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| 1 | The willow genome and divergent evolution from poplar after the common genome duplication显示文摘 | Xiaogang Dai Quanjun Hu Qingle Cai Kai Feng Ning Ye Gerald A Tuskan Richard Milne Yingnan Chen Zhibing Wan Zefu Wang Wenchun Luo Kun Wang Dongshi Wan Mingxiu Wang Jun Wang Jianquan Liu Tongming Yin | 2014 | Cell Research2014，24，10： | 28 |
| 2 | A chromosome-scale genome assembly of Isatis indigotica,an important medicinal plant used in traditional Chinese medicine显示文摘Isatis indigotica(2n=14)is an important medicinal plant in China.Its dried leaves and roots(called Isatidis Folium and Isatidis Radix,respectively)are broadly used in traditional Chinese medicine for curing diseases caused by bacteria and viruses such as influenza and viral pneumonia.Various classes of compounds isolated from this species have been identified as effective ingredients.Previous studies based on transcriptomes revealed only a few candidate genes for the biosynthesis of these active compounds in this medicinal plant.Here,we report a high-quality chromosome-scale genome assembly of I.indigotica with a total size of 293.88 Mb and scaffold N50=36.16 Mb using single-molecule real-time long reads and high-throughput chromosome conformation capture techniques.We annotated 30,323 highconfidence protein-coding genes.Based on homolog searching and functional annotations,we identified many candidate genes involved in the biosynthesis of main active components such as indoles,terpenoids,and phenylpropanoids.In addition,we found that some key enzyme-coding gene families related to the biosynthesis of these components were expanded due to tandem duplications,which likely drove the production of these major active compounds and explained why I.indigotica has excellent antibacterial and antiviral activities.Our results highlighted the importance of genome sequencing in identifying candidate genes for metabolite synthesis in medicinal plants. | Minghui Kang Haolin Wu Qiao Yang Li Huang Quanjun Hu Tao Ma Zaiyun Li Jianquan Liu | 2020 | Horticulture Research2020，7，1： | 9 |
| 3 | Hybrid speciation via inheritance of alternate alleles of parental isolating genes显示文摘It is increasingly realized that homoploid hybrid speciation(HHS),which involves no change in chromosome number,is an important mechanism of speciation.HHS will likely increase in frequency as ecological and geographical barriers between species are continuing to be disrupted by human activities.HHS requires the establishment of reproductive isolation between a hybrid and its parents,but the underlying genes and genetic mechanisms remain largely unknown.In this study,we reveal by integrated approaches that reproductive isolation originates in one homoploid hybrid plant species through the inheritance of altemate alleles at genes that determine parental premating isolation.The parent species of this hybrid species are reproductively isolated by differences in flowering time and survivorship on soils containing high concentrations of iron.We found that the hybrid species inherits alleles of parental isolating major genes related to flowering time from one parent and alleles of major genes related to iron tolerance from the other parent.In this way,it became reproductively isolated from one parent by the difference in flowering time and from the other by habitat adaptation(iron tolerance).These findings and further modeling results suggest that HHS may occur relatively easily via the inheritance of alternate parental premating isolating genes and barriers. | Zefu Wang Yuanzhong Jiang Hao Bi Zhiqiang Lu Yazhen Ma Xiaoyue Yang Ningning Chen Bin Tian Bingbing Liu Xingxing Mao Tao Ma Stephen P.DiFazio Quanjun Hu Richard J.Abbott Jianquan Liu | 2021 | Molecular Plant2021，14，2： | 4 |
| 4 | Pervasive hybridization during evolutionary radiation of Rhododendron subgenus Hymenanthes in mountains of southwest China显示文摘Radiations are especially important for generating species biodiversity in mountainous ecosystems.The contribution of hybridization to such radiations has rarely been examined.Here,we use extensive genomic data to test whether hybridization was involved in evolutionary radiation within Rhododendron subgenus Hymenanthes,whose members show strong geographic isolation in the mountains of southwest China.We sequenced genomes for 143 species of this subgenus and 93 species of four other subgenera,and found that Hymenanthes was monophyletic and radiated during the late Oligocene to middle Miocene.Widespread hybridization events were inferred within and between the identified clades and subclades.This suggests that hybridization occurred both early and late during diversification of subgenus Hymenan thes,although the extent to which hybridization,speciation through mixing-isolation-mixing or hybrid speciation,accelerated the diversification needs further exploration.Cycles of isolation and contact in such and other montane ecosystems may have together promoted species radiation through hybridization between diverging populations and species.Similar radiation processes may apply to other montane floras in this region and elsewhere. | Yazhen Ma Xingxing Mao Ji Wang Lei Zhang Yuanzhong Jiang Yuying Geng Tao Ma Liming Cai Shuangquan Huang Pete Hollingsworth Kangshan Mao Minghui Kang Yiling Li Wenlu Yang Haolin Wu Yang Chen Charles C.Davis Nawal Shrestha Richard H.Ree Zhenxiang Xi Quanjun Hu Richard I.Milne Jianquan Liu | 2022 | National Science Review2022，9，12： | 1 |
| 5 | Phylotranscriptomics of Swertiinae(Gentianaceae)reveals that key floral traits are not phylogenetically correlated显示文摘Establishing how lineages with similar traits are phylogenetically related remains critical for understanding the origin of biodiversity on Earth.Floral traits in plants are widely used to explore phylogenetic relationships and to delineate taxonomic groups.The subtribe Swertiinae(Gentianaceae)comprises more than 350 species with high floral diversity ranging from rotate to tubular corollas and possessing diverse nectaries.Here we performed phylogenetic analysis of 60 species from all 15 genera of the subtribe Swertiinae sensu Ho and Liu,representing the range of floral diversity,using data from the nuclear and plastid genomes.Extensive topological conflicts were present between the nuclear and plastome trees.Three of the 15 genera represented by multiple species are polyphyletic in both trees.Key floral traits including corolla type,absence or presence of lobe scales,nectary type,nectary position,and stigma type are randomly distributed in the nuclear and plastome trees without phylogenetic correlation.We also revealed the likely ancient hybrid origin of one large clade comprising 10 genera with diverse floral traits.These results highlight the complex evolutionary history of this subtribe.The phylogenies constructed here provide a basic framework for further exploring the ecological and genetic mechanisms underlying both species diversification and floral diversity. | Chunlin Chen Brad R.Ruhfel Jialiang Li Zefu Wang Lushui Zhang Lei Zhang Xingxing Mao Ji Wang Dashan He Yue Luo Quanjun Hu Yuanwen Duan Xiaoting Xu Zhenxiang Xi Jianquan Liu | 2023 | Journal of Integrative Plant Biology2023，65，6： | 1 |
| 6 | Genome-scale transcriptome analysis of the desert poplar, Populus euphratica显示文摘 | QIU Qiang MA Tao HU Quanjun | 2011 | Tree physiology2011，31，4： | 1 |
| 7 | Generation of gene-target dogs using CRISPR/Cas9 system显示文摘Dear Editor,Dogs(Canis familiaris)serve as human companions and are raised to herd livestock,aid hunters,guard homes,perform police and rescue work,and guide the blind.Dogs exhibit close similarities to humans in terms of metabolic,physiological,and anatomical characteristics,and thus are ideal genetic and clinical models to study human diseases(Tsai et al.,2007).Gene target technology is a powerful tool to create new strains of animals with favorable traits.However,thus far,gene-target dogs have not been developed due to their unique species-specific reproductive characteristics,which limits the applications of dogs especially in the field of biomedical research.Recently,clustered regularly interspaced short palindromic repeats(CRISPRs)/CRISPR-associated(Cas)9 system was applied to edit specific genes with a high efficiency(Cong et al.,2013;Mali et al.,2013).Here we attempt to explore the feasibility of producing gene knockout(KO)dogs by using this technology.Beagle dog,the most widely used breed in biomedical research,was used as our animal model.Myostatin(MSTN)was chosen as the first gene of interest. | Qingjian Zou Xiaomin Wang Yunzhong Liu Zhen Ouyang Haibin Long Shu Wei Jige Xin Bentian Zhao Sisi Lai Jun Shen Qingchun Ni Huaqiang Yang Huilin Zhong Li Li Minhua Hu Quanjun Zhang Zhidong Zhou Jiaxin He Quanmei Yan Nana Fan Yu Zhao Zhaoming Liu Lin Guo Jiao Huang Guanguan Zhang Jun Ying Liangxue Lai Xiang Gao | 2015 | Journal of Molecular Cell Biology2015，7，6： | 1 |
| 8 | Genome-scale transcrip- tome analysis of the desert poplar, Populus euphratica 显示文摘 | Qiu Qiang Ma Tao Hu Quanjun | 2011 | Tree Physiology2011，，4： | 1 |
| 9 | Transformation Design of Old Parks Based on Behavior Psychology: A Case Study of Hefei Xiaoyaojin Park显示文摘City park undertakes the function of urban core green island. Hefei Xiaoyaojin Park providesa leisure and entertainment place for Hefei citizens. Although it has been continuously transformed andupgraded, there are still many places to be improved. Through behavior observation and questionnaire,the usage and satisfaction evaluation of tourists in Xiaoyaojin Park were obtained, and the transformationdesign of Xiaoyaojin Park was analyzed from the perspective of behavior psychology by analyzing thebehavior of tourists in different zones of Xiaoyaojin. Based on the premise of exploring the behaviorof tourists in different spaces, a city park environment that meets the needs of tourists can be created bypromoting the cultural context of the Three Kingdoms, improving the plant landscape and infrastructureof the site, optimizing the spatial function, and exploring the park design and transformation strategy that ismore in line with the needs of people, in order to provide new ideas for the future landscape transformationof Xiaoyaojin park, and offer reference suggestions for the future transformation design of old city parks. | GE Juan CAO Menghan CHEN Jiaxin HU Yueyue LI Quanjun LI Yinan | 2023 | Journal of Landscape Research2023，15，5： | 0 |
| 10 | Urban Waterfront Space Design under the Concept of Ecological Conservation:A Case Study of Hefei Swan Lake显示文摘With the proposal of the concept that lucid waters and lush mountains are invaluable assets,ecological issues have become increasingly important issues of concern to people.The process of urbanization is accelerating,and the importance of urban waterfront space in improving the environmental quality of the city and people’s quality of life,enhancing the vitality of the city,the overall appearance of the city,and the competitiveness of the city,is receiving increasing attention.And how to properly handle the construction and development of urban waterfront space has become increasingly prominent in urban planning.Under the the concept of“ecological conservation”,it is thought that the construction of urban waterfront space should follow the principle of harmony between nature and man,and strengthen the multifaceted connection of the city.Through field research on Swan Lake,a comprehensive evaluation of the problems in the plank road and land ecology is conducted.It is proposed to improve the current situation of Swan Lake by grasping the two keywords of“waterfront”and“city”,and starting from the improvement of water body and the enhancement of urban cultural construction in the lake area. | LI Quanjun GE Juan WANG Mengqing HU Yueyue | 2023 | Journal of Landscape Research2023，15，4： | 0 |
| 11 | A chromosome-scale reference genome of Lobularia maritima,an ornamental plant with high stress tolerance显示文摘Lobularia maritima(L.)Desv.is an ornamental plant cultivated across the world.It belongs to the family Brassicaceae and can tolerate dry,poor and contaminated habitats.Here,we present a chromosome-scale,high-quality genome assembly of L.maritima based on integrated approaches combining Illumina short reads and Hi–C chromosome conformation data.The genome was assembled into 12 pseudochromosomes with a 197.70 Mb length,and it includes 25,813 protein-coding genes.Approximately 41.94%of the genome consists of repetitive sequences,with abundant long terminal repeat transposable elements.Comparative genomic analysis confirmed that L.maritima underwent a species-specific whole-genome duplication(WGD)event~22.99 million years ago.We identified~1900 species-specific genes,25 expanded gene families,and 50 positively selected genes in L.maritima.Functional annotations of these genes indicated that they are mainly related to stress tolerance.These results provide new insights into the stress tolerance of L.maritima,and this genomic resource will be valuable for further genetic improvement of this important ornamental plant. | Li Huang Yazhen Ma Jiebei Jiang Ting Li Wenjie Yang Lei Zhang Lei Wu Landi Feng Zhenxiang Xi Xiaoting Xu Jianquan Liu Quanjun Hu | 2020 | Horticulture Research2020，7，1： | 0 |
| 12 | Application of Shrub Landscape on Campus from the Perspective of Ornamental Characteristics of Plants显示文摘In the campus greening design,the shrub height is generally consistent with people’s horizontal line of sight,which plays a significant role in people’s visual focus.From the perspective of ornamental characteristics of plants,the application of shrub landscape is explored in a campus environment.Based on the analysis of the selection,arrangement and maintenance of shrub plants in campus gardens,the application of shrub landscape on campus was evaluated comprehensively from the theoretical analysis of plant ornamental characteristics and campus shrub landscape.Based on the research background of the problems existing in the application of shrub landscape on campus,this paper first collected and sorted out the relevant theories extensively,and then conducted in-depth research on the relevant theories by using analysis methods such as literature data,field investigation and questionnaire survey.The results will provide a theoretical guidance and practical advocacy for campus garden planning and design,and help to create a livable and comfortable campus environment.It is hoped that the results will have some references for future campus shrub landscape and play a certain promoting role. | HU Yueyue CAO Menghan GE Juan LI Quanjun CHEN Long LI Yanfei | 2023 | Journal of Landscape Research2023，15，4： | 0 |
| 13 | Ensemble learning system to identify nutritional risk and malnutrition in cancer patients without weight loss information显示文摘Dear Editor,Malnutrition is a prevalent disease in oncology practice(Arends et al.,2017).With its cancer-specific prevalence ranging from 21%–72%,malnutrition is responsible for 10%–20% cancer deaths(Yin et al.,2021b).However,malnutrition is often underestimated,misclassified,or left untreated in cancer care(Hébuterne et al.,2014). | Liangyu Yin Jie Liu Ming Liu Jin Zheng Aiguo Xu Quanjun Lyu Yongdong Feng Zengqing Guo Hu Ma Jipeng Li Zhikang Chen Hui Wang Zengning Li Chunling Zhou Xi Gao Min Weng Qinghua Yao Wei Li Tao Li Hanping Shi Hongxia Xu | 2023 | Science China(Life Sciences)2023，66，5： | 0 |
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