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| 1 | Genome analysis of Taraxacum kok-saghyz Rodin provides new insights into rubber biosynthesis显示文摘The Russian dandelion Taraxacum kok-saghyz Rodin(TKS), a member of the Composite family and a potential alternative source of natural rubber(NR) and inulin, is an ideal model system for studying rubber biosynthesis. Here we present the draft genome of TKS, the first assembled NR-producing weed plant. The draft TKS genome assembly has a length of 1.29 Gb, containing 46 731 predicted protein-coding genes and68.56% repeats, in which the LTR-RT elements predominantly contribute to the genome enlargement. We analyzed the heterozygous regions/genes, suggesting its possible involvement in inbreeding depression.Through comparative studies between rubber-producing and non-rubber-producing plants, we found that enzymes of the mevalonate(MVA) pathway and rubber elongation might be critical for rubber biosynthesis, and several key isoforms have been isolated and shown to be predominantly expressed in the latex, indicating their crucial functions in rubber biosynthesis. Moreover, for two important families in rubber elongation, the CPT/CPTL and REF/SRPP families, diverse evolutionary tracks have been revealed. These results provide valuable resources and new insights into the mechanism of NR biosynthesis,and facilitate the development of alternative NR-producing crops. | Tao Lin Xia Xu Jue Ruan Shizhong Liu Shigang Wu Xiujuan Shao Xiaobo Wang Lin Gan Bi Qin Yushuang Yang Zhukuan Cheng Suhua Yang Zhonghua Zhang Guosheng Xiong Sanwen Huang Hong Yu Jiayang Li | 2018 | National Science Review2018，5，1： | 22 |
| 2 | 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 |
| 3 | Structural variation during dog domestication: insights from gray wolf and dhole genomes显示文摘Several processes like phenotypic evolution, disease susceptibility and environmental adaptations, which fashion the domestication of animals, are largely attributable to structural variations(SVs) in the genome.Here, we present high-quality draft genomes of the gray wolf(Canis lupus) and dhole(Cuon alpinus) with scaffold N50 of 6.04 Mb and 3.96 Mb, respectively. Sequence alignment comprising genomes of three canid species reveals SVs specific to the dog, particularly 16 315 insertions, 2565 deletions, 443 repeats, 16 inversions and 15 translocations. Functional annotation of the dog SVs associated with genes indicates their enrichments in energy metabolisms, neurological processes and immune systems. Interestingly, we identify and verify at population level an insertion fully covering a copy of the AKR1 B1(Aldo-Keto Reductase Family 1 Member B) transcript. Transcriptome analysis reveals a high level of expression of the new AKR1 B1 copy in the small intestine and liver, implying an increase in de novo fatty acid synthesis and antioxidant ability in dog compared to gray wolf, likely in response to dietary shifts during the agricultural revolution. For the first time, we report a comprehensive analysis of the evolutionary dynamics of SVs during the domestication step of dogs. Our findings demonstrate that retroposition can birth new genes to facilitate domestication, and affirm the importance of large-scale genomic variants in domestication studies. | Guo-Dong Wang Xiu-Juan Shao Bing Bai Junlong Wang Xiaobo Wang Xue Cao Yan-Hu Liu Xuan Wang Ting-Ting Yin Shao-Jie Zhang Yan Lu Zechong Wang Lu Wang Wenming Zhao Bing Zhang Jue Ruan Ya-Ping Zhang | 2019 | National Science Review2019，6，1： | 3 |
| 4 | Understanding divergent domestication traits from the whole-genome sequencing of swamp-and river-buffalo populations显示文摘Domesticated buffaloes have been integral to rice-paddy agro-ecosystems formillennia,yet relatively little is known about the buffalo genomics.Here,we sequenced and assembled reference genomes for both swamp and river buffaloes and we re-sequenced 230 individuals(132 swamp buffaloes and 98 river buffaloes)sampled from across Asia and Europe.Beyond the many actionable insights that our study revealed about the domestication,basic physiology and breeding of buffalo,we made the striking discovery that the divergent domestication traits between swamp and river buffaloes can be explained with recent selections of genes on social behavior,digestion metabolism,strengths and milk production. | Xier Luo Yu Zhou Bing Zhang Yi Zhang Xiaobo Wang Tong Feng Zhipeng Li Kuiqing Cui Zhiqiang Wang Chan Luo Hui Li Yanfei Deng Fenghua Lu Jianlin Han Yongwang Miao Huaming Mao Xiaoyan Yi Cheng Ai Shigang Wu Alun Li Zhichao Wu Zijun Zhuo Do Da Giang Bikash Mitra Mohammad Farhad Vahidi Shahid Mansoor Sahar Ahmed Al-Bayatti Eka Meutia Sari Neena Amatya Gorkhali Sigit Prastowo Laiba Shafique Guoyou Ye Qian Qian Baoshan Chen Deshun Shi Jue Ruan Qingyou Liu | 2020 | National Science Review2020，7，3： | 3 |
| 5 | 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 |
| 6 | The First High-quality Reference Genome of Sika Deer Provides Insights into High-tannin Adaptation显示文摘Sika deer are known to prefer oak leaves,which are rich in tannins and toxic to most mammals;however,the genetic mechanisms underlying their unique ability to adapt to living in the jungle are still unclear.In identifying the mechanism responsible for the tolerance of a highly toxic diet,we have made a major advancement by explaining the genome of sika deer.We generated the first high-quality,chromosome-level genome assembly of sika deer and measured the correlation between tannin intake and RNA expression in 15 tissues through 180 experiments.Comparative genome analyses showed that the UGT and CYP gene families are functionally involved in the adaptation of sika deer to high-tannin food,especially the expansion of the UGT family 2 subfamily B of UGT genes.The first chromosome-level assembly and genetic characterization of the tolerance to a highly toxic diet suggest that the sika deer genome may serve as an essential resource for understanding evolutionary events and tannin adaptation.Our study provides a paradigm of comparative expressive genomics that can be applied to the study of unique biological features in non-model animals. | Xiumei Xing Cheng Ai Tianjiao Wang Yang Li Huitao Liu Pengfei Hu Guiwu Wang Huamiao Liu Hongliang Wang Ranran Zhang Junjun Zheng Xiaobo Wang Lei Wang Yuxiao Chang Qian Qian Jinghua Yu Lixin Tang Shigang Wu Xiujuan Shao Alun Li Peng Cui Wei Zhan Sheng Zhao Zhichao Wu Xiqun Shao Yimeng Dong Min Rong Yihong Tan Xuezhe Cui Shuzhuo Chang Xingchao Song Tongao Yang Limin Sun Yan Ju Pei Zhao Huanhuan Fan Ying Liu Xinhui Wang Wanyun Yang Min Yang Tao Wei Shanshan Song Jiaping Xu Zhigang Yue Qiqi Liang Chunyi Li Jue Ruan Fuhe Yang | 2023 | Genomics, Proteomics & Bioinformatics2023，21，1： | 1 |
| 7 | De novo assembly of human genomes with massively parallel short read sequencing显示文摘 | Li Rui-qiang Zhu Hong-mei Ruan Jue | 2010 | Genome Res2010，20，： | 1 |
| 8 | Mapping short DNAsequencing reads and calling variants using mapping qualityscores显示文摘 | LIHENG RUAN JUE DURBIN R | 2008 | Genome Research2008，18，11： | 1 |
| 9 | A prolific and robust whole-genome genotyping method using PCR amplification via primer-template mismatched annealing显示文摘Whole-genome genotyping methods are important for breeding.However,it has been challenging to develop a robust method for simultaneous foreground and background genotyping that can easily be adapted to different genes and species.In our study,we accidently discovered that in adapter ligation-mediated PCR,the amplification by primertemplate mismatched annealing(PTMA)along the genome could generate thousands of stable PCR products.Based on this observation,we consequently developed a novel method for simultaneous foreground and background integrated genotyping by sequencing(FBI-seq)using one specific primer,in which foreground genotyping is performed by primer-template perfect annealing(PTPA),while background genotyping employs PTMA.Unlike DNA arrays,multiple PCR,or genome target enrichments,FBI-seq requires little preliminary work for primer design and synthesis,and it is easily adaptable to different foreground genes and species.FBI-seq therefore provides a prolific,robust,and accurate method for simultaneous foreground and background genotyping to facilitate breeding in the postgenomics era. | Sheng Zhao Cuicui Zhang Liqun Wang Minxuan Luo Peng Zhang Yue Wang Waqar Afzal Malik Yue Wang Peng Chen Xianjin Qiu Chongrong Wang Hong Lu Yong Xiang Yuwen Liu Jue Ruan Qian Qian Haijian Zhi Yuxiao Chang | 2023 | Journal of Integrative Plant Biology2023，65，3： | 0 |
| 10 | Multi-omics analysis reveals the evolutionary origin of diterpenoid alkaloid biosynthesis pathways in Aconitum显示文摘Diterpenoid alkaloids(DAs) have been often utilized in clinical practice due to their analgesic and anti-infammatory properties. Natural DAs are prevalent in the family Ranunculaceae, notably in the Aconitum genus. Nevertheless, the evolutionary origin of the biosynthesis pathway responsible for DA production remains unknown.In this study, we successfully assembled a highquality, pseudochromosome-level genome of the DA-rich species Aconitum vilmorinianum(A.vilmorinianum)(5.76 Gb). An A. vilmorinianumspecific whole-genome duplication event was discovered using comparative genomic analysis,which may aid in the evolution of the DA biosynthesis pathway. We identified several genes involved in DA biosynthesis via integrated genomic, transcriptomic, and metabolomic analyses. These genes included enzymes encoding target ent-kaurene oxidases and aminotransferases, which facilitated the activation of diterpenes and insertion of nitrogen atoms into diterpene skeletons, thereby mediating the transformation of diterpenes into DAs. The divergence periods of these genes in A. vilmorinianum were further assessed, and it was shown that two major types of genes were involved in the establishment of the DA biosynthesis pathway. Our integrated analysis offers fresh insights into the evolutionary origin of DAs in A.vilmorinianum as well as suggestions for engineering the biosynthetic pathways to obtain desired DAs. | Dake Zhao Ya Zhang Huanxing Ren Yana Shi Ding Dong Zonghang Li Guanghong Cui Yong Shen Zongmin Mou Edward JKennelly Luqi Huang Jue Ruan Suiyun Chen Diqiu Yu Yupeng Cun | 2023 | Journal of Integrative Plant Biology2023，65，10： | 0 |
| 11 | BARMR1-mediated sorafenib resistance is derived through stem-like property acquisition by activating integrin-FAK signaling pathways显示文摘Dear Editor,BARMR1(alternatively named FAM92A1 or FAM92A)gene was first identified in 2002 and is a highly conserved gene and widely expressed in most tissues in mammals.1 We first cloned the complete CDS sequence of BARMR1 in 2007,2 which encodes a protein with a Bin-Amphiphysin-Rvs(BAR)domain.BARcontaining proteins are known to bind onto lipid membrane surface and generate membrane curvature and have been demonstrated to play diverse roles in cell growth,inflammation and cell migration. | Xing Rong Guo Meng Ye Shan Yu Huang Zong Li Zhang Yue Yuan Long Jun Dai Jue Wang Xue Peng Zhou Fu Yun Ji Jun Ming Tang Zhong Ji Meng Xu Zhi Ruan | 2020 | Signal Transduction and Targeted Therapy2020，5，1： | 0 |
| 12 | The complete and fully-phased diploid genome of a male Han Chinese显示文摘Since the release of the complete human genome,the priority of human genomic study has now been shifting towards closing gaps in ethnic diversity.Here,we present a fully phased and well-annotated diploid human genome from a Han Chinese male individual(CN1),in which the assemblies of both haploids achieve the telomere-to-telomere(T2T)level.Comparison of this diploid genome with the CHM13 haploid T2T genome revealed significant variations in the centromere.Outside the centromere,we discovered 11,413 structural variations,including numerous novel ones.We also detected thousands of CN1 alleles that have accumulated high substitution rates and a few that have been under positive selection in the East Asian population.Further,we found that CN1 outperforms CHM13 as a reference genome in mapping and variant calling for the East Asian population owing to the distinct structural variants of the two references.Comparison of SNP calling for a large cohort of 8869 Chinese genomes using CN1 and CHM13 as reference respectively showed that the reference bias profoundly impacts rare SNP calling,with nearly 2 million rare SNPs miss-called with different reference genomes.Finally,applying the CN1 as a reference,we discovered 5.80 Mb and 4.21 Mb putative introgression sequences from Neanderthal and Denisovan,respectively,including many East Asian specific ones undetected using CHM13 as the reference.Our analyses reveal the advances of using CN1 as a reference for population genomic studies and paleo-genomic studies.This complete genome will serve as an alternative reference for future genomic studies on the East Asian population. | Chentao Yang Yang Zhou Yanni Song Dongya Wu Yan Zeng Lei Nie Panhong Liu Shilong Zhang Guangji Chen Jinjin Xu Hongling Zhou Long Zhou Xiaobo Qian Chenlu Liu Shangjin Tan Chengran Zhou Wei Dai Mengyang Xu Yanwei Qi Xiaobo Wang Lidong Guo Guangyi Fan Aijun Wang Yuan Deng Yong Zhang Jiazheng Jin Yunqiu He Chunxue Guo Guoji Guo Qing Zhou Xun Xu Huanming Yang Jian Wang Shuhua Xu Yafei Mao Xin Jin Jue Ruan Guojie Zhang | 2023 | Cell Research2023，33，10： | 0 |
| 13 | En Route to Completion:What Is An Ideal Reference Genome?显示文摘Since the Human Genome Project assembled the first draft human genome 20 years ago[1],immense manpower,material,and financial resources have been cast for generating accurate,continuous,complete,and informative reference genome for each important species.Nowadays,although the qualities of these genome assemblies have been significantly improved compared to their initial draft versions. | Weihua Pan Jue Ruan | 2022 | Genomics, Proteomics & Bioinformatics2022，20，1： | 0 |
| 14 | A Chromosome-level Genome Assembly of Wild Castor Provides New Insights into Its Adaptive Evolution in Tropical Desert显示文摘Wild castor grows in the high-altitude tropical desert of the African Plateau,a region known for high ultraviolet radiation,strong light,and extremely dry condition.To investigate the potential genetic basis of adaptation to both highland and tropical deserts,we generated a chromosome-level genome sequence assembly of the wild castor accession WT05,with a genome size of 316 Mb,a scaffold N50 of 31.93 Mb,and a contig N50 of 8.96 Mb,respectively.Compared with cultivated castor and other Euphorbiaceae species,the wild castor exhibits positive selection and gene family expansion for genes involved in DNA repair,photosynthesis,and abiotic stress responses.Genetic variations associated with positive selection were identified in several key genes,such as LIG1,DDB2,and RECG1,involved in nucleotide excision repair.Moreover,a study of genomic diversity among wild and cultivated accessions revealed genomic regions containing selection signatures associated with the adaptation to extreme environments.The identification of the genes and alleles with selection signatures provides insights into the genetic mechanisms underlying the adaptation of wild castor to the high-altitude tropical desert and would facilitate direct improvement of modern castor varieties. | Jianjun Lu Cheng Pan Wei Fan Wanfei Liu Huayan Zhao Donghai Li Sen Wang Lianlian Hu Bing He Kun Qian Rui Qin Jue Ruan Qiang Lin Shiyou Lü Peng Cui | 2022 | Genomics, Proteomics & Bioinformatics2022，20，1： | 0 |
| 15 | GAEP:a comprehensive genome assembly evaluating pipeline显示文摘With the rapid development of sequencing technologies,especially the maturity of third-generation sequencing technologies,there has been a significant increase in the number and quality of published genome assemblies.The emergence of these high-quality genomes has raised higher requirements for genome evaluation.Although numerous computational methods have been developed to evaluate assembly quality from various perspectives,the selective use of these evaluation methods can be arbitrary and inconvenient for fairly comparing the assembly quality.To address this issue,we have developed the Genome Assembly Evaluating Pipeline(GAEP),which provides a comprehensive assessment pipeline for evaluating genome quality from multiple perspectives,including continuity,completeness,and correctness.Additionally,GAEP includes new functions for detecting misassemblies and evaluating the assembly redundancy,which performs well in our testing.GAEP is publicly available at https://github.com/zyoptimistic/GAEP under the GPL3.0 License.With GAEP,users can quickly obtain accurate and reliable evaluation results,facilitating the comparison and selection of high-quality genome assemblies. | Yong Zhang Hong-Wei Lu Jue Ruan | 2023 | Journal of Genetics and Genomics2023，50，10： | 0 |
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