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| 1 | Genetic Contribution of Paleopolyploidy to Adaptive Evolution in Angiosperms显示文摘Ancient whole-genome duplications (WGDs or polyploidy) are prevalent in plants, and some WGDs occurred during the timing of severe global environmental changes. It has been suggested that WGDs may have contributed to plant adaptation. However, this still lacks empirical evidence at the genetic level to support the hypothesis. Here, we investigated the survivors of gene duplicates from multiple ancient WGD events on the major branches of angiosperm phylogeny, and aimed to explore genetic evidence supporting the significance of polyploidy. Duplicated genes co-retained from three waves of independent WGDs (~120 million years ago [Ma], ~66, and <20 Ma) were investigated in 25 selected species. Gene families functioning in low temperature and darkness were commonly retained gene duplicates after the eight independently occurring WGDs in many lineages around the Cretaceous-Paleocene boundary, when the global cooling and darkness were the two main stresses. Moreover, the commonly retained duplicates could be key factors which may have contributed to the robustness of the critical stress-related pathways. In addition, genome-wide transcription factors (TFs) functioning in stresses tend to retain duplicates after waves of WGDs, and the coselected gene duplicates in many lineages may play critical roles during severe environmental stresses. Collectively, these results shed new light on the significant contribution of paleopolyploidy to plant adaptation during global environmental changes in the evolutionary history of angiosperms. | Shengdan Wu Baocai Han Yuannian Jiao | 2020 | Molecular Plant2020，13，1： | 21 |
| 2 | 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://gffzz6c7fcf032cb94ff5swvqbo05bcbv56kpx.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://gffzzaeec8df70e7c4b21hwvqbo05bcbv56kpx.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 |
| 3 | 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 |
| 4 | Comparison of fatty acid profile of three adipose tissues in Ningxiang pigs显示文摘The present study is conducted to determinate fatty acids(FA) composition in 3 adipose tissues. Subcutaneous and perirenal adipose tissues were prepared from 24 Ningxiang castrated boars and 24 castrated gilts fattened by a traditional diet for 56 d, respectively. The results showed that the FA profile in the 3 adipose tissues(dorsal subcutaneous adipose [DSA], abdominal subcutaneous adipose [ASA], and perirenal adipose [PA]) differed greatly. In boars, the proportions of oleic acid(c18:1 n9 c)(P < 0.05), cis-11-20 c acid(c20:1)(P < 0.05), and a-linolenic acid(c18:3 n3)(P < 0.05) in DSA were the highest among 3 adipose tissues, whereas palmitic acid(c16:0)(P < 0.05) and stearic acid(c18:0)(P < 0.05) in DSA had the lowest proportion. In gilts, cis-11-20 c acid(c20:1)(P < 0.05) in DSA was the highest, while stearic acid(c18:0)(P < 0.05) in subcutaneous adipose was the lowest among these deposits. Overall, the results indicate that from external to inner carcass of boars, the sum of saturated fatty acids(SFA) increase, but the sum of monounsaturated fatty acids(MUFA) decrease, while ASA of gilts have the greatest proportion of MUFA and the lowest SFA. Sex and adipose locations as significant effects on the FA profile are interaction. | Qianming Jiang Chenyan Li Yuannian Yu Yueteng Xing Dingfu Xiao Bin Zhang | 2018 | Animal Nutrition2018，，3： | 3 |
| 5 | Double the Genome, Double the Fun: Genome Duplications in Angiosperms显示文摘 | Yuannian,Jiao | 2018 | Molecular Plant2018，11，3： | 3 |
| 6 | A chromosome-scale genome assembly of Artemisia argyi reveals unbiased subgenome evolution and key contributions of gene duplication to volatile terpenoid diversity显示文摘Artemisia argyi Le´vl.et Vant.,a perennial Artemisia herb with an intense fragrance,is widely used in traditional medicine in China and many other Asian countries.Here,we present a chromosome-scale genome assembly of A.argyi comprising 3.89 Gb assembled into 17 pseudochromosomes.Phylogenetic and comparative genomic analyses revealed that A.argyi underwent a recent lineage-specificwhole-genomeduplication(WGD)event after divergence fromArtemisia annua,resulting in two subgenomes.Wedeciphered the diploid ancestral genome of A.argyi,and unbiased subgenome evolution was observed.The recent WGD led to a large number of duplicated genes in the A.argyi genome.Expansion of the terpene synthase(TPS)gene family through various types of gene duplication may have greatly contributed to the diversity of volatile terpenoids in A.argyi.In particular,we identified a typical germacrene D synthase gene cluster within the expanded TPS gene family.The entire biosynthetic pathways of germacrenes,(+)-borneol,and(+)-camphor were elucidated in A.argyi.In addition,partial deletion of the amorpha-4,11-diene synthase(ADS)gene and loss of function of ADS homologs may have resulted in the lack of artemisinin production in A.argyi.Our study provides newinsights into the genome evolution of Artemisia and lays a foundation for further improvement of the quality of this important medicinal plant. | Hongyu Chen Miaoxian Guo Shuting Dong Xinling Wu Guobin Zhang Liu He Yuannian Jiao Shilin Chen Li Li Hongmei Luo | 2023 | Plant Communications2023，4，3： | 2 |
| 7 | 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 |
| 8 | 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 |
| 9 | 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 |
| 10 | 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 |
| 11 | 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 |
| 12 | 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 |
| 13 | 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 |
| 14 | 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 |
| 15 | 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 |
| 16 | New insights into the dispersion history and adaptive evolution of taxon Aegilops tauschii in China显示文摘Aegilops tauschii,the wild progenitor of wheat D-genome and a valuable germplasm for wheat improvement,has a wide natural distribution from eastern Turkey to China.However,the phylogenetic relationship and dispersion history of Ae.tauschii in China has not been scientifically clarified.In this study,we genotyped 208 accessions(with 104 in China)using dd RAD sequencing and 55K SNP array,and classified the population into six sublineages.Three possible spreading routes or events were identified,resulting in specific distribution patterns,with four sublineages found in Xinjiang,one in Qinghai,two in Shaanxi and one in Henan.We also established the correlation of SNP-based,karyotypebased and spike-morphology-based techniques to demonstrate the internal classification of Ae.tauschii,and developed consensus dataset with 1245 putative accessions by merging data previously published.Our analysis suggested that eight inter-lineage accessions could be assigned to the putative Lineage 3and these accessions would help to conserve the genetic diversity of the species.By developing the consensus phylogenetic relationships of Ae.tauschii,our work validated the hypothesis on the dispersal history of Ae.tauschii in China,and contributed to the efficient and comprehensive germplasm-mining of the species. | Hao Li Fang Nie Lele Zhu Menghua Mu Ruixiao Fan Jingyao Li Aaqib Shaheen Yifan Liu Can Li Wenjuan Liu Huihui Liang Xinpeng Zhao Shenglong Bai Guanghui Guo Zheng Li Yiheng Hu Yuannian Jiao Jonathan Adams Assaf Distelfeld Guiling Sun Suoping Li Yun Zhou Chun-Peng Song | 2022 | Journal of Genetics and Genomics2022，49，3： | 0 |
| 17 | The Genome of Opium Poppy Reveals Evolutionary History of Morphinan Pathway显示文摘Plants, as primary producers, have been playing an indispensable role in other organisms’ survival and the balance of whole ecosystem on Earth. Especially, they provide the main source of energy, food, and medicine for human beings, some of which are derived from the primary or secondary metabolites[1].Angiosperms,with more than 300,000 species on Earth,are the largest group of land plants by far. | Yiheng Hu Ran Zhao Peng Xu Yuannian Jiao | 2018 | Genomics, Proteomics & Bioinformatics2018，16，6： | 0 |
| 18 | WheatCENet:A Database for Comparative Co-expression Network Analysis of Allohexaploid Wheat and Its Progenitors显示文摘Genetic and epigenetic changes after polyploidization events could result in variable gene expression and modified regulatory networks.Here,using large-scale transcriptome data,we constructed co-expression networks for diploid,tetraploid,and hexaploid wheat species,and built a platform for comparing co-expression networks of allohexaploid wheat and its progenitors,named WheatCENet.WheatCENet is a platform for searching and comparing specific functional coexpression networks,as well as identifying the related functions of the genes clustered therein.Functional annotations like pathways,gene families,protein-protein interactions,microRNAs(miRNAs),and several lines of epigenome data are integrated into this platform,and Gene Ontology(GO)annotation,gene set enrichment analysis(GSEA),motif identification,and other useful tools are also included.Using WheatCENet,we found that the network of WHEAT ABERRANT PANICLE ORGANIZATION I(WAPOI)has more co-expressed genes related to spike development in hexaploid wheat than its progenitors.We also found a novel motif of CCWWWWWWGG(CArG)specifically in the promoter region of WAPO-Al,suggesting that neofunctionalization of the WAPO-AI gene affects spikelet development in hexaploid wheat.WheatCENet is useful for investigating co-expression networks and conducting other analyses,and thus facilitates comparative and functional genomic studies in wheat. | Zhongqiu Li Yiheng Hu Xuelian Ma Lingling Da Jiajie She Yue Liu Xin Yi Yaxin Cao Wenying Xu Yuannian Jiao Zhen Su | 2023 | Genomics, Proteomics & Bioinformatics2023，21，2： | 0 |
| 19 | 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 |
| 20 | Data-Driven Joint Estimation for Blind Signal Based on GA-PSO Algorithm显示文摘Without any prior information about related wireless transmitting nodes,joint estimation of the position and power of a blind signal combined with multiple co-frequency radio waves is a challenging task.Measuring the signal related data based on a group distributed sensor is an efficient way to infer the various characteristics of the signal sources.In this paper,we propose a particle swarm optimization to estimate multiple co-frequency'blind'source nodes,which is based on the received power data measured by the sensors.To distract the mix signals precisely,a genetic algorithm is applied,and it further improves the estimation performance of the system.The simulation results show the efficiency of the proposed algorithm. | LIU Shen QIN Yuannian LI Xiaofan ZHAO Yubin XU Chengzhong | 2019 | ZTE Communications2019，17，3： | 0 |
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