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| 1 | A Collinearity-Incorporating Homology Inference Strategy for Connecting Emerging Assemblies in the Triticeae Tribe as a Pilot Practice in the Plant Pangenomic Era显示文摘Plant genome sequencing has dramatically increased,and some species even have multiple high-quality reference versions.Demands for clade-specific homology inference and analysis have increased in the pangenomic era.Here we present a novel method,GeneTribe(http://gffzz6c7fcf032cb94ff5sq0un99np9bwx6559.ffgz.tsg.suse.edu.cn/genetribe/),for homology inference among genetically similar genomes that incorporates gene collinearity and shows bet-ter performance than traditional sequence-similarity-based methods in terms of accuracy and scalability.The Triticeae tribe is a typical allopolyploid-rich clade with complex species relationships that includes many important crops,such as wheat,barley,and rye.We built Triticeae-GeneTribe(http://gffzzaeec8df70e7c4b21hq0un99np9bwx6559.ffgz.tsg.suse.edu.cn/TGT/),a homology database,by integrating 12 Triticeae genomes and 3 outgroup model genomes and implemented versatile analysis and visualization functions.With macrocollinearity analysis,we were able to construct a refined model illustrating the structural rearrangements of the 4A-5A-7B chromosomes in wheat as two major translocation events.With collinearity analysis at both the macro-and microscale,we illustrated the complex evolutionary history of homologs of the wheat vernalization gene Vm2,which evolved as a combined result of genome translocation,duplication,and polyploidization and gene loss events.Our work provides a useful practice for connecting emerging genome assemblies,with awareness of the extensive polyploidy in plants,and will help researchers efficiently exploit genome sequence re-sources. | Yongming Chen Wanjun Song Xiaoming Xie Zihao Wang Panfeng Guan Huiru Peng Yuannian Jiao Zhongfu Ni Qixin Sun Weilong Guo | 2020 | Molecular Plant2020，13，12： | 14 |
| 2 | Wheat genomic study for genetic improvement of traits in China显示文摘Bread wheat(Triticum aestivum L.)is a major crop that feeds 40%of the world’s population.Over the past several decades,advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat,and the genetic basis of agronomically important traits,which promote the breeding of elite varieties.In this review,we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield,end-use traits,flowering regulation,nutrient use efficiency,and biotic and abiotic stress responses,and various breeding strategies that contributed mainly by Chinese scientists.Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools,highthroughput phenotyping platforms,sequencing-based cloning strategies,high-efficiency genetic transformation systems,and speed-breeding facilities.These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process,ultimately contributing to more sustainable agriculture in China and throughout the world. | Jun Xiao Bao Liu Yingyin Yao Zifeng Guo Haiyan Jia Lingrang Kong Aimin Zhang Wujun Ma Zhongfu Ni Shengbao Xu Fei Lu Yuannian Jiao Wuyun Yang Xuelei Lin Silong Sun Zefu Lu Lifeng Gao Guangyao Zhao Shuanghe Cao Qian Chen Kunpu Zhang Mengcheng Wang Meng Wang Zhaorong Hu Weilong Guo Guoqiang Li Xin Ma Junming Li Fangpu Han Xiangdong Fu Zhengqiang Ma Daowen Wang Xueyong Zhang Hong-Qing Ling Guangmin Xia Yiping Tong Zhiyong Liu Zhonghu He Jizeng Jia Kang Chong | 2022 | Science China(Life Sciences)2022，65，9： | 9 |
| 3 | Calibration of a discrete element model for intact rock up to its peak strength 显示文摘 | Wang Yuannian Tonon F | 2010 | Interna- tional Journal for Numerical and Analytical Methods in Geomechanics2010，34，5： | 1 |
| 4 | A new numerical method for dem?block and particle model显示文摘 | Shihai Li Manhong Zhao Yuannian Wang Ying Rao | 2004 | International Journal of Rock Mechanics and Mining Sciences2004，，3： | 1 |
| 5 | Modeling Lac du Bonnet granite using a discrete element model显示文摘 | Yuannian Wang Fulvio Tonon | 2009 | International Journal of Rock Mechanics and Mining Sciences2009，，7： | 1 |
| 6 | A chromosome-scale reference genome of Aquilegia oxysepala var.kansuensis显示文摘The genus Aquilegia(Ranunculaceae)has been cultivated as ornamental and medicinal plants for centuries.With petal spurs of strikingly diverse size and shape,Aquilegia has also been recognized as an excellent system for evolutionary studies.Pollinator‐mediated selection for longer spurs is believed to have shaped the evolution of this genus,especially the North American taxa.Recently,however,an opposite evolutionary trend was reported in an Asian lineage,where multiple origins of mini-or even nonspurred morphs have occurred.Interesting as it is,the lack of genomic resources has limited our ability to decipher the molecular and evolutionary mechanisms underlying spur reduction in this special lineage.Using long-read sequencing(PacBio Sequel),in combination with optical maps(BioNano DLS)and Hi–C,we assembled a high-quality reference genome of A.oxysepala var.kansuensis,a sister species to the nonspurred taxon.The final assembly is approximately 293.2 Mb,94.6%(277.4 Mb)of which has been anchored to 7 pseudochromosomes.A total of 25,571 protein-coding genes were predicted,with 97.2%being functionally annotated.When comparing this genome with that of A.coerulea,we detected a large rearrangement between Chr1 and Chr4,which might have caused the Chr4 of A.oxysepala var.kansuensis to partly deviate from the“decaying”path that was taken before the split of Aquilegia and Semiaquilegia.This high-quality reference genome is fundamental to further investigations on the development and evolution of petal spurs and provides a strong foundation for the breeding of new horticultural Aquilegia cultivars. | Jinghe Xie Haifeng Zhao Kunpeng Li Rui Zhang Yongchao Jiang Meimei Wang Xuelian Guo Ben Yu Hongzhi Kong Yuannian Jiao Guixia Xu | 2020 | Horticulture Research2020，7，1： | 1 |
| 7 | A new numerical method for dem?block and particle model显示文摘 | Shihai Li Manhong Zhao Yuannian Wang Ying Rao | 2004 | International Journal of Rock Mechanics and Mining Sciences2004，，3： | 1 |
| 8 | A new numerical method for 'DEM block and particle model 显示文摘 | Shihai Li Manhong Zhao Yuannian Wang | 2004 | International Journal of Rock Mechanics and Mining Sciences2004，41，3： | 1 |
| 9 | A new numerical method for dem?block and particle model显示文摘 | Shihai Li Manhong Zhao Yuannian Wang Ying Rao | 2004 | International Journal of Rock Mechanics and Mining Sciences2004，，3： | 1 |
| 10 | A new numerical method for dem-block and particle model 显示文摘 | LI Shihai ZHAO Manhong WANG Yuannian | 2004 | International Journal of Rock Mechanics and Mining Sciences2004，41，3： | 1 |
| 11 | Alterations of endotoxin distribution across different biofluids and relevant inflammatory responses by supplementing L-theanine in dairy cows during heat stress显示文摘The present trial was performed to reveal the regulatory effects of L-theanine on the levels of lipopolysaccharide(LPS)endotoxin within different biofluids,as well as relevant inflammatory responses of dairy cattle under heat stress conditions.Thirty lactating Chinese Holstein dairy cattle(189±47 d in milk,and 2±1 parities)were allocated in a completely randomized design to each of 3 dietary treatments:the control(CON,0 g/d per cow L-theanine),the low L-theanine dosage treatment(LL,16 g/d per cow L-theanine),and the high L-theanine dosage treatment(HL,32 g/d per cow L-theanine).This trial consisted of 38 d(7 d for adaption and 31 d for data and sample collection),and sample collection for rumen liquid,blood plasma or serum,and milk were conducted on the d 27 and 38,respectively.Dairy cattle were constantly exposed to environmental heat stress during this experiment according to the recorded temperature-humidity index(THI).In the LL treatment,LPS concentration in rumen liquid was higher(P<0.05),whilst LPS densities in plasma and milk were lower(P<0.05)than those of the CON.Supplementing L-theanine at 2 dosages both significantly lowered(P<0.05)the level of interleukin(IL)-1βin the serum.Results of the present study suggested that L-theanine could be a promising additive in reducing the detrimental effects of heat stress on dairy cows,and L-theanine supplementation at 16 g/d per cow is preferred because it reduced the LPS translocation into the peripheral blood and LPS accumulation in the milk,as well as mitigated LPS-induced inflammatory reactions in dairy cows during heat stress.Further studies are necessitated to investigate the underlying mechanisms of L-theanine in LPS alteration and inflammation alleviation. | Zuo Wang Lingmei Zhang Zhicai Li Yuannian Yu Lingyuan Yang Peihua Zhang Weijun Shen Fachun Wan Jianhua He Wenjun Xiao Dasheng Yang Zhiliang Tan Shaoxun Tang | 2021 | Animal Nutrition2021，，4： | 1 |
| 12 | The Physalis floridana genome provides insights into the biochemical and morphological evolution of Physalis fruits显示文摘The fruits of Physalis(Solanaceae)have a unique structure,a lantern-like fruiting calyx known as inflated calyx syndrome(ICS)or the Chinese lantern,and are rich in steroid-related compounds.However,the genetic variations underlying the origin of these characteristic traits and diversity in Physalis remain largely unknown.Here,we present a high-quality chromosome-level reference genome assembly of Physalis floridana(~1.40Gb in size)with a contig N50 of~4.87Mb.Through evolutionary genomics and experimental approaches,we found that the loss of the SEP-like MADS-box gene MBP21 subclade is likely a key mutation that,together with the previously revealed mutation affecting floral MPF2 expression,might have contributed to the origination of ICS in Physaleae,suggesting that the origination of a morphological novelty may have resulted from an evolutionary scenario in which one mutation compensated for another deleterious mutation.Moreover,the significant expansion of squalene epoxidase genes is potentially associated with the natural variation of steroid-related compounds in Physalis fruits.The results reveal the importance of gene gains(duplication)and/or subsequent losses as genetic bases of the evolution of distinct fruit traits,and the data serve as a valuable resource for the evolutionary genetics and breeding of solanaceous crops. | Jiangjie Lu Meifang Luo Li Wang Kunpeng Li Yongyi Yu Weifei Yang Pichang Gong Huihui Gao Qiaoru Li Jing Zhao Lanfeng Wu Mingshu Zhang Xueyang Liu Xuemei Zhang Xian Zhang Jieyu Kang Tongyuan Yu Zhimin Li Yuannian Jiao Huizhong Wang Chaoying He | 2021 | Horticulture Research2021，8，1： | 0 |
| 13 | A recent burst of gene duplications in Triticeae显示文摘Gene duplication provides raw genetic materials for evolution and potentially novel genes for crop improvement.The two seminal genomic studies of Aegilops tauschii both mentioned the large number of genes independently duplicated in recent years,but the duplication mechanism and the evolutionary significance of these gene duplicates have not yet been investigated.Here,we found that a recent burst of gene duplications(hereafter abbreviated as the RBGD)has probably occurred in all sequenced Triticeae species.Further investigations of the characteristics of the gene duplicates and their flanking sequences suggested that transposable element(TE)activity may have been involved in generating the RBGD.We also characterized the duplication timing,retention pattern,diversification,and expression of the duplicates following the evolution of Triticeae.Multiple subgenome-specific comparisons of the duplicated gene pairs clearly supported extensive differential regulation and related functional diversity among such pairs in the three subgenomes of bread wheat.Moreover,several duplicated genes from the RBGD have evolved into key factors that influence important agronomic traits of wheat.Our results provide insights into a unique source of gene duplicates in Triticeae species,which has increased the gene dosage together with the two polyploidization events in the evolutionary history of wheat. | Xiaoliang Wang Xueqing Yan Yiheng Hu Liuyu Qin Daowen Wang Jizeng Jia Yuannian Jiao | 2022 | Plant Communications2022，3，2： | 0 |
| 14 | Genome resources for the elite bread wheat cultivar Aikang 58 and mining of elite homeologous haplotypes for accelerating wheat improvement显示文摘Despite recent progress in crop genomics studies,the genomic changes brought about by modern breeding selection are still poorly understood,thus hampering genomics-assisted breeding,especially in polyploid crops with compound genomes such as common wheat(Triticum aestivum).In this work,we constructed genome resources for the modern elite common wheat variety Aikang 58(AK58).Comparative genomics between AK58 and the landrace cultivar Chinese Spring(CS)shed light on genomic changes that occurred through recent varietal improvement.We also explored subgenome diploidization and divergence in common wheat and developed a homoeologous locus-based genome-wide association study(HGWAS)approach,which was more effective than single homoeolog-based GWAS in unraveling agronomic trait-associated loci.A total of 123 major HGWAs loci were detected using a genetic population derived from AK58 and cs.Elite homoeologous haplotypes(HHs),formed by combinations of subgenomic homoeologs of the associated loci,were found in both parents and progeny,and many could substantially improve wheat yield and related traits.We built a website where users can download genome assembly sequence and annotation data for AK58,perform blast analysis,and run JBrowse.Our work enriches genome resources for wheat,provides new insights into genomic changes during modern wheat improve-.ment,and suggests that efficientmining of elite HHs can make a substantial contribuutionto genomics-assisted breeding in common wheat and other polyploid crops. | Jizeng Jia Guangyao Zhao Danping Li Kai Wang Chuizheng Kong Pingchuan Deng Xueqing Yan Xueyong Zhang Zefu Lu Shujuan Xu Yuannian Jiao Kang Chong Xu Liu Dangqun Cui Guangwei Li Yijing Zhang Chunguang Du Liang Wu Tianbao Li Dong Yan Kehui Zhan Feng Chen Zhiyong Wang Lichao Zhang Xiuying Kong Zhengang Ru Daowen Wang Lifeng Gao | 2023 | Molecular Plant2023，16，12： | 0 |
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