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Gap-free genome assembly and CYP450 gene family analysis reveal the biosynthesis of anthocyanins in Scutellaria baicalensis

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Horticulture Research 2023年第12期10卷 217-231页

作者： Tianlin Pei Sanming Zhu Weizhi Liao Yumin Fang Jie Liu Yu Kong mengxiao yan Mengying Cui Qing Zhao Shanghai Key Laboratory of Plant Functional Genomics and Resources CAS Center for Excellence in Molecular Plant Sciences Chenshan Plant Science Research CenterShanghai Chenshan Botanical GardenShanghai201602China State Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai200032China National Key Laboratory of Wheat Improvement College of Life SciencesShandong Agricultural UniversityTaian271018China Shanghai Key Laboratory of Plant Molecular Sciences College of Life SciencesShanghai Normal UniversityShanghai200234China

Scutellaria baicalensis Georgi,a member of the Lamiaceae family,is a widely utilized medicinal *** flavones extracted from *** contribute to numerous health benefits,including anti-inflammatory,antiviral,and anti-tumor ***,the incomplete genome assembly hinders biological studies on *** study presents the first telomere-to-telomere(T2T)gap-free genome assembly of *** through the integration of Pacbio HiFi,Nanopore ultra-long and Hi-C technologies.A total of 384.59 Mb of genome size with a contig N50 of 42.44 Mb was obtained,and all sequences were anchored into nine pseudochromosomes without any gap or *** addition,we analysed the major cyanidin-and delphinidin-based anthocyanins involved in the determination of blue-purple flower using a widely-targeted metabolome *** on the genome-wide identification of Cytochrome P450(CYP450)gene family,three genes(SbFBH1,2,and 5)encoding flavonoid 3′-hydroxylases(F3′Hs)and one gene(SbFBH7)encoding flavonoid 3′5′-hydroxylase(F3′5′H)were found to hydroxylate the B-ring of *** studies enrich the genomic information available for the Lamiaceae family and provide a toolkit for discovering CYP450 genes involved in the flavonoid decoration.

关键词： CYP450 incomplete utilized

Exploring and exploiting genetics and genomicsfor sweetpotato improvement: Status andperspectives

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Plant Communications 2022年第5期3卷 38-62页

作者： mengxiao yan Haozhen Nie Yunze Wang Xinyi Wang Robert Jarret Jiamin Zhao Hongxia Wang Jun yang Shanghai Key Laboratory of Plant Functional Genomics and Resources Shanghai Chenshan Botanical GardenShanghai 201602China College of Life Sciences Shanghai Normal UniversityShanghai 200234China USDA-ARS/PGRU GriffinGA 30223USA National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai 200032China

Sweetpotato(Ipomoea batatas(L.)Lam.)is one of the most important root crops cultivated *** of its adaptability,high yield potential,and nutritional value,sweetpotato has become an important food crop,particularly in developing *** ensure adequate crop yields to meet increasing demand,it is essential to enhance the tolerance of sweetpotato to environmental stresses and other yield-limiting *** highly heterozygous hexaploid genome of *** complicates genetic studies and limits improvement of sweetpotato through traditional ***,application of next-generation sequencing and high-throughput genotyping and phenotyping technologies to sweetpotato genetics and genomics research has provided new tools and resources for crop *** this review,we discuss the genomics resources that are available for sweetpotato,including the current reference genome,databases,and available bioinformatics *** systematically review the current state of knowledge on the polyploid genetics of sweetpotato,including studies of its origin and germplasm diversity and the associated mapping of important agricultural *** then outline the conventional and molecular breeding approaches that have been applied to ***,we discuss future goals for genetic studies of sweetpotato and crop improvement via breeding in combination with state-of-the-art multi-omics approaches such as genomic selection and gene *** approaches will advance and accelerate genetic improvement of this important root crop and facilitate its sustainable global production.

关键词： sweetpotato polyploid genetics genomics breeding

The Reference Genome Sequence of Scutellaria baicalensis Provides Insights into the Evolution of Wogonin Biosynthesis

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Molecular Plant 2019年第7期12卷 935-950页

作者： Qing Zhao Jun yang Meng-Ying Cui Jie Liu Yumin Fang mengxiao yan Wenqing Qiu Huiwen Shang Zhicheng Xu Reheman Yidiresi Jing-Ke Weng Tomas Pluskal Marielle Vigouroux Burkhard Steuernagel Yukun Wei Lei yang Yonghong Hu Xiao-Ya Chen Cathie Martin Shanghai Key Laboratory of Plant Functional Genomics and Resources Shanghai Chenshan Botanical Garden Shanghai Chenshan Plant Science Research Center Chinese Academy of Sciences Shanghai China State Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant Sciences Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences Shanghai China Key Laboratory of Metabolism and Molecular Medicine Department of Biochemistry and Molecular Biology School of Basic Medical Sciences Fudan University Shanghai China Novogene Bioinformatics Institute Beijing China Whitehead Institute for Biomedical Research 455 Main Street Cambridge MA 02142 USA Department of Biology Massachusetts Institute of Technology Cambridge MA 02139 USA John Innes Centre Norwich NR4 7UH UK

Scutellaria baicalensis Georgi is important in Chinese traditional medicine where preparations of dried roots,"Huang Qin," are used for liver and lung complaints and as complementary cancer treatments. We report a high-quality reference genome sequence for S. baicalensis where 93% of the 408.14-Mb genome has been assembled into nine pseudochromosomes with a super-N50 of 33.2 Mb. Comparison of this sequence with those of closely related species in the order Lamiales, sesamum indicum and Salvia splendens,revealed that a specialized metabolic pathway for the synthesis of 4'-deoxyflavone bioactives evolved in the genus Scu-tellaria. We found that the gene encoding a specific cinnamate coenzyme A ligase likely obtained its newfunc- tion following recent mutations, and that four genes encoding enzymes in the 4'-deoxyflavone pathway are present as tandem repeats in the genome of S. baicalensis. Further analyses revealed that gene duplications, segmental duplication, gene amplification, and point mutations coupled to gene neo- and subfunctionaliza-tions were involved in the evolution of 4'-deoxyflavone synthesis in the genus Scutellaria. Our study not only provides significant insight into the evolution of specific flavone biosynthetic pathways in the mint family, Lamiaceae, but also will facilitate the development of tools for enhancing bioactive productivity by metabolic engineering in microbes or by molecular breeding in plants. The reference genome of S. baicalensis is also useful for improving the genome assemblies for other members of the mint family and offers an important foundation for decoding the synthetic pathways of bioactive compounds in medicinal plants.

关键词： genome skullcap 4’-deoxyflavone traditional Chinese medicine Huang Qin:evolution specialized metabolism

Haplotype-based phylogenetic analysis and population genomics uncover the origin and domestication of sweetpotato

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Molecular Plant 2024年第2期17卷 277-296页

作者： mengxiao yan Ming Li Yunze Wang Xinyi Wang M-Hossein Moeinzadeh Dora G.Quispe-Huamanquispe Weijuan Fan Yijie Fang Yuqin Wang Haozhen Nie Zhangying Wang Aiko Tanaka Bettina Heider Jan F.Kreuze Godelieve Gheysen Hongxia Wang Martin Vingron Ralph Bock Jun yang Shanghai Key Laboratory of Plant Functional Genomics and Resources Shanghai Chenshan Botanical GardenShanghai 201602China College of Life Sciences Chongqing Normal UniversityChongqing 401331China Biotechnology and Nuclear Technology Research Institute Sichuan Academy of Agricultural SciencesChengdu 610061China College of Life Sciences Shanghai Normal UniversityShanghai 200234China Department of Computational Molecular Biology Max Planck Institute for Molecular GeneticsIhnestraBe 63-7314195 BerlinGermany Department of Biotechnology Ghent University9000 GhentBelgium Guangdong Provincial Key Laboratory of Crops Genetics and Improvement Crop Research InstituteGuangdong Academy of Agricultural SciencesGuangzhou 510640China Graduate School of Bioagricultural Sciences Nagoya UniversityChikusaNagoya 464-8601Japan international Potato Center(CIP) LimaPeru CAS Center for Excellence of Molecular Plant Sciences Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai 200233China Max-Planck-Institut fur Molekulare Pflanzenphysiologie Am Muhlenberg 114476 Potsdam-GolmGermany

The hexaploid sweetpotato(lpomoea batatas)is one of the most important root crops ***,its genetic origin remains controversial,and its domestication history remains *** this study,we used a range of genetic evidence and a newly developed haplotype-based phylogenetic analysis to identify two probable progenitors of *** diploid progenitor was likely closely related to lpomoea ae-quatoriensis and contributed the B,subgenome,IbT-DNA2,and the lineage 1 type of chloroplast genome to *** tetraploid progenitor of sweetpotato was most likely *** 4x,which donated the B2 subgenome,IbT-DNA1,and the lineage 2 type of chloroplast *** most likely originated from reciprocal crosses between the diploid and tetraploid progenitors,followed by a subsequent whole-genome *** addition,we detected biased gene exchanges between the subgenomes;the rate of B,to B2 subgenome conversions was nearly three times higher than that of B2 to B subgenome *** analyses revealed that genes involved in storage root formation,maintenance of genome stabil-ity,biotic resistance,sugar transport,and potassium uptake were selected during the speciation and domestication of *** study sheds light on the evolution of sweetpotato and paves the way forimprovementofthiscrop.

关键词： sweetpotato origin gene conversion domestication IbT-DNA HPA

Genome-wide identification of agronomically important genes in outcrossing crops using OutcrossSeq

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Molecular Plant 2021年第4期14卷 556-570页

作者： Mengjiao Chen Weijuan Fan Feiyang Ji Hua Hua Jie Liu mengxiao yan Qingguo Ma Jiongjiong Fan Qin Wang Shufeng Zhang Guiling Liu Zhe Sun Changgeng Tian Fengling Zhao Jianli Zheng Qi Zhang Jiaxin Chen Jie Qiu Xin Wei Ziru Chen Peng Zhang Dong Pei Jun yang Xuehui Huang Shanghai Key Laboratory of Plant Molecular Sciences College of Life SciencesShanghai Normal UniversityShanghai 200234China Shanghai Key Laboratory of Plant Functional Genomics and Resources Shanghai Chenshan Plant Science Research CenterChinese Academy of SciencesShanghai Chenshan Botanical GardenShanghai 201602China State Key Laboratory of Tree Genetics and Breeding Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland AdministrationResearch Institute of ForestryChinese Academy of ForestryBeijing 100091China Tai'an Academy of Agricultural Sciences Tai'an 271000ShandongChina National Genomics Data Center Bio-Med Big Data CenterCAS Key Laboratory of Computational BiologyCAS-MPG Partner Institute for Computational BiologyShanghai Institute of Nutrition and HealthChinese Academy of SciencesShanghai 200031China CAS Center for Excellence of Molecular Plant Sciences Institute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghai 200233China These authors contributed equally to this article.

Many important crops(e.g.,tuber,root,and tree crops)are *** these crops,no inbred lines are available for genetic study and breeding because they are self-incompatible,clonally propagated,or have a long generation time,making the identification of agronomically important genes difficult,particularly in crops with a complex autopolyploid *** this study,we developed a method,OutcrossSeq,for mapping agronomically important loci in outcrossing crops based on whole-genome low-coverage resequencing of a large genetic population,and designed three computation algorithms in OutcrossSeq for different types of outcrossing *** applied OutcrossSeq to a tuberous root crop(sweet potato,autopolyploid),a tree crop(walnut tree,highly heterozygous diploid),and hybrid crops(double-cross populations)to generate high-density genotype maps for the outcrossing populations,which enable precise identification of genomic loci underlying important agronomic *** causative genes at these loci were detected based on functional *** together,our results indicate that OutcrossSeq is a robust and powerful method for identifying agronomically important genes in heterozygous species,including polyploids,in a cost-efficient *** OutcrossSeq software and its instruction manual are available for downloading at ***/tool/***.

关键词： genotyping genetic mapping outcrossing polyploid

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历史教学中的道德评价问题

天津师范大学学报（基础教育版） 2024年第1期25卷 59-63页

作者：张汉林颜孟晓首都师范大学教师教育学院北京100048 首都师范大学教育学院齐鲁师范学院

道德评价是指以道德观念为标准,在历史评价的基础上,对历史人物在公共领域的言行或历史事件进行评价。在历史教学中,道德评价至关重要,这是因为:道德是历史研究的重要范畴;道德评价是历史学的重要传统;培养道德评价能力是历史教育的重... 详细信息

道德评价是指以道德观念为标准,在历史评价的基础上,对历史人物在公共领域的言行或历史事件进行评价。在历史教学中,道德评价至关重要,这是因为:道德是历史研究的重要范畴;道德评价是历史学的重要传统;培养道德评价能力是历史教育的重要使命。研究认为,道德评价的关键在于评价标准的选择,将古人和今人的道德标准结合起来,就形成了四种情况,由此构成了历史教学中的道德评价矩阵。道德评价矩阵属于理想类型,除此之外,还有道德两难困境。经由历史教育,我们要培养道德践行者和道德促进者,落实立德树人根本任务。

关键词：道德评价历史评价道德实践道德经验

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改进的轻量级行人目标检测算法

计量学报 2024年第2期45卷 186-193页

作者：金梅任婷婷张立国闫梦萧沈明浩燕山大学电气工程学院河北秦皇岛066004

针对行人目标数量密集、目标尺度小和目标周围背景光照强弱不一而导致的检测精度低的问题,提出一种基于特征融合的轻量化行人检测算法。以TinyYOLOv4为基础框架,首先,搭建新的主干特征提取网络(CSPDarknet53-S),在原主干网络的基础上加... 详细信息

针对行人目标数量密集、目标尺度小和目标周围背景光照强弱不一而导致的检测精度低的问题,提出一种基于特征融合的轻量化行人检测算法。以TinyYOLOv4为基础框架,首先,搭建新的主干特征提取网络(CSPDarknet53-S),在原主干网络的基础上加入新的特征提取模块(REM)来增强网络提取行人特征的能力。其次,改进特征融合结构,在主干网络提取高低层特征图后,先是在主干网络与特征融合网络间加入特征融合模块(RM-block)来增大感受野;然后引入浅层特征信息保留更多小目标特征,形成新的特征融合网络(IFFM)。最后,通过YOLO Head对融合来的特征图进行处理获得输出结果。实验结果表明,提出的算法在行人数据集(PASCAL VOC2007和VOC2012的person数据)上取得了较高的检测精度以及较好的检测效果。

关键词：目标检测特征融合浅层特征 TinyYOLOv4算法注意力机制

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不同倍性甘薯及近缘材料的SNP鉴定流程

分子植物育种 2024年第20期22卷 6747-6756页

作者：王心怡李明颜梦晓王红霞杨俊上海辰山植物园上海市资源植物功能基因组学重点实验室上海201602 四川省农业科学院生物技术核技术研究所成都610061 中国科学院分子植物科学卓越创新中心植物分子遗传国家重点实验室上海200032

基因组上的SNP变异具有丰富的数量和多态性的特点,SNP鉴定在作物遗传多样性、群体结构关系、育种等方面有重要作用。然而多倍体作物由于倍性高、杂合性高等问题,使得SNP的开发、验证和检测较为困难。甘薯及不同倍性近缘野生种均属于番薯... 详细信息

基因组上的SNP变异具有丰富的数量和多态性的特点,SNP鉴定在作物遗传多样性、群体结构关系、育种等方面有重要作用。然而多倍体作物由于倍性高、杂合性高等问题,使得SNP的开发、验证和检测较为困难。甘薯及不同倍性近缘野生种均属于番薯属,由于甘薯近缘物种倍性变化较大,本研究选取二倍体、四倍体、六倍体的Ipomoea trifida以及五倍体和六倍体的甘薯为材料,采用简化基因组测序技术——RAD-seq进行测序,以栽培甘薯‘泰中6号’基因组序列为参考,通过与参考基因组的比对、排序、PCR标记去重复以及变异检测,建立了一套基于甘薯参考基因组进行不同倍性材料SNP鉴定的分析流程。通过IQ-TREE对SNP标记进行系统发育树构建,结果验证了本流程具有较高的可靠性。本研究开发的数据处理流程,不仅可用于不同倍性野生材料遗传关系的鉴定,还可为甘薯品种的遗传多样性分析和育种的亲本选择以及其他多倍体植物SNP标记开发鉴定提供借鉴和参考。

关键词：甘薯 Ipomoea trifida 多倍体 SNP 简化基因组测序

伴精神病性症状及童年期创伤的重度抑郁发作青少年患者执行功能情况

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四川精神卫生 2023年第3期36卷 202-208页

作者：宋仕琪刘剑波闫梦霄周敏思高铭冯文泰卢建平安徽医科大学深圳精神卫生临床学院广东深圳518000 深圳市精神卫生中心/深圳市康宁医院广东深圳518000

背景有无精神病性症状的重度抑郁发作患者执行功能存在差异,且童年期创伤可能影响重度抑郁发作患者的执行功能,既往研究对象大多为成年抑郁发作患者,缺少对重度抑郁发作青少年患者的相关研究。目的比较有无精神病性症状及童年期创伤的... 详细信息

背景有无精神病性症状的重度抑郁发作患者执行功能存在差异,且童年期创伤可能影响重度抑郁发作患者的执行功能,既往研究对象大多为成年抑郁发作患者,缺少对重度抑郁发作青少年患者的相关研究。目的比较有无精神病性症状及童年期创伤的重度抑郁发作青少年患者执行功能的差异。方法纳入2020年8月-2021年11月在深圳市康宁医院儿少精神科住院的、符合《国际疾病分类(第10版)》(ICD-10)重度抑郁发作诊断标准的青少年患者共112例,同期通过公开宣传招募健康对照组27例。使用剑桥神经心理自动化成套测试(CANTAB)中的运动控制任务(MOT)、空间工作记忆(SWM)、快速视觉信息处理(RVP)三个任务评定患者的执行功能,采用儿童期创伤问卷(CTQ-SF)评定童年期创伤类型。结果与健康对照组相比,重度抑郁发作患者MOT任务平均延迟时更长(Z=-3.407,P=0.001),SWM任务中的组间错误反应总数更多(Z=-3.291,P=0.001)、组内错误反应总数更多(Z=-3.461,P=0.001)、双重错误反应总数更多(Z=-3.218,P=0.001)、错误反应总数更多(Z=-3.312,P=0.001)、策略分数更高(Z=-2.437,P=0.015)以及平均延迟时更长(Z=-2.055,P=0.040),RVP任务中的击中总数更少(Z=-3.196,P=0.001)、漏报总数更多(Z=-3.179,P=0.001)、拒绝总数更少(Z=-2.772,P=0.006)、击中概率更低(Z=-3.187,P=0.001)以及A'分数更低(Z=-3.070,P=0.002)。与不伴精神病性症状的重度抑郁发作青少年患者相比,伴精神病性症状者SWM任务中的双重错误反应总数更少(Z=-2.566,P=0.010)。相较于未经历过情感忽视的重度抑郁发作青少年患者,经历过情感忽视者MOT任务中的平均延迟时更长(Z=-3.183,P=0.001),RVP任务中的击中总数更少(Z=-2.445,P=0.014)、漏报总数更多(Z=-2.467,P=0.014)、击中概率更低(Z=-2.445,P=0.014)、A'分数更低(Z=-2.089,P=0.037)。相较于未经历过情感虐待的重度抑郁发作青少年患者,经历过情感虐待的患者MOT任务中的平均延迟时更长(Z=-2.552,P=0.011)。结论重度抑郁发作青少年患者存在大部分类型的执行功能异常,不伴精神病性症状和伴有童年期创伤的患者执行功能更差。

关键词：青少年重度抑郁发作精神病性症状童年期创伤执行功能