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| 1 | The Tartary Buckwheat Genome Provides Insights into Rutin Biosynthesis and Abiotic Stress Tolerance显示文摘 | Zhang, Lijun Li, Xiuxiu Ma, Bin Gao, Qiang Du, Huilong Han, Yuanhuai Li, Yan Cao, Yinghao Qi, Ming Zhu, Yaxin Lu, Hongwei Ma, Mingchuan Liu, Longlong Zhou, Jianping Nan, Chenghu Qin, Yongjun Wang, Jun Cui, Lin Liu, Huimin Liang, Chengzhi Qiao, Zhijun | 2017 | Molecular Plant2017，10，9： | 53 |
| 2 | The Chromosome-Level Genome Sequence of the Autotetraploid Alfalfa and Resequencing of Core Germplasms Provide Genomic Resources for Alfalfa Research显示文摘Alfalfa(Medicago sativa)is one of the most important forage crops in the world;however,its molecular genetics and breeding research are hindered due to the lack of a high-quality reference genome.Here,we report a de novo assembled 816-Mb high-quality,chromosome-level haploid genome sequence for‘Zhongmu No.1’alfalfa,a heterozygous autotetraploid.The contig N50 is 3.92 Mb,and 49165 genes are annotated in the genome.The alfalfa genome is estimated to have diverged from M.truncatula approximately 8 million years ago.Genomic population analysis of 162 alfalfa accessions revealed high genetic diversity,weak population structure,and extensive gene flow from wild to cultivated alfalfa.Genome-wide association studies identified many candidate genes associated with important agronomic traits.Furthermore,we showed that MsFTa2,a Flowering Locus T homolog,whose expression is upregulated in salt-resistant germplasms,may be associated with fall dormancy and salt resistance.Taken together,these genomic resources will facilitate alfalfa genetic research and agronomic improvement. | Chen Shen Huilong Du Zhuo Chen Hongwei Lu Fugui Zhu Hong Chen Xiangzhao Meng Qianwen Liu Peng Liu Lihua Zheng Xiuxiu Li Jiangli Dong Chengzhi Liang Tao Wang | 2020 | Molecular Plant2020，13，9： | 21 |
| 3 | Update soybean Zhonghuang 13 genome to a golden reference显示文摘Dear Editor,Soybean is one of the most important crops worldwide.A high-quality reference genome will facilitate its functional analysis and molecular breeding (Wang and Tian,2015).Previously,we de novo assembled a high-quality Chinese soybean genome Gmax_ZH13 (Shen et al.,2018,Yang and Huang,2018).However,due to technical limitations at the time when we generated Gmax_ZH13,a large number of small contigs were not anchored onto chromosomes.Therefore,we here build a new golden reference genome for Zhonghuang 13 consisting of 20 nearly complete chromosomes by adding more single-molecule real time (SMRT) sequencing reads.Furthermore,we add large RNA-seq and smRNA-seq datasets for improving the annotation of its protein coding genes. | Yanting Shen Huilong Du Yucheng Liu Lingbin Ni Zheng Wang Chengzhi Liang Zhixi Tian | 2019 | Science China(Life Sciences)2019，62，9： | 6 |
| 4 | Evolution and Domestication Footprints Uncovered from the Genomes of Coix显示文摘Coix lacryma-jobi,a plant species closely related to Zea and Sorghum,is an important food and medicinal crop in Asia.However,no reference genome of this species has been reported,and its exact phylogeny within the Andropogoneae remains unresolved.Here,we generated a high-quality genome assembly of coix comprising~1.73 Gb with 44485 predicted protein-coding genes.We found coix to be a typical diploid plant with an overall 1-to-1 syntenic relationship with the Sorghum genome,despite its drastic genome expansion(~2.3-fold)due mainly to the activity of transposable elements.Phylogenetic analysis revealed that coix diverged with sorghum~10.41 million years ago,which was~1.49 million years later than the divergence between sorghum and maize.Resequencing of 27 additional coix accessions revealed that they could be unambiguously separated into wild relatives and cultivars,and suggested that coix experienced a strong genetic bottleneck,resulting in the loss of about half of the genetic diversity during domestication,even though many traits have remained undomesticated.Our data not only provide novel comparative genomic and evolutionary insights into the Andropogoneae lineage,but also an important resource that will greatly benefit molecular breeding of this important crop. | Hongbing Liu Junpeng Shi Zexi Cai Yumin Huang Menglu Lv Huilong Du Qiang Gao Yi Zuo Zhaobin Dong Wei Huang Rui Qin Chengzhi Liang Jinsheng Lai Weiwei Jin | 2020 | Molecular Plant2020，13，2： | 4 |
| 5 | A chromosome-level genome assembly of the wild rice Oryza rufipogon facilitates tracing the origins of Asian cultivated rice显示文摘Oryza rufipogon Griff.is a wild progenitor of the Asian cultivated rice Oryza sativa.To better understand the genomic diversity of the wild rice,high-quality reference genomes of O.rufipogon populations are needed,which also facilitate utilization of the wild genetic resources in rice breeding.In this study,we generated a chromosome-level genome assembly of O.rufipogon using a combination of short-read sequencing,single-molecule sequencing,BioNano and Hi-C platforms.The genome sequence(399.8 Mb)was assembled into 46 scaffolds on the 12 chromosomes,with contig N50 and scaffold N50 of 13.2 Mb and 20.3 Mb,respectively.The genome contains 36,520 protein-coding genes,and 49.37% of the genome consists of repetitive elements.The genome has strong synteny with those of the O.sativa subspecies indica and japonica,but containing some large structural variations.Evolutionary analysis unveiled the polyphyletic origins of O.sativa,in which the japonica and indica genome formations involved different divergent O.rufipogon(including O.nivara)lineages,accompanied by introgression of genomic regions between japonica and indica.This high-quality reference genome provides insight on the genome evolution of the wild rice and the origins of the O.sativa subspecies,and valuable information for basic research and rice breeding. | Xianrong Xie Huilong Du Huiwu Tang Jianian Tang Xiyu Tan Weizhi Liu Tie Li Zhansheng Lin Chengzhi Liang Yao-Guang Liu | 2021 | Science China(Life Sciences)2021，64，2： | 4 |
| 6 | SNX14 deficiency-induced defective axonal mitochondrial transport in Purkinje cells underlies cerebellar ataxia and can be reversed by valproate显示文摘Loss-of-function mutations in sorting nexin 14(SNX14)cause autosomal recessive spinocerebellar ataxia 20,which is a form of early-onset cerebellar ataxia that lacks molecular mechanisms and mouse models.We generated Snx14-deficient mouse models and observed severe motor deficits and cell-autonomous Purkinje cell degeneration.SNX14 deficiency disrupted microtubule organization and mitochondrial transport in axons by destabilizing the microtubule-severing enzyme spastin,which is implicated in dominant hereditary spastic paraplegia with cerebellar ataxia,and compromised axonal integrity and mitochondrial function.Axonal transport disruption and mitochondrial dysfunction further led to degeneration of high-energy-demanding Purkinje cells,which resulted in the pathogenesis of cerebellar ataxia.The antiepileptic drug valproate ameliorated motor deficits and cerebellar degeneration in Snx14-deficient mice via the restoration of mitochondrial transport and function in Purkinje cells.Our study revealed an unprecedented role for SNX14-dependent axonal transport in cerebellar ataxia,demonstrated the convergence of SNX14 and spastin in mitochondrial dysfunction,and suggested valproate as a potential therapeutic agent. | Hongfeng Zhang Yujuan Hong Weijie Yang Ruimin Wang Ting Yao Jian Wang Ke Liu Huilong Yuan Chaoqun Xu Yuanyuan Zhou Guanxian Li Lishan Zhang Hong Luo Xian Zhang Dan Du Hao Sun Qiuyang Zheng Yun-Wu Zhang Yingjun Zhao Ying Zhou Huaxi Xu Xin Wang | 2021 | National Science Review2021，8，7： | 1 |
| 7 | Miningassociation rules to support resource allocation in businessprocess management显示文摘 | HUANG Zhengxing LU Xudong DU AN Huilong | 2011 | Expert Systems with Applications2011，38，8： | 1 |
| 8 | Advanced Process and Electron Device Technology显示文摘This article reviews advanced process and electron device technology of integrated circuits,including recent featuring progress and potential solutions for future development.In 5 years,for pushing the performance of fin field-effect transistors(FinFET)to its limitations,several processes and device boosters are provided.Then,the three-dimensional(3 D)integration schemes with alternative materials and device architectures will pave paths for future technology evolution.Finally,it could be concluded that Moore’s law will undoubtedly continue in the next 15 years. | Dan Zhang Xiaojing Su Hao Chang Hao Xu Xiaolei Wang Xiaobin He Junjie Li Fei Zhao Qide Yao Yanna Luo Xueli Ma Hong Yang Yongliang Li Zhenhua Wu Yajuan Su Tao Yang Yayi Wei Anyan Du Huilong Zhu Junfeng Li Huaxiang Yin Jun Luo Tianchun Ye Wenwu Wang | 2022 | Tsinghua Science and Technology2022，27，3： | 1 |
| 9 | Plant pan-genomics:recent advances,new challenges,and roads ahead显示文摘Pan-genomics can encompass most of the genetic diversity of a species or population and has proved to be a powerful tool for studying genomic evolution and the origin and domestication of species,and for providing information for plant improvement.Plant genomics has greatly progressed because of improvements in sequencing technologies and the rapid reduction of sequencing costs.Nevertheless,pangenomics still presents many challenges,including computationally intensive assembly methods,high costs with large numbers of samples,ineffective integration of big data,and difficulty in applying it to downstream multi-omics analysis and breeding research.In this review,we summarize the definition and recent achievements of plant pan-genomics,computational technologies used for pan-genome construction,and the applications of pan-genomes in plant genomics and molecular breeding.We also discuss challenges and perspectives for future pan-genomics studies and provide a detailed pipeline for sample selection,genome assembly and annotation,structural variation identification,and construction and application of graph-based pan-genomes.The aim is to provide important guidance for plant pan-genome research and a better understanding of the genetic basis of genome evolution,crop domestication,and phenotypic diversity for future studies. | Wei Li Jianan Liu Hongyu Zhang Ze Liu Yu Wang Longsheng Xing Qiang He Huilong Du | 2022 | Journal of Genetics and Genomics2022，49，9： | 1 |
| 10 | The genome of okra (Abelmoschus esculentus) provides insights into its genome evolution and high nutrient content显示文摘Okra(Abelmoschus esculentus)is an important vegetable crop with high nutritional value.However,the mechanism underlying its high nutrient content remains poorly understood.Here,we present a chromosome-scale genome of okra with a size of 1.19 Gb.Comparative genomics analysis revealed the phylogenetic status of A.esculentus,as well as whole-genome duplication(WGD)events that have occurred widely across the Malvaceae species.We found that okra has experienced three additional WGDs compared with the diploid cotton Gossypium raimondii,resulting in a large chromosome number(2n=130).After three WGDs,okra has undergone extensive genomic deletions and retained substantial numbers of genes related to secondary metabolite biosynthesis and environmental adaptation,resulting in significant differences between okra and G.raimondii in the gene families related to cellulose synthesis.Combining transcriptomic and metabolomic analysis,we revealed the relationship between gene expression and metabolite content change across different okra developmental stages.Furthermore,the sinapic acid/S-lignin biosynthesis-related gene families have experienced remarkable expansion in okra,and the expression of key enzymes involved in the sinapic acid/S-lignin biosynthesis pathway vary greatly across developmental periods,which partially explains the differences in metabolite content across the different stages.Our study gains insights into the comprehensive evolutionary history of Malvaceae species and the genetic basis that underlies the nutrient content changes in okra,which will facilitate the functional study and genetic improvement of okra varieties. | Ruyu Wang Wei Li Qiang He Hongyu Zhang Meijia Wang Xinyuan Zheng Ze Liu Yu Wang Cailian Du Huilong Du Longsheng Xing | 2023 | Horticulture Research2023，10，8： | 0 |
| 11 | High-quality Fagopyrum esculentum genome provides insights into the flavonoid accumulation among different tissues and self-incompatibility显示文摘Common buckwheat(Fagopyrum esculentum)and Tartary buckwheat(Fagopyrum tataricum),the two most widely cultivated buckwheat species,differ greatly in flavonoid content and reproductive mode.Here,we report the first high-quality and chromosome-level genome assembly of common buckwheat with 1.2 Gb.Comparative genomic analysis revealed that common buckwheat underwent a burst of long terminal repeat retrotransposons insertion accompanied by numerous large chromosome rearrangements after divergence from Tartary buckwheat.Moreover,multiple gene families involved in stress tolerance and flavonoid biosynthesis such as multidrug and toxic compound extrusion(MATE)and chalcone synthase(CHS)underwent significant expansion in buckwheat,especially in common buckwheat.Integrated multi-omics analysis identified high expression of catechin biosynthesis-related genes in flower and seed in common buckwheat and high expression of rutin biosynthesis-related genes in seed in Tartary buckwheat as being important for the differences in flavonoid type and content between these buckwheat species.We also identified a candidate key rutindegrading enzyme gene(Ft8.2377)that was highly expressed in Tartary buckwheat seed.In addition,we identified a haplotype-resolved candidate locus containing many genes reportedly associated with the development of flower and pollen,which was potentially related to self-incompatibility in common buckwheat.Our study provides important resources facilitating future functional genomics-related research of flavonoid biosynthesis and selfincompatibility in buckwheat. | Qiang He Dan Ma Wei Li Longsheng Xing Hongyu Zhang Yu Wang Cailian Du Xuanzhao Li Zheng Jia Xiuxiu Li Jianan Liu Ze Liu Yuqing Miao Rui Feng Yang Lv Meijia Wang Hongwei Lu Xiaochen Li Yao Xiao Ruyu Wang Hanfei Liang Qinghong Zhou Lijun Zhang Chengzhi Liang Huilong Du | 2023 | Journal of Integrative Plant Biology2023，65，6： | 0 |
| 12 | A backbone parent contributes core genomic architecture to pedigree breeding of early-season indica rice显示文摘Due to the capacity to deliver favorable target traits to offspring via breeder selection,backbone parents carrying accumulated favorable agronomic traits have been used widely in breeding programs in crop species,such as rice,wheat,cotton,and maize(Zhou et al.,2016;Fradgley et al.,2019;Li et al.,2019;Ma et al.,2019;Han et al.,2020).It is estimated that 3656(~70%)of the major Chinese rice varieties released from the year 1950e2008 were found to be derived from as few as 35 backbone parents(Tang et al.,2012).Large-scale genome sequencing of diverse rice accessions has been emerged as a promising technology for the identification of key genomic regions or loci under selection during rice domestication(Huang et al.,2012;Wang et al.,2018)and genetic improvement(Xie et al.,2015).On the other hand,sequence information derived from breeding pedigrees could also help to unravel how favorable genomic regions were transmitted from parents to their offspring,as demonstrated by the researches on the pedigrees of the wellknown rice varieties Minghui 63 and Huanghuazhan(Zhou et al.,2016;Chen et al.,2017;Huang et al.,2018).These researches enhanced the understanding of the cumulative effects of beneficial alleles at limited loci in selected offspring varieties.A few examples include IPA1,Gn1a,GW5,GS3,and GS5 for high grain yield,Waxy for good grain eating quality,and Xa21 for high adversity adaptability. | Junyu Chen Huali Zhang Shuhan Deng Huilong Du Zhuo Chen Yuhui Zhao Dongqing Dai Chengzhen Liang Ximing Li Chengzhi Liang Rui Zhang Liangyong Ma | 2021 | Journal of Genetics and Genomics2021，48，11： | 0 |
| 13 | Extensive sequence divergence between the reference genomes of Taraxacum kok-saghyz and Taraxacum mongolicum显示文摘Plants belonging to the genus Taraxacum are widespread all over the world,which contain rubber-producing and non-rubberproducing species.However,the genomic basis underlying natural rubber(NR)biosynthesis still needs more investigation.Here,we presented high-quality genome assemblies of rubber-producing T.kok-saghyz TK1151 and non-rubber-producing T.mongolicum TM5.Comparative analyses uncovered a large number of genetic variations,including inversions,translocations,presence/absence variations,as well as considerable protein divergences between the two species.Two gene duplication events were found in these two Taraxacum species,including one common ancestral whole-genome triplication and one subsequent round of gene amplification.In genomes of both TK1151 and TM5,we identified the genes encoding for each step in the NR biosynthesis pathway and found that the SRPP and CPT gene families have experienced a more obvious expansion in TK1151 compared to TM5.This study will have large-ranging implications for the mechanism of NR biosynthesis and genetic improvement of NR-producing crops. | Tao Lin Xia Xu Huilong Du Xiuli Fan Qingwen Chen Chunyan Hai Zijian Zhou Xiao Su Liquan Kou Qiang Gao Lingwei Deng Jinsheng Jiang Hanli You Yihua Ma Zhukuan Cheng Guodong Wang Chengzhi Liang Guomin Zhang Hong Yu Jiayang Li | 2022 | Science China(Life Sciences)2022，65，3： | 0 |
| 14 | A complete reference genome assembly for foxtail millet and Setaria-db, a comprehensive database for Setaria显示文摘Dear Editor,,Foxtail millet(Setaria italica)and its wild ancestor green foxtail(S.viridis),are two C4 genetic model plants known for their desirable traits,such as small size,short life cycle,ease of transformation,and a compact genome size(~420 Mb)(He et al.,2023).Foxtail millet stands out as the only cultivated species within the Setaria genus.As a foundational crop for ancient east Asian agriculture civilization,it possesses remarkable drought and soil-nutrient deficiency tolerance. | Qiang He Chunchao Wang Qiang He Jun Zhang Hongkai Liang Zefu Lui Kun Xie Sha Tang Yuhan Zhou Bin Liu Hui Zhi Guanqing Jia Ganggang Guo Huilong Du Xianmin Diao | 2024 | Molecular Plant2024，17，2： | 0 |
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