects/ingap-family/.

关键词： inGAP-family Genomic variation Structural variation Meiotic analysis Genetic mapping Causal mutation

Mutation of DELAYED GREENING1 impairs chloroplast RNA editing at elevated ambient temperature in Arabidopsis

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Journal of Genetics and Genomics 2020年第4期47卷 201-212页

作者： Jingliang Sun Yingying Tian qichao lian Jian-Xiang Liu State Key Laboratory of Genetic Engineering School of Life SciencesFudan UniversityShanghai200433China State Key Laboratory of Plant Physiology and Biochemistry College of Life SciencesZhejiang UniversityHangzhou310027China

Chloroplasts are important for plant growth and development.RNA editing in chloroplast converts cytidines(Cs)to uridine s(Us)at specific transcript positions and provides a correction mechanism to restore conserved codons or creates start or stop codons.However,the underlined molecular mechanism is not yet fully unders tood.In the present study,we identi fied a thermo-sensi tive mutantin leaf color 1(tst1)and found that TSL1 is allelic to DELAYED GREENING 1(DG1).The mis sense mutation of DG1 in tsl1 mutant confers a high temperature sensitivity and impaired chloroplast development at an elevated ambient temperature in Arabidopsis.Subsequent analysis showed that chloroplast RNA editing at seve ral sites including accD-2568,ndhD-2,and petL-5 is impaired in tsl1 mutant plants grown at an elevated temperature.DG1 interacts with MORF2 and other proteins such as DYW1 and DYW2 involved in chloroplast RNA editing.In vitro RNA electrophoretic mobility shift assay demonstrated that DG1 binds to RNA targets such as accD,ndhD,and petL.Thus,our results revealed that DG1 is important for maintaining chloroplast mRNA editing in Arabidopsis.

关键词： Chloroplast development mRNA editing Warm temperature

Changing Gly311 to an acidic amino acid in the MATE family protein DTX6 enhances Arabidopsis resistance to the dihydropyridine herbicides

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Molecular Plant 2021年第12期14卷 2115-2125页

作者： Zeyu Lv Mingming Zhao Wenjing Wang Qi Wang Mengqi Huang Chaoqun Li qichao lian Jinqiu Xia Ji Qi Chengbin Xiang Huiru Tang Xiaochun Ge State Key Laboratory of Genetic Engineering Department of Biochemistry and BiophysicsSchool of Life SciencesFudan UniversityShanghai 200438China School of Life Sciences and Division of Molecular&Cell Biophysics Hefei National Science Center for Physical Sciences at the MicroscaleUniversity of Science and Technology of ChinaHefeiAnhui Province 230027China

In modern agriculture,frequent application of herbicides may induce the evolution of resistance in plants,but the mechanisms underlying herbicide resistance remain largely unexplored.Here,we report the char-acterization of rtp 1(resistant to paraquat 1),an Arabidopsis mutant showing strong resistance to the widely used herbicides paraquat and diquat.The rtp1 mutant is semi-dominant and carries a point mutation in the gene encoding the multidrug and toxic compound extrusion family protein DTX6,leading to the change of glycine to glutamic acid at residue 311(G311E).The wild-type DTX6 with glycine 311 conferred weak para-quat and diquat resistance when overexpressed,while mutation of glycine 311 to a negatively charged amino acid(G311E or G311D)markedly increased the paraquat and diquat resistance of plants,whereas mutation to a positively charged amino acid(G311R or G311K)compromised the resistance,suggesting that the charge property of residue 311 of DTX6 is critical for the paraquat and diquat resistance of Arabi-dopsis plants.DTX6 is localized in the endomembrane trafficking system and may undergo the endosomal sorting to localize to the vacuole and plasma membrane.Treatment with the V-ATPase inhibitor ConA reduced the paraquat resistance of the rtp1 mutant.Paraquat release and uptake assays demonstrated that DTX6 is involved in both exocytosis and vacuolar sequestration of paraquat.DTX6 and DTX5 show functional redundancy as the dtx5 dtx6 double mutant but not the dtx6 single mutant plants were more sen-sitive to paraquat and diquat than the wild-type plants.Collectively,our work reveals a potential mecha-nism for the evolution of herbicide resistance in weeds and provides a promising gene for the manipulation of plant herbicide resistance.

关键词： paraquat diquat point mutation DTX6 gene function multidrug and toxic compound extrusion

Modulation of evening complex activity enables north-to-south adaptation of soybean

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Science China(Life Sciences) 2021年第2期64卷 179-195页

作者： Xiaolong Fang Yapeng Han Mengshi Liu Jiacan Jiang Xiang Li qichao lian Xianrong Xie Yian Huang Qibin Ma Hai Nian Ji Qi Cunyi Yang Yingxiang Wang State Key Laboratory of Genetic Engineering and Institute of Genetics Institute of Plant BiologySchool of Life SciencesFudan UniversityShanghai 200438China Guangdong Provincial Key Laboratory of Plant Molecular Breeding Guangdong Sub-center of National Center for Soybean ImprovementCollege of AgricultureSouth China Agricultural UniversityGuangzhou 510642China The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources South China Agricultural UniversityGuangzhou 510642China

Soybean,a typical short-day crop,is sensitive to photoperiod,which is a major limiting factor defining its north-to-south cultivation range.The long-juvenile(LJ)trait is controlled primarily by the J locus which has been used for decades by soybean breeders to delay flowering and improve grain yield in tropical regions.The J gene encodes an ortholog of the Arabidopsis Evening Complex(EC)component EARLY FLOWERING 3(ELF3).To identify modifiers of J,we conducted a forward genetic screen and isolated a mutant(eoj57)that in combination with j has longer flowering delay compared with j single mutant plants.Map-based cloning and genome re-sequencing identified eoj57(designated as GmLUX2)as an ortholog of the Arabidopsis EC component LUX ARRHYTHMO(LUX).To validate that GmLUX2 is a modifier of J,we used trans-complementation and identified a natural variant allele with a similar phenotype.We also show that GmLUX2 physically interacts with GmELF3a/b and binds DNA,whereas the mutant and natural variant are attenuated in both activities.Transcriptome analysis shows that the GmLUX2-GmELF3a complex co-regulates the expression of several circadian clock-associated genes and directly represses E1 expression.These results provide mechanistic insight into how GmLUX2-GmELF3 controls flowering time via synergistic regulation of gene expression.These novel insights expand our understanding of the regulation of the EC complex,and facilitate the development of soybean varieties adapted for growth at lower latitudes.

关键词： soybean flowering time circadian clock Evening Complex geographic adaptation

Environmental selection and evolutionary process jointly shape genomic and functional profiles of mangrove rhizosphere microbiomes

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mLife 2023年第3期2卷 253-266页

作者： Xiaoli Yu qichao Tu Jihua Liu Yisheng Peng Cheng Wang Fanshu Xiao Yingli lian Xueqin Yang Ruiwen Hu Huang Yu Lu Qian Daoming Wu Ziying He Longfei Shu Qiang He Yun Tian Faming Wang Shanquan Wang Bo Wu Zhijian Huang Jianguo He Qingyun Yan Zhili He State Key Laboratory for Biocontrol Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)School of Environmental Science and EngineeringEnvironmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina Institute of Marine Science and Technology Shandong UniversityQingdaoChina College of Forestry&Landscape Architecture South China Agricultural UniversityGuangzhouChina Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai) School of Marine ScienceSun Yat‐sen UniversityGuangzhouChina Department of Civil and Environmental Engineering The University of TennesseeKnoxvilleTennesseeUSA Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems School of Life SciencesXiamen UniversityXiamenChina Xiaoliang Research Station for Tropical Coastal Ecosystems and Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems South China Botanical GardenChinese Academy of SciencesGuangzhouChina School of Life Sciences Sun Yat‐sen UniversityGuangzhouChina

Mangrove reforestation with introduced species has been an important strategy to restore mangrove ecosystem functioning.However,how such activities affect microbially driven methane(CH4),nitrogen(N),and sulfur(S)cycling of rhizosphere microbiomes remains unclear.To understand the effect of environmental selection and the evolutionary process on microbially driven biogeochemical cycles in native and introduced mangrove rhizospheres,we analyzed key genomic and functional profiles of rhizosphere microbiomes from native and introduced mangrove species by metagenome sequencing technologies.Compared with the native mangrove(Kandelia obovata,KO),the introduced mangrove(Sonneratia apetala,SA)rhizosphere microbiome had significantly(p<0.05)higher average genome size(AGS)(5.8 vs.5.5 Mb),average 16S ribosomal RNA gene copy number(3.5 vs.3.1),relative abundances of mobile genetic elements,and functional diversity in terms of the Shannon index(7.88 vs.7.84)but lower functional potentials involved in CH4 cycling(e.g.,mcrABCDG and pmoABC),N2 fixation(nifHDK),and inorganic S cycling(dsrAB,dsrC,dsrMKJOP,soxB,sqr,and fccAB).Similar results were also observed from the recovered Proteobacterial metagenome-assembled genomes with a higher AGS and distinct functions in the introduced mangrove rhizosphere.Additionally,salinity and ammonium were identified as the main environmental drivers of functional profiles of mangrove rhizosphere microbiomes through deterministic processes.This study advances our understanding of microbially mediated biogeochemical cycling of CH_(4),N,and S in the mangrove rhizosphere and provides novel insights into the influence of environmental selection and evolutionary processes on ecosystem functions,which has important implications for future mangrove reforestation.

关键词： average genome size functional potential mangrove rhizosphere metagenome metagenome-assembled genome

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区块链技术及其潜在的军事价值

国防科技 2016年第2期37卷 30-34页

作者：廉蔺朱启超赵炤国防科技大学国家安全与军事战略研究中心湖南长沙410073

区块链技术是对等网络上的一次重大创新,使各网络节点在没有第三方权威认证的情况下达成可信的共识,并可以对形成的共识进行只读、分布式记录。阐释了区块、区块链及其技术原理,提出了区块链技术的基础应用、升级应用和扩展应用三个层级... 详细信息

区块链技术是对等网络上的一次重大创新,使各网络节点在没有第三方权威认证的情况下达成可信的共识,并可以对形成的共识进行只读、分布式记录。阐释了区块、区块链及其技术原理,提出了区块链技术的基础应用、升级应用和扩展应用三个层级,分析了该技术在情报工作绩效激励、武器装备全寿命管理和军用物流等军事领域中的潜在价值,未来在军事应用中可能面临的一些难题。

关键词：区块链对等网络(P2P) 军事应用

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苜蓿皂苷研究进展

河南农业科学 2015年第7期44卷 11-16页

作者：陈燕绘周岩陈亚东郝薇薇魏琦超连杰白红霞河南科技学院生命科技学院/现代生物育种河南省协同创新中心河南新乡453003 河南省华隆生物技术有限公司河南新乡453003

苜蓿是当今世界分布最广泛的栽培牧草,其富含皂苷、叶蛋白、多糖和类黄酮等多种生物活性成分,在生物制药及畜牧业生产中有着广泛的应用,具有重要的研究价值。其中皂苷是苜蓿中重要的生物及药理活性物质,也是苜蓿的主要次生代谢产物之一... 详细信息

苜蓿是当今世界分布最广泛的栽培牧草,其富含皂苷、叶蛋白、多糖和类黄酮等多种生物活性成分,在生物制药及畜牧业生产中有着广泛的应用,具有重要的研究价值。其中皂苷是苜蓿中重要的生物及药理活性物质,也是苜蓿的主要次生代谢产物之一,具有抑菌、抗氧化、降低胆固醇以及调节脂类代谢等多种功能。介绍了不同地区不同苜蓿品种植株在各部位和不同生长期皂苷含量的变化情况及现阶段苜蓿皂苷的主要提取技术,并对其生物学功能和应用的研究进展作了综述,为苜蓿皂苷的进一步研究、开发和利用提供参考。

关键词：苜蓿皂苷提取技术生物学功能应用

“愚民”与“不可使知”之间——论清末民初学人对“民可使由之”章的解释

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开放时代 2020年第4期 114-124,M0006页

作者：练亚坤中山大学哲学系

《论语·泰伯》篇中的"民可使由之"章在清末民初引起了很大的争议,争议的焦点主要集中在愚民的问题上。有关此章是否愚民的讨论在戊戌变法之前就已经出现,并在20世纪初吸引了不少学者的注意,康有为、梁启超等人都试图为此章进行辩护。然... 详细信息

《论语·泰伯》篇中的"民可使由之"章在清末民初引起了很大的争议,争议的焦点主要集中在愚民的问题上。有关此章是否愚民的讨论在戊戌变法之前就已经出现,并在20世纪初吸引了不少学者的注意,康有为、梁启超等人都试图为此章进行辩护。然而,这些辩护并未止息这场论争,相反,从清末至民初,围绕此章的争议已经延伸到孔子以及儒家是否愚民的问题。而学界较少关注的是,这场论争还有另外一个侧面,即由"不可使知"引出的儒家是否为宗教的问题。"愚民"和"非宗教"是近代儒家面临的两大质疑,而同时出现在围绕"民可使由之"章的论争中,透过这场论争,或许有助于我们理解近代儒家在"教化"与"宗教"问题上的双重困境。

关键词：愚民开民智宗教不可使知

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20世纪我国早期画论中的“写实”概念

云南师范大学学报（哲学社会科学版） 2017年第6期49卷 143-150页

作者：刘连杰云南师范大学美术学院云南昆明650500

"写实主义"通常被作为"现实主义"的初级阶段,附属于"现实主义"并遵循西方科学方法的绘画技法。但实际上,在20世纪早期画论中,它是一个独立的概念,其内涵从梁启超、王国维的绘画风格,到康有为的古今之异,再到陈独秀、蔡元培、林风眠等人... 详细信息

"写实主义"通常被作为"现实主义"的初级阶段,附属于"现实主义"并遵循西方科学方法的绘画技法。但实际上,在20世纪早期画论中,它是一个独立的概念,其内涵从梁启超、王国维的绘画风格,到康有为的古今之异,再到陈独秀、蔡元培、林风眠等人的中西之别,有一个逐渐演变的过程。即使作为追求"逼真"科学写实技法,对于中国传统绘画而言,也是一种训练出来的新的视觉方式,其背后隐藏着某种特定的民族趣味和文化传统,并不具有普遍性。认真梳理"写实"概念在20世纪早期文献中的确切用法,可以为中国画的未来发展提供更多的思考方向。

关键词：写实绘画风格古今之异中西之别科学方法

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戊戌变法前光绪帝所做的政策准备

吕梁学院学报 2011年第6期1卷 37-40页

作者：王玉莲大同口泉中学山西大同037000

戊戌变法前,光绪帝受康梁维新思想的影响,在政治、经济、文化教育等方面做了一系列的政策准备,如驱逐异己,提拔帝党,御用新人;推行经济改革,积极发展资本主义;发展文化教育,积极培养近代人才等等,为戊戌变法的展开奠定了坚实的基础。

关键词：戊戌变法前光绪帝反思政策准备