A complete assembly of the rice Nipponbare reference genome

作     者：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 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

作者机构：Shenzhen BranchGuangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China Yazhouwan National LaboratoryNo.8 Huanjin RoadYazhou DistrictSanya CityHainan Province 572024China State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhou 310006China National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China Key Laboratory of Plant Functional Genomics of the Ministry of EducationJiangsu Co-Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhou 225009China 

出 版 物：《Molecular Plant》 (分子植物（英文版）)

年 卷 期：2023年第16卷第8期

页      面：1232-1236页

核心收录：

学科分类：0710[理学-生物学] 09[农学] 0901[农学-作物学] 

基　　金：supported by the National Natural Science Foundation of China(32188102,32101718) Guangdong Basic and Applied Basic Research Foundation(2023B1515020053) the Youth Innovation of Chinese Academy of Agricultural Sciences(Y20230C36) the specific research fund of The Innovation Platform for Academicians of Hainan Province(YSPTZX202303) 

主　　题：Sakai bases assembly 

摘      要：Dear Editor,In 2005,the current commonly used rice reference genome(Oryza sativa *** ***)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 *** 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 ***,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 of
3%of the genome unsolved.