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Unveiling the distinctive traits of functional rye centromeres:minisatellites,retrotransposons,and R-loop formation

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Science China(Life Sciences) 2024年第9期67卷 1989-2002页

作者： Chang Liu Shulan Fu Congyang Yi Yang Liu Yuhong Huang xianrui guo Kaibiao Zhang Qian Liu James A.Birchler Fangpu Han State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Key Laboratory for Plant Genetics and Breeding Sichuan Agricultural UniversityChengdu 611130China Division of Biological Science University of MissouriColumbia 65211-7400USA

Centromeres play a vital role in cellular division by facilitating kinetochore assembly and spindle *** their conserved functionality,centromeric DNA sequences exhibit rapid evolution,presenting diverse sizes and compositions across *** functional significance of rye centromeric DNA sequences,particularly in centromere identity,remains *** this study,we comprehensively characterized the sequence composition and organization of rye *** findings revealed that these centromeres are primarily composed of long terminal repeat retrotransposons(LTR-RTs)and interspersed *** systematically classified LTR-RTs into five categories,highlighting the prevalence of younger CRS1,CRS2,and CRS3 of CRSs(centromeric retrotransposons of Secale cereale)were primarily located in the core centromeres and exhibited a higher association with CENH3 *** minisatellites,mainly derived from retrotransposons,along with CRSs,played a pivotal role in establishing functional centromeres in ***,we observed the formation of R-loops at specific regions of CRS1,CRS2,and CRS3,with both rye pericentromeres and centromeres exhibiting enrichment in ***,these R-loops selectively formed at binding regions of the CENH3 nucleosome in rye centromeres,suggesting a potential role in mediating the precise loading of CENH3 to centromeres and contributing to centromere *** work provides insights into the DNA sequence composition,distribution,and potential function of R-loops in rye *** knowledge contributes valuable information to understanding the genetics and epigenetics of rye centromeres,offering implications for the development of synthetic centromeres in future plant modifications and beyond.

关键词： centromere LTR-RTs minisatellite rye R-loop

Establishment and characterization of a complete set of Triticum durum-Thinopyrum elongatum monosomic addition lines with resistance to Fusarium head blight in wheat

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Journal of Genetics and Genomics 2019年第11期46卷 547-549页

作者： Jing Wang Qinghua Shi xianrui guo Fangpu Han Center for Agricultural Resources Research Institute of Genetics and Developmental BiologyChinese Academy of SciencesShijiazhuang 050022China State Kay Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

Durum wheat(Triticum durum Desf.,2n=28,AABB),which is mainly used to make pasta,is the second cultivated wheat variety ***,the durum wheat production is severely affected by a number of diseases,such as Fusarium head blight(FHB)and stem rust(Klindworth et al.,2017;Zhao et al.,2018).Thinopyrum elongatum(2n=4x=28),a close relative of wheat.

关键词： Establishment characterization Thinopyrum

Site-specific transfer of chromosomal segments and genes in wheat engineered chromosomes

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Journal of Genetics and Genomics 2017年第11期44卷 531-539页

作者： Jing Yuan Qinghua Shi Xiang guo Yalin Liu Handong Su xianrui guo Zhenling Lv Fangpu Han State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

Recently, engineered minichromosomes have been produced using a telomere-mediated truncation technique in some plants. However, the study on transferring genes to minichromosomes is very ***, telomere-mediated truncation was successfully performed in common wheat（Triticum aestivum）to generate stable truncated chromosomes accompanied by a relatively high frequency of chromosomal rearrangements. After the cross between transgenic parents, a promoter-less DsRed gene in a chromosome from one parent was transferred to another chromosome from the other parent at the site behind a maize ubiquitin promoter via the Cre/lox system. DsRed transcripts and red fluorescent proteins were detected in the recombinant plants. In one such seedling, transgenic signals were detected at the centric terminus of chromosome 4D and the distal terminus of chromosome 3A. Clear translocations could be detected at the transgenic loci of these two chromosomes. Intriguingly, signals of centric-specific sequences were co-localized with the translocated D-group chromosomal segment in the terminal region of chromosome 3A. Our results indicate that the Cre/lox system induces the gene swapping to the target chromosome and non-homologous chromosomal recombination simultaneously. These approaches could offer a platform to transfer large DNA fragments or even terminal chromosomal segments to other chromosomes of the natural genome.

关键词： Telomere-mediated truncation Engineered chromosome Crellox system Chromosomal recombination Chromosome translocation Triticum aestivum

Development and genetic analysis of wheat double substitution lines carrying Hordeum vulgare 2H and Thinopyrum intermedium 2Ai#2 chromosomes

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The Crop Journal 2019年第2期7卷 163-175页

作者： Jing Wang Chang Liu xianrui guo Ke Wang Lipu Du Zhishan Lin Xingguo Ye National Key Facility of Crop Gene Resources and Genetic Improvement Institute of Crop Sciences Chinese Academy of Agricultural Sciences State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental Biology Chinese Academy of Sciences

Thinopyrum intermedium and barley are two close relatives of wheat and carry many genes that are potentially valuable for the improvement of various wheat traits. In this study we created wheat double substitution lines by hybridizing different wheat–Th. intermedium and wheat–barley disomic alien substitution lines, with the aim of using genes in Th. intermedium and barley for wheat breeding and investigating the genetic behavior of alien chromosomes and their wheat homoeologs. As expected, we obtained two types of wheat double substitution lines,2D2Ai#2(2B)2H( A) and 2A2 Ai#2(2B)2H(2D), in which different group 2 wheat chromosomes were replaced by barley chromosome 2 H and Th. intermedium chromosome 2Ai#2. The new materials were characterized using molecular markers, genomic in situ hybridization(GISH), and fluorescent in situ hybridization(FISH). GISH and FISH experiments revealed that the double substitution lines harbor 42 chromosomes including 38 wheat chromosomes, a pair of barley chromosomes, and a pair of Th. intermedium chromosomes. Analysis using specific DNA markers showed that two pairs of wheat homoeologous group 2 chromosomes in the new lines were substituted by a pair of 2H and a pair of 2Ai#2 chromosomes. Chromosome 2H showed a higher transmission rate than 2Ai#2, and both chromosomes were preferentially transmitted between generations via female gametes. Evaluation of botanic and agronomic traits demonstrated that,compared with their parents, the new lines showed similar growth habits and plant type but differences in plant height, flowering date, and self-fertility. Cytological observations using different probes suggested that the double substitution lines showed nearly normal genetic behavior before and during meiosis. The novel substitution lines can potentially be used in wheat meiosis research and breeding programs.

关键词： Wheat Double substitution lines Molecular markers Transmission rate of alien chromosomes Genomic in situ hybridization

Development and genetic analysis of wheat double substitution lines carrying Hordeum vulgare 2H and Thinopyrum intermedium 2Ai#2 chromosomes

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基于Random Forest和UHPLC-QTOF-MS^(E)对不同来源龟甲基原的鉴定

The Crop Journal 2019年第2期

作者： Jing Wang Chang Liu xianrui guo Ke Wang Lipu Du Zhishan Lin Xingguo Ye National Key Facility of Crop Gene Resources and Genetic Improvement，Institute of Crop Sciences，Chinese Academy of Agricultural Sciences State Key Laboratory of Plant Cell and Chromosome Engineering，Institute of Genetics and Developmental Biology，Chinese Academy of Sciences

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中国药事 2024年第9期38卷 1008-1019页

作者：王献瑞张佳婷张宇李明华郭晓晗荆文光程显隆魏锋中国食品药品检定研究院药品监管科学全国重点实验室北京102629

目的:基于超高效液相色谱串联四极杆飞行时间质谱(UHPLC-QTOF-MS^(E))分析并经数字量化处理,结合随机森林(Random Forest,RF)算法构建数据辨识模型,以实现中华草龟、巴西龟、台湾龟、鳄鱼龟、鳖甲基原的数字化鉴定。方法:经样品预处理后... 详细信息

目的:基于超高效液相色谱串联四极杆飞行时间质谱(UHPLC-QTOF-MS^(E))分析并经数字量化处理,结合随机森林(Random Forest,RF)算法构建数据辨识模型,以实现中华草龟、巴西龟、台湾龟、鳄鱼龟、鳖甲基原的数字化鉴定。方法:经样品预处理后,对不同来源、不同批次的龟甲进行UPLC-QTOF-MS^(E)分析,并以混合样品为基准进行峰位校正、提取并经量化处理,获取反映多肽离子信息的精确质量数-保留时间数据对(Exact Mass Retention Time,EMRT)。然后基于信息增益率的特征筛选获取重要多肽离子信息,结合随机森林(RF)算法进行数据建模,同时基于内部交叉验证中的准确率(Acc)、精确率(P)、曲线下面积(AUC)等参数进行模型评价。最后基于最优模型进行龟甲基原的鉴定验证分析。结果:基于信息增益率的特征筛选,得到71个特征多肽信息,建立的RF模型具有优秀的辨识效果,准确率、精确率以及AUC均大于0.950且外部鉴定验证的正确率为100.0%。结论:基于UHPLC-QTOF-MS^(E)分析,并结合RF算法能够高效准确地实现不同来源龟甲基原的数字化鉴定,可为龟甲的质量控制及基原考证提供参考和帮助。

关键词：龟甲基原鉴定机器学习随机森林超高效液相色谱串联四极杆飞行时间质谱

Fragmentation pathways of chiral pyrrole derivatives using electrospray ionization ion trap and electrospray ionization quadrupole time-of-flight mass spectrometry

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Fragmentation pathways of chiral pyrrole derivatives using e...

2012长三角药物化学研讨会

作者： xianrui Liang Zili guo Chuanming Yu Key Laboratory for Green Pharmaceutical Technologies and Related Equipment of Ministry of Education College of Pharmaceutical SciencesZhejiang University of Technology

A study on the fragmentation pathways of chiral pyrrole derivatives becomes more and more *** trap mass spectrometry(ITMS) and the hybrid quadrupole-time of flight-mass spectrometry (QTOFMS) are thought be a suitable choice to discuss the fragmentation *** analysis was carried out using electrospray ionization(ESI) in positive mode in conjunction with a LCQ Ion-trap ***-resolution quadrupole-time of flight-mass spectrometry(QTOFMS) was employed as a

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一类强非线性双曲方程组解的存在性和唯一性

吉林大学自然科学学报 1994年第2期 5-10页

作者：吕显瑞郭庆尧吉林大学数学系

本文研究了一类强非线性双曲方程组ｕ＿（ｔｔ）－ｕ＿（ｘｘ）＝ｆ（ｕ，ｖ），ｖ＿（ｔｔ）－ｖ＿（ｘｘ）＝ｇ（ｕ，ｖ）解的存在和唯一性，还证明了解的Ｈｏｌｄｅｒ连续性。

关键词：存在性唯一性双曲型方程组

基于超高效液相色谱-四极杆-飞行时间质谱法的兴安升麻甲醇提取物化学成分分析

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食品科学 2019年第16期40卷 169-176页

作者：吕弘王晓明刘小梅张帆王献瑞郭亚卿潘桂湘天津中医药大学天津市现代中药重点实验室-省部共建国家重点实验室培育基地天津301617 天津中医药大学第二附属医院天津300250

目的:鉴定兴安升麻甲醇提取物中的化学成分。方法:采用超高效液相色谱仪分离兴安升麻甲醇提取物化学成分,四极杆-飞行时间质谱采集其一级和二级高分辨质谱数据,并用Masshunter软件对原始质谱数据进行分子特征提取,得到可能与兴安升麻相... 详细信息

目的:鉴定兴安升麻甲醇提取物中的化学成分。方法:采用超高效液相色谱仪分离兴安升麻甲醇提取物化学成分,四极杆-飞行时间质谱采集其一级和二级高分辨质谱数据,并用Masshunter软件对原始质谱数据进行分子特征提取,得到可能与兴安升麻相关的候选成分,根据化合物质谱裂解规律及部分标准品确证,鉴定化合物的结构。结果:共鉴定兴安升麻甲醇提取物中的38个成分,包括苯丙素类、皂苷类,色原酮类、含氮化合物4类成分。结论:超高效液相色谱-四极杆-飞行时间质谱可应用于升麻化学成分的鉴定。

关键词：兴安升麻超高效液相色谱-四极杆-飞行时间质谱化学成分定性分析