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Improved genome annotation of Brassica oleracea highlights the importance of alternative splicing

Horticultural Plant Journal 2024年第4期10卷 961-970页

作者： yinqing yang Lei Zhang Qi Tang Lingkui Zhang Xing Li Shumin Chen Kang Zhang Ying Li Xilin Hou Feng Cheng State Key Laboratory of Crop Genetics and Germplasm Enhancement College of HorticultureNanjing Agricultural UniversityNanjing 210095China State Key Laboratory of Vegetable Biobreeding Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural AffairsSino-Dutch Joint Laboratory of Horticultural GenomicsBeijing 100081China

Brassica oleracea has been developed into many important crops,including cabbage,kale,cauliflower,broccoli and so *** genome and gene annotation of cabbage(cultivar JZS),a representative morphotype of ***,has been widely used as a common reference in biological *** its genome assembly has been updated twice,the current gene annotation still lacks information on untranslated regions(UTRs)and alternative splicing(AS).Here,we constructed a high-quality gene annotation(JZSv3)using a full-length transcriptome acquired by nanopore sequencing,yielding a total of 59452 genes and 75684 ***,we re-analyzed the previously reported transcriptome data related to the development of different tissues and cold response using JZSv3 as a reference,and found that 3843 out of 11908 differentially expressed genes(DEGs)underwent AS during the development of different tissues and 309 out of 903 cold-related genes underwent AS in response to cold ***,we also identified many AS genes,including BolLHCB5 and BolHSP70,that displayed distinct expression patterns within variant transcripts of the same gene,highlighting the importance of JZSv3 as a pivotal reference for AS ***,JZSv3 provides a valuable resource for exploring gene function,especially for obtaining a deeper understanding of AS regulation mechanisms.

关键词： Brassica oleracea Oxford nanopore technologies Gene annotation Alternative splicing

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Genome Assembly and Population Resequencing Reveal the Geographical Divergence of Shanmei(Rubus corchorifolius)

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Genomics, Proteomics & Bioinformatics 2022年第6期20卷 1106-1118页

作者： yinqing yang Kang Zhang Ya Xiao Lingkui Zhang Yile Huang Xing Li Shumin Chen Yansong Peng Shuhua yang Yongbo Liu Feng Cheng Institute of Vegetables and Flowers Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Horticultural CropsMinistry of Agriculture and Rural AffairsSino-Dutch Joint Laboratory of Horticultural GenomicsBeijing 100081China Biotechnology Research Center Xiangxi Academy of Agricultural SciencesJishou 416000China Lushan Botanical Garden Chinese Academy of SciencesJiujiang 332900China State Environmental Protection Key Laboratory of Regional Eco-process and Function Assessment Chinese Research Academy of Environmental SciencesBeijing 100012China

Rubus corchorifolius(Shanmei or mountain berry,2n=14)is widely distributed in China,and its fruits possess high nutritional and medicinal ***,we reported a highquality chromosome-scale genome assembly of Shanmei,with contig size of 215.69 Mb and 26,696 *** comparison among Rosaceae species showed that Shanmei and Fupenzi(Rubus chingii Hu)were most closely related,followed by blackberry(Rubus occidentalis),and that environmental adaptation-related genes were expanded in the Shanmei *** resequencing of 101 samples of Shanmei collected from four regions in the provinces of Yunnan,Hunan,Jiangxi,and Sichuan in China revealed that among these samples,the Hunan population of Shanmei possessed the highest diversity and represented the more ancestral ***,the Yunnan population underwent strong selection based on the nucleotide diversity,linkage disequilibrium,and historical effective population size ***,genes from candidate genomic regions that showed strong divergence were significantly enriched in the flavonoid biosynthesis and plant hormone signal transduction pathways,indicating the genetic basis of adaptation of Shanmei to the local *** high-quality assembled genome and the variome dataset of Shanmei provide valuable resources for breeding applications and for elucidating the genome evolution and ecological adaptation of Rubus species.

关键词： Rubus corchorifolius Genome assembly Resequencing Divergence Genome evolution

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The gap-free potato genome assembly reveals large tandem gene clusters of agronomical importance in highly repeated genomic regions

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Molecular Plant 2023年第2期16卷 314-317页

作者： Xiaohui yang Lingkui Zhang Xiao Guo Jianfei Xu Kang Zhang yinqing yang Yu yang Yinqiao Jian Daofeng Dong Sanwen Huang Feng Cheng Guangcun Li Institute of Vegetables Shandong Academy of Agricultural SciencesJinan 250100China Institute of Vegetables and Flowers Chinese Academy of Agricultural SciencesBeijing100081China Institute of Vegetables and Flowers Chinese Academy of Agricultural Sciences/State Key Laboratory of Vegetable Biobreeding/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural AffairsBeijing100081China Institute of Vegetables Shandong Academy of Agricultural Sciences/Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Sub-CenterJinan 250100China Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural SciencesShenzhen518120China Chinese Academy of Tropical Agricultural Sciences Haikou 571101China

Dear Editor,Potato is a vital food security crop and is ranked as the world’s third most important food crop after rice and *** 2011,the first genome assembly of a doubled monoploid potato DM1-3516 R44(DM)was released(Potato Genome Sequencing Consortium,2011),which has been widely used as one of the most popular reference genomes in the last decade and served as a valuable resource in plant genomics and potato genetics community(Leisner et al.,2018;yang et al.,2020;Zheng et al.,2020).

关键词： agronomic doubled potato

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Clinical features, treatment strategies and outcomes of craniocervical junction arteriovenous fistulas: a cohort study of 193 patients

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Stroke & Vascular Neurology 2024年第1期9卷 18-29页

作者： Yongjie Ma Zihao Song yinqing Wang Jiachen Wang Chuan He Guilin Li Peng Zhang Tao Hong Liyong Sun Peng Hu Ming Ye Hongqi Zhang Department of Neurosurgery Xuanwu Hospital Capital Medical University Beijing China

Background Craniocervical junction(CCJ)arteriovenous fistulas(AVFs)are *** current treatment strategies for AVFs with different angioarchitecture need to be *** present study aimed to analyse the correlation between angioarchitecture and clinical characteristics,share our experience in treating this disease and identify risk factors associated with subarachnoid haemorrhage(SAH)and poor *** A total of 198 consecutive patients with CCJ AVFs from our neurosurgical centre were retrospectively *** patients were grouped according to their clinical manifestations,and their baseline clinical characteristics,angioarchitecture,treatment strategies and outcomes were *** The patients’median age was 56 years(IQR 47–62 years).The majority of patients were men with 166(83.8%)*** most common clinical manifestation was SAH(52.0%),followed by venous hypertensive myelopathy(VHM)(45.5%).The most common CCJ AVFs type was dural AVF,with 132(63.5%)*** most frequent fistula location was C-1(68.7%)and dural branch of vertebral artery(70.2%)was the most involved arterial feeders for *** most common direction of venous drainage was descending intradural drainage(40.9%),followed by ascending intradural drainage(36.5%).Microsurgery was the most common treatment strategy applied for 151(76.3%)patients,15(7.6%)patients were treated with interventional embolisation only,and 27(13.6%)received both interventional embolisation and microsurgical *** learning curve for microsurgery only was analysed by cumulative summation method,and the turning point was the 70th case,and blood loss in post-group was lower than that in pre-group(p=0.034).At the last follow-up,there were 155(78.3%)patients with favourable outcomes(modified Rankin Scale(mRS)<3).Age≥56(OR 2.038,95%CI 1.039 to 3.998,p=0.038),VHM as the clinical manifestation(OR 4.102,95%CI 2.108 to 7.982,p<0.001)and pretreatment mRS≥3(OR 3.127,95%CI 1.617 to 6.047,p<0

关键词： patients treatment hypertensive

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Pepper variome reveals the history and key loci associated with fruit domestication and diversification

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Molecular Plant 2022年第11期15卷 1744-1758页

作者： Yacong Cao Kang Zhang Hailong Yu Shumin Chen Donghui Xu Hong Zhao Zhenghai Zhang yinqing yang Xiaozhen Gu Xinyan Liu Haiping Wang Yaxin Jing Yajie Mei Xiang Wang Véronique Lefebvre Weili Zhang Yuan Jin Dongliang An Risheng Wang Paul Bosland Xixiang Li IIan Paran Baoxi Zhang Giovanni Giuliano Lihao Wang Feng Cheng Key Laboratory of Vegetables Geneticsand Physiology of China Ministry of Agriculture and Rural AffairsKey Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural AffairsSino-Dutch Joint Laboratory of Horticultural GenomicsInstitute of Vegetables and FlowersCAAS(Chinese Academy of Agricultural Sciences)12 Zhongguancun South StreetBeijing 100081P.R.China INRAE GAFLUnitéde Génétique et Amélioration des Fruits et Légumes84140 MontfavetFrance Institute of Vegetables Academy of Agricultural Sciences of Guangxi174 Daxue East RoadNanning 53007P.R.China Department of Plant and Environmental Sciences NMSULas CrucesNM 88003USA Institute of Plant Sciences Agricultural Research OrganizationThe Volcani CenterRishon LeZionIsrael Biotechnology and Agroindustry Division ENEAItalian National Agency for New TechnologiesEnergy and Sustainable DevelopmentVia Anguillarese301-00123 RomaItaly

Pepper(Capsicum spp.)is an important vegetable crop that provides a unique pungent sensation when *** construction of a pepper variome map,we examined the main groups that emerged during domestication and breeding of ***,their relationships and temporal succession,and the molecular events underlying the main *** results showed that the initial differentiation in fruit shape and pungency,increase in fruit weight,and transition from erect to pendent fruits,as well as the recent appearance of large,blocky,sweet fruits(bell peppers),were accompanied by strong selection/fixation of key alleles and introgressions in two large genomic ***,we identified Up,which encodes a BIG GRAIN protein involved in auxin transport,as a key domestication gene that controls erect vs pendent fruit *** up mutation gained increased expression especially in the fruit pedicel through a 579-bp sequence deletion in its 5′upstream region,resulting in the phenotype of pendent *** function of Up was confirmed by virus-induced gene *** together,these findings constitute a cornerstone for understanding the domestication and differentiation of a key horticultural crop.

关键词： Capsicum variome domestication fruit orientation pungency fruit shape sweet pepper blocky fruit pepper narrow fruit pepper

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客运专线大跨度T构墩梁固结处优化措施研究

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高速铁路技术 2016年第3期7卷 87-90页

作者：杨银庆铁道第三勘察设计院集团有限公司天津300142

大跨度T构桥墩梁固结区域是设计的关键部位,需确定合理的墩梁固结构造措施,以保证此处结构受力的合理性。但墩梁固结处的局部应力状态及构造措施有待进一步深入研究。文章以长昆客运专线龙溪大桥70 m T构为依托,采用有限元程序对墩梁固... 详细信息

大跨度T构桥墩梁固结区域是设计的关键部位,需确定合理的墩梁固结构造措施,以保证此处结构受力的合理性。但墩梁固结处的局部应力状态及构造措施有待进一步深入研究。文章以长昆客运专线龙溪大桥70 m T构为依托,采用有限元程序对墩梁固结处进行了精细化模拟。在对局部应力分析结果的基础上,对墩梁固结的细节提出了墩梁固结下腋处设倒角、墩顶设帮宽和箱体内设倒角3处优化措施,并对优化前后的应力进行了对照分析。结构优化后,主拉、主压应力峰值消减效果较好,主拉应力最大可下降64.78%,主压应力可下降14.71%。经研究表明,墩梁固结处局部应力分析方法可行,措施优化有效,对类似工程有借鉴意义。

关键词： T构墩梁固结局部应力优化措施

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The genome of Orychophragmus violaceus provides genomic insights into the evolution of Brassicaceaepolyploidizationandits distinct traits

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Plant Communications 2023年第2期4卷 77-92页

作者： Kang Zhang yinqing yang Xin Zhang Lingkui Zhang Yu Fu Zhongwei Guo Shumin Chen Jian Wu James C.Schnable Keke Yi Xiaowu Wang Feng Cheng Institute of Vegetables and Flowers Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of AgricultureSino-Dutch Joint Laboratory of Horticultural GenomicsBeijing 10008China Department of Agronomy and Horticulture University of NebraskaLincolnNE 68588USA Key Laboratory of Plant Nutrition and Fertilizer Ministry of AgricultureInstitute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijing 100081China

Orychophragmus violaceus,referred to as‘‘eryuelan’’(February orchid)in China,is an early-flowering ornamental *** high oil content and abundance of unsaturated fatty acids in *** seeds make it a potential high-quality oilseed ***,we generated a whole-genome assembly for *** using Nanopore and Hi-C sequencing *** assembled genome of *** was~1.3 Gb in size,with 12 pairs of *** investigation of ancestral genome evolution,we determined that the genome of *** experienced a tetraploidization event from a diploid progenitor with the translocated proto-Calepineae *** between the reconstructed subgenomes of *** identified indicators of subgenome dominance,indicating that subgenomes likely originated via *** was phylogenetically close to the Brassica genus,and tetraploidy in *** occurred approximately 8.57 million years ago,close in time to the whole-genome triplication of Brassica that likely arose via an intermediate tetraploid ***,the tetraploidization in Orychophragmus was independent of the hexaploidization in Brassica,as evidenced by the results from detailed phylogenetic analyses and comparisons of the break and fusion points of ancestral genomic ***,identification of multi-copy genes regulating the production of high-quality oil highlighted the contributions of both tetraploidization and tandem duplication to functional innovation in *** findings provide novel insights into the polyploidization evolution of plant species and will promote both functional genomic studies and domestication/breeding efforts in ***.

关键词： Orychophragmus violaceus eryuelan genome assembly polyploidization subgenome differentiation function innovation

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足疗与保健服务质量评价模型研究

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中国卫生质量管理 2006年第6期13卷 38-40页

作者：杨胤清成都中医药大学四川成都610075

足疗保健行业的快速发展产生了服务质量问题,如何科学评价服务质量已成为重要课题。文章论述了已有服务质量评价模型的特点,探索了服务质量评价模型研究的方向,提出了足疗保健服务质量评价模型的建立步骤。

关键词：足疗保健服务质量评价模型

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童年期不可预测性与精神病理学关系的研究进展

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中华精神科杂志 2024年第2期57卷 108-114页

作者：范尹晴袁晨语王振上海交通大学医学院附属精神卫生中心上海200030

童年期不可预测性是童年不良经历的独立维度,对个体的心身健康发展及精神病理学风险有独特且重要的影响,而国内精神科少有关注。本文综述了童年期不可预测性对精神病理学症状及生存和繁衍相关行为选择的影响,以及可能影响心身症状的生... 详细信息

童年期不可预测性是童年不良经历的独立维度,对个体的心身健康发展及精神病理学风险有独特且重要的影响,而国内精神科少有关注。本文综述了童年期不可预测性对精神病理学症状及生存和繁衍相关行为选择的影响,以及可能影响心身症状的生物学改变机制,并介绍了对于不可预测性概念的测量,希望有助于精神科医生及临床研究者进一步理解童年不良经历对精神疾病及心身健康的影响。

关键词：精神病理学青少年童年期不可预测性童年不良经历

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7种茄科植物染色体的演化关系研究

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园艺学报 2023年第5期50卷 1009-1024页

作者：付钰张令奎黄议乐杨印庆陈姝敏张亢李良俊程锋扬州大学园艺与植物保护学院江苏扬州225000 中国农业科学院蔬菜花卉研究所北京100081

为了追溯茄科(Solanaceae)物种染色体的演化关系,对7种茄科物种进行了系统的比较基因组学分析,利用模式植物番茄的基因组为参考模板,全面鉴定7个物种间的基因组共线性关系,以此为基础建立了茄科的基因组片段单元系统,并基于该系统重建... 详细信息

为了追溯茄科(Solanaceae)物种染色体的演化关系,对7种茄科物种进行了系统的比较基因组学分析,利用模式植物番茄的基因组为参考模板,全面鉴定7个物种间的基因组共线性关系,以此为基础建立了茄科的基因组片段单元系统,并基于该系统重建了具有12条染色体的祖先基因组,阐明祖先基因组主要通过基因组片段的易位和倒位逐步形成目前的茄科基因组结构,且这些重排事件多发生在着丝粒等重复序列富集的区域。研究结果为深入认识茄科以及其他植物的基因组进化和物种分化等提供理论参考。

关键词：茄科比较基因组祖先基因组染色体重排着丝粒重复序列

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