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The Dark Side of the Genome： Revealing the Native Transposable Element/Repeat Content of Eukaryotic Genomes

Molecular Plant 2016年第12期9卷 1664-1666页

作者： dario copetti Rod A. Wing Arizona Genomics Institute BIO5 Institute and School of Plant Sciences University of Arizona Tucson AZ 85721 USA International Rice Research Institute T.T. Chang Genetic Resources Center Los Baños Laguna 63108 Philippines

Dear Editor,The majority of genome assemblies to date fail to represent the true structure of native genomes. This lack of completeness is largely due to the inability to assemble the variable （often significant） fraction of nuclear genomes that is composed primarily of repeated sequences （with either a structural function such as satellite DNA and simple sequence repeats or ＂selfish DNA＂ such as high-copy transposable elements [TEs]）, herein defined as the ＂dark side of the genome.＂

关键词： Specialized Metabolites Flavonol

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Dissect the rice immune system using a whole-genome sequenced mutant population

Dissect the rice immune system using a whole-genome sequence...

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中国植物病理学会2019年学术年会

作者： Li Guotian Sha Gan Jain Rashmi Jenkins Jerry Shu Shengqiang Chern Mawsheng copetti dario Xing Feng Xie Weibo Wing Rod A Schmutz Jeremy Ronald Pamela C State Key Laboratory of Agricultural Microbiology and College of Plant Science and Technology Huazhong Agricultural University Department of Plant Pathology University of California Joint BioEnergy Institute Lawrence Berkeley National Laboratory U.S.Department of Energy Joint Genome Institute Arizona Genomics Institute School of Plant SciencesUniversity of Arizona National Key Laboratory of Crop Genetic Improvement National Center of Plant Gene ResearchHuazhong Agricultural University HudsonAlpha Institute for Biotechnology

Rice provides food for more than half of the world’s population and also serves as a model for studies of other monocotyledonous ***,we report the de novo genome sequencing and analysis of an early flowering Geng/japonica variety KitaakeX,which completes its life cycle in 9 *** KitaakeX sequence assembly contains 377.6 Mb,consisting of 33 scaffolds（476 contigs） with a contig N50 of 1.4 *** the assembly are detailed gene annotations of 35 594 protein coding *** high-quality genome of the model rice plant KitaakeX will accelerate rice functional *** further facilitate rice research,we generated and sequenced a fast-neutron-induced mutant population in *** sequenced 1 504 mutant lines at 45-fold coverage and identified 91 513 mutations affecting 32 307 genes,i.e.,58% of all rice *** detected an average of 61 mutations per *** types include single-base substitutions,deletions,insertions,inversions,translocations,and tandem *** observed a high proportion of loss-of-function *** facilitate public access to this genetic resource,we established an open access database called KitBase that provides access to sequence data and seed *** have screened this mutant population for lines altered in plant immunity and identified multiple mutant *** on these mutants will be presented.

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The Genomic Variation of 3,000 diverse Rice (Oryza sativa L.)Accessions:Discoveries And Applications In Rice Improvement

The Genomic Variation of 3,000 diverse Rice (Oryza sativa L....

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2018中国作物学会学术年会

作者：黎志康 Fan Zhang Whensheng Wang Ramil Mauleon Zhiqiang Hu Dmytro Chebotarov Shuaishuai Tai Zhichao Min Li Tianqing Zheng Roven Rommel Fuentes Locedie Mansueto dario copetti Millicent Sanciangco Kevin Christian Palis Jianlong Xu Chen Sun Hongliang Zhang Binying Fu Yongming Gao Xiuqin Zhao Fei Shen Xiao Cui Hong Yu Zichao Li Miaolin Chen Jeffery Detras Yongli Zhou Xinyuan Zhang Yue Zhao Dave Kudrna Chunchao Wang Rui Li Ben Jia Jinyuan Lu Xianchang He Zhaotong Dong Jiabao Xu Yanhong Li Miao Wang Jianxin Shi Jing Li Dabing Zhang Seunhee Lee Wushu Hu Alexander Poliakov Inna Dubchak Victor Jun Ulat Frances Nikki Borja John Robert Mendoza Jauhar Ali Ming Yang Yongchao Niu Zhen Yue Ma.Elizabeth B.Naredo Jayson Talag Xueqiang Wang Jinjie Li Xiaodong Fang Ye Yin Jean-Christophe Glaszmann Jianwei Zhang Jiayang Li Ruaraidh Sackville Hamilton Rod A.Wing Chaochun Wei Jue Ruan Gengyun Zhang Kenneth L.Mcnally Nickolai Alexandrov Hei Leung Hei Institute of Crop Sciences Chinese Academy of Agricultural Sciences Shenzhen Institute for Innovative Breeding Chinese Academy of Agricultural Sciences International Rice Research Institute School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai Center for Bioinformation Technology BGI Genomics BGI-Shenzhen Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Anhui Agricultural University Arizona Genomics Institute School of Plant SciencesUniversity of Arizona China Agricultural University Institute of Genetics and Developmental Biology Chinese Academy of Sciences Lawrence Berkeley National Laboratory

Asian cultivated rice(Oryza sativa L.) is the staple food for the half world population with rich within species *** analyses of the genome resequencing data of a core collection of 3,010 rice accessions revealed four important aspects of the genomic diversity within ***,over 42 million SNPs and >3 million small InDels were discovered against five reference ***,we discovered more than 90,000 structural(>100 bps) variations(SVs) when compared with the Geng reference genome,consisting primarily of small-sized deletions and translocations,plus many duplications and *** SVs accounted for significant portion of the rice genome and involved most(～80%) rice ***,we discovered >12,000 full-length novel protein-coding genes plus 9000+ novel genes of partial sequences that are absent in the Nipponbare reference *** rice pan genome consists of ～62%core genes/gene families that are present in all rice lines,and ～38%distributed genes that are present only some of rice ***,using large-effect SNPs and InDels of all loci in the PG,a rice functional haplotype database was *** SNP,PG and SV variation clearly resolve the 3,010 rice accessions into two major subspecies,Xian(indica) and Geng(japonica),plus Aus and Aro groups and multiple subpopulations within Xian and *** reduced diversity was found in genomic regions where over 1,000 agronomically important and domestication-related genes *** efforts have been taken to identify and mine genes/QTLs/alleles associated with a wide range of important traits in rice using the 3 k materials and SNP *** demonstrate how the results of the 3 k RGP could be used in rice improvement,genomic constitutions of 476 BC F introgression lines(ILs) from our breeding program were constructed using high-quality reference genomes of their 9 parents and the 3 k RGP *** compared with their recurrent parent,Huang-hua-

关键词： Rice genome diversity population structure pan genomes genomics-based breeding by design

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