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| 1 | A super pan-genomic landscape of rice显示文摘Pan-genomes from large natural populations can capture genetic diversity and reveal genomic complexity.Using de novo longread assembly,we generated a graph-based super pan-genome of rice consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice.Our pan-genome reveals extensive structural variations(SVs)and gene presence/absence variations.Additionally,our pan-genome enables the accurate identification of nucleotide-binding leucine-rich repeat genes and characterization of their inter-and intraspecific diversity.Moreover,we uncovered grain weight-associated SVs which specify traits by affecting the expression of their nearby genes.We characterized genetic variants associated with submergence tolerance,seed shattering and plant architecture and found independent selection for a common set of genes that drove adaptation and domestication in Asian and African rice.This super pan-genome facilitates pinpointing of lineage-specific haplotypes for trait-associated genes and provides insights into the evolutionary events that have shaped the genomic architecture of various rice species. | Lianguang Shang Xiaoxia Li Huiying He Qiaoling Yuan Yanni Song Zhaoran Wei Hai Lin Min Hu Fengli Zhao Chao Zhang Yuhua Li Hongsheng Gao Tianyi Wang Xiangpei Liu Hong Zhang Ya Zhang Shuaimin Cao Xiaoman Yu Bintao Zhang Yong Zhang Yiqing Tan Mao Qin Cheng Ai Yingxue Yang Bin Zhang Zhiqiang Hu Hongru Wang Yang Lv Yuexing Wang Jie Ma Quan Wang Hongwei Lu Zhe Wu Shanlin Liu Zongyi Sun Hongliang Zhang Longbiao Guo Zichao Li Yongfeng Zhou Jiayang Li Zuofeng Zhu Guosheng Xiong Jue Ruan Qian Qian | 2022 | Cell Research2022，32，10： | 3 |
| 2 | Exploration on crystallization habit of rare earth fluoride crystal BaY2F8 显示文摘 | LIN Junyi RUAN Yongfeng WANG Jun | 2004 | J Rare Earth2004，22，12： | 1 |
| 3 | Exploration on Crystallization Habit of Rare Earth Fluoride Crystal BaY2F8显示文摘 | Lin Junyi Ruan Yongfeng Wang Jun Liu Jian Huan Boxian | 2004 | Journal of Rare Earth2004，22，3： | 1 |
| 4 | A complete assembly of the rice Nipponbare reference genome显示文摘Dear Editor,In 2005,the current commonly used rice reference genome(Oryza sativa ssp.japonica cv.Nipponbare)was initially released by the International Rice Genome Sequencing Project(International Rice Genome Sequencing Project,2005).Thereafter,the reference genome was further updated in 2013 with improved genome assembly(IRGSP-1.0)and gene annotations(MSU7,RAP-DB)(Kawahara et al.,2013;Sakai et al.,2013).In the past 10 years,this reference has been serving as one of the most important genetic resources for subsequent rice functional genomics efforts.As several rice genomes had been assembled into gapless chromosomes with only 2–5 telomeres absent(Li et al.,2021;Song et al.,2021;Zhang et al.,2022),the IRGSP1.0 and its annotations still performed as the most widely used reference.However,limitations of sequencing technology and intricate genomic organization led to an under-representation of complex regions in this reference,leaving a total of 72 major gaps(including 19 telomeres),167 minor gaps,and 779 unknown bases(Kawahara et al.,2013),with an estimated length of3%of the genome unsolved. | Lianguang Shang Wenchuang He Tianyi Wang Yingxue Yang Qiang Xu Xianjia Zhao Longbo Yang Hong Zhang Xiaoxia Li Yang Lv Wu Chen Shuo Cao Xianmeng Wang Bin Zhang Xiangpei Liu Xiaoman Yu Huiying He Hua Wei Yue Leng Chuanlin Shi Mingliang Guo Zhipeng Zhang Bintao Zhang Qiaoling Yuan Hongge Qian Xinglan Cao Yan Cui Qianqian Zhang Xiaofan Dai Congcong Liu Longbiao Guo Yongfeng Zhou Xiaoming Zheng Jue Ruan Zhukuan Cheng Weihua Pan Qian Qian | 2023 | Molecular Plant2023，16，8： | 1 |
| 5 | Exploration on Crystallization Habit of Rare Earth Fluoride Crystal BaY2F8显示文摘 | Lin Junyi Ruan Yongfeng Wang Jun Liu Jian Huan Boxian | 2004 | Journal of Rare Earth2004，22，： | 1 |
| 6 | Frequency Shifts of Luminescence for ZnO Nanoparticles in Porous Alumina Template显示文摘ZnO nanoparticles in porous anodized alumina were fabricated by sol-gel method. The PL spectra of pure ZnO nanoparticles, porous alumina template and the ZnO/PAA composite system were investigated after annealed at different temperatures. The annealing of ZnO/PAA composite system displays very complicated behavior, where changing of luminescence intensity and a 'red shift' of emission frequency were observed at less or higher than 500 ℃ of the annealing temperature, respectively. To explain the phenomenon, it is considered that the emission origin of the green luminescence of ZnO nanoparticles came from OZn. It is suggested that the ZnO/PAA composite system should be annealed at the temperature above 500 ℃ in order to get intense luminescence of ZnO nanoparticle. | Ruan Yongfeng Jing Hongqi Huang Boxian Lu Shuhua Zhan Shouchao | 2006 | Journal of Rare Earths2006，24，z1： | 1 |
| 7 | Genetic similarity among cuhivars of Phyllostachys pubescens 显示文摘 | LIN Xinchun RUAN Xiaosai LOU Yongfeng | 2009 | Plant Syst Evol2009，277，： | 1 |
| 8 | PHOTOIONIZATION AND TUNABLE LASER OF COLOR CENTERS IN KMgF_(3)显示文摘The density of 570nm centers in KMgF_(3) crystals colored by electron beam bombardment at 200K could be increased by irradiating the crystals with 337nm,400nm,and 445nm lasers at room temperature or 200K,respectively.The near infrared laser operation using 570nm centers in KMgF_(3) crystals was realized at room temperature.The tunable range of the laser is from 720nm to 820nm. | GU Hongen QI Lan RUAN Yongfeng | 1990 | Chinese Physics Letters1990，7，6： | 0 |
| 9 | Radiation Damage and Recovery in Neutron-Irradiated MgO Crystal显示文摘MgO single crystal was irradiated by neutron up to a dose of 5.74×1018 cm-2. The radiation damage and its recovery were studied by means of UV-VIS and EM spectroscopy. The results indicate that the irradiation generates large amount of optically detectable defects such as single anion vacancies (F+ center), anion divacancies (F2) and some higher order defects. Through isochronal annealing, these defects started a series of processes of diminishing and transforming, and finally all disappeared while annealing at 900 ℃. It seems that the absorption bands of 573 nm are resulted from a higher order and more complex aggregated center than that of 424, 451 nm bands. | Ruan Yongfeng Ma Pengfei Liu Jian Li Wenrun Liu Changlong | 2006 | Journal of Rare Earths2006，24，z1： | 0 |
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