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| 1 | Chromosome-scale assembly of the Dendrobium chrysotoxum genome enhances the understanding of orchid evolution显示文摘As one of the largest families of angiosperms,the Orchidaceae family is diverse.Dendrobium represents the second largest genus of the Orchidaceae.However,an assembled high-quality genome of species in this genus is lacking.Here,we report a chromosome-scale reference genome of Dendrobium chrysotoxum,an important ornamental and medicinal orchid species.The assembled genome size of D.chrysotoxum was 1.37 Gb,with a contig N50 value of 1.54 Mb.Of the sequences,95.75%were anchored to 19 pseudochromosomes.There were 30,044 genes predicted in the D.chrysotoxum genome.Two whole-genome polyploidization events occurred in D.chrysotoxum.In terms of the second event,whole-genome duplication(WGD)was also found to have occurred in other Orchidaceae members,which diverged mainly via gene loss immediately after the WGD event occurred;the first duplication was found to have occurred in most monocots(tau event).We identified sugar transporter(SWEET)gene family expansion,which might be related to the abundant medicinal compounds and fleshy stems of D.chrysotoxum.MADS-box genes were identified in D.chrysotoxum,as well as members of TPS and Hsp90 gene families,which are associated with resistance,which may contribute to the adaptive evolution of orchids.We also investigated the interplay among carotenoid,ABA,and ethylene biosynthesis in D.chrysotoxum to elucidate the regulatory mechanisms of the short flowering period of orchids with yellow flowers.The reference D.chrysotoxum genome will provide important insights for further research on medicinal active ingredients and breeding and enhances the understanding of orchid evolution. | Yongxia Zhang Guo-Qiang Zhang Diyang Zhang Xue-Die Liu Xin-Yu Xu Wei-Hong Sun Xia Yu Xiaoen Zhu Zhi-Wen Wang Xiang Zhao Wen-Ying Zhong Hongfeng Chen Wei-Lun Yin Tengbo Huang Shan-Ce Niu Zhong-Jian Liu | 2021 | Horticulture Research2021，8，1： | 3 |
| 2 | Targeting a novel inducible GPX4 alternative isoform to alleviate ferroptosis and treat metabolic-associated fatty liver disease显示文摘Metabolic-associated fatty liver disease(MAFLD),which is previously known as non-alcoholic fatty liver disease(NAFLD),represents a major health concern worldwide with limited therapy.Here,we provide evidence that ferroptosis,a novel form of regulated cell death characterized by iron-driven lipid peroxidation,was comprehensively activated in liver tissues from MAFLD patients.The canonical-GPX4(cGPX4),which is the most important negative controller of ferroptosis,is downregulated at protein but not mRNA level.Interestingly,a non-canonical GPX4 transcript-variant is induced(inducible-GPX4,iGPX4)in MAFLD condition.The high fat-fructose/sucrose diet(HFFD)and methionine/choline-deficient diet(MCD)-induced MAFLD pathologies,including hepatocellular ballooning,steatohepatitis andfibrosis,were attenuated and aggravated,respectively,in cGPX4-and iGPX4-knockin mice.cGPX4 and iGPX4 isoforms also displayed opposing effects on oxidative stress and ferroptosis in hepatocytes.Knockdown of iGPX4 by siRNA alleviated lipid stress,ferroptosis and cell injury.Mechanistically,the triggered iGPX4 interacts with cGPX4 to facilitate the transformation of cGPX4 from enzymatic-active monomer to enzymatic-inactive oligomers upon lipid stress,and thus promotes ferroptosis.Co-immunoprecipitation and nano LC–MS/MS analyses confirmed the interaction between iGPX4 and cGPX4.Our results reveal a detrimental role of non-canonical GPX4 isoform in ferroptosis,and indicate selectively targeting iGPX4 may be a promising therapeutic strategy for MAFLD. | Jie Tong Dongjie Li Hongbo Meng Diyang Sun Xiuting Lan Min Ni Jiawei Ma Feiyan Zeng Sijia Sun Jiangtao Fu Guoqiang Li Qingxin Ji Guoyan Zhang Qirui Shen Yuanyuan Wang Jiahui Zhu Yi Zhao Xujie Wang Yi Liu Shenxi Ouyang Chunquan Sheng Fuming Shen Pei Wang | 2022 | Acta Pharmaceutica Sinica B2022，12，9： | 3 |
| 3 | The Cymbidium genome reveals the evolution of unique morphological traits显示文摘The marvelously diverse Orchidaceae constitutes the largest family of angiosperms.The genus Cymbidium in Orchidaceae is well known for its unique vegetation,floral morphology,and flower scent traits.Here,a chromosomescale assembly of the genome of Cymbidium ensifolium(Jianlan)is presented.Comparative genomic analysis showed that C.ensifolium has experienced two whole-genome duplication(WGD)events,the most recent of which was shared by all orchids,while the older event was the t event shared by most monocots.The results of MADS-box genes analysis provided support for establishing a unique gene model of orchid flower development regulation,and flower shape mutations in C.ensifolium were shown to be associated with the abnormal expression of MADS-box genes.The most abundant floral scent components identi fied included methyl jasmonate,acacia alcohol and linalool,and the genes involved in the floral scent component network of C.ensifolium were determined.Furthermore,the decreased expression of photosynthesis-antennae and photosynthesis metabolic pathway genes in leaves was shown to result in colorful striped leaves,while the increased expression of MADS-box genes in leaves led to perianth-like leaves.Our results provide fundamental insights into orchid evolution and diversi fication. | Ye Ai Zhen Li Wei-Hong Sun Juan Chen Diyang Zhang Liang Ma Qing-Hua Zhang Ming-Kun Chen Qing-Dong Zheng Jiang-Feng Liu Yu-Ting Jiang Bai-Jun Li Xuedie Liu Xin-Yu Xu Xia Yu Yu Zheng Xing-Yu Liao Zhuang Zhou Jie-Yu Wang Zhi-Wen Wang Tai-Xiang Xie Shan-Hu Ma Jie Zhou Yu-Jie Ke Yu-Zhen Zhou Hsiang-Chia Lu Ke-Wei Liu Feng-Xi Yang Gen-Fa Zhu Laiqiang Huang Dong-Hui Peng Shi-Pin Chen Siren Lan Yves Van de Peer Zhong-Jian Liu | 2021 | Horticulture Research2021，8，1： | 1 |
| 4 | The genome sequence of star fruit(Averrhoa carambola)显示文摘Oxalidaceae is one of the most important plant families in horticulture,and its key commercially relevant genus,Averrhoa,has diverse growth habits and fruit types.Here,we describe the assembly of a high-quality chromosomescale genome sequence for Averrhoa carambola(star fruit).Ks distribution analysis showed that A.carambola underwent a whole-genome triplication event,i.e.,the gamma event shared by most eudicots.Comparisons between A.carambola and other angiosperms also permitted the generation of Oxalidaceae gene annotations.We identified unique gene families and analyzed gene family expansion and contraction.This analysis revealed significant changes in MADS-box gene family content,which might be related to the cauliflory of A.carambola.In addition,we identified and analyzed a total of 204 nucleotide-binding site,leucine-rich repeat receptor(NLR)genes and 58 WRKY genes in the genome,which may be related to the defense response.Our results provide insights into the origin,evolution and diversification of star fruit. | Shasha Wu Wei Sun Zhichao Xu Junwen Zhai Xiaoping Li Chengru Li Diyang Zhang Xiaoqian Wu Liming Shen Junhao Chen Hui Ren Xiaoyu Dai Zhongwu Dai Yamei Zhao Lei Chen Mengxia Cao Xinyu Xie Xuedie Liu Donghui Peng Jianwen Dong Yu-Yun Hsiao Shi-lin Chen Wen-Chieh Tsai Siren Lan Zhong-Jian Liu | 2020 | Horticulture Research2020，7，1： | 1 |
| 5 | Correction: The Cymbidium genome reveals the evolution of unique morphological traits显示文摘After online publication of the article 1 the author noticed minor typo in Fig.4c.CeSEP1/2/3/4 should be read as CeSEP1/3/4.Revised figure supplied during the proof correction was inadvertently not reproduced in the final version.In addition,the affiliation numbers of the authors revised in the original article during proof correction,but not reflected in the title page in Supplementary Information. | Ye Ai Zhen Li Wei-Hong Sun Juan Chen Diyang Zhang Liang Ma Qing-Hua Zhang Ming-Kun Chen Qing-Dong Zheng Jiang-Feng Liu Yu-Ting Jiang Bai-Jun Li Xuedie Liu Xin-Yu Xu Xia Yu Yu Zheng Xing-Yu Liao Zhuang Zhou Jie-Yu Wang Zhi-Wen Wang Tai-Xiang Xie Shan-Hu Ma Jie Zhou Yu-Jie Ke Yu-Zhen Zhou Hsiang-Chia Lu Ke-Wei Liu Feng-Xi Yang Gen-Fa Zhu Laiqiang Huang Dong-Hui Peng Shi-Pin Chen Siren Lan Yves Van de Peer Zhong-Jian Liu | 2021 | Horticulture Research2021，8，1： | 1 |
| 6 | The Cymbidium goeringii genome provides insight into organ development and adaptive evolution in orchids显示文摘Cymbidium goeringii is one of the important ornamental orchids,but its high-quality genome has not been previously published.Here,we report a chromosome-level genome of C.goeringii and report the gene family expansion,and contraction of the C.goeringii genome and the regulation mechanism of MADS-box genes in floral organ development.We constructed the pathways of carotenoids and anthocyanins that contribute to the different flower colors of C.goeringii and the metabolic pathways of the main components of flower fragrance.Moreover,we found the genes that regulate colourful leaves and analyzed the resistance genes involved in the adaptive evolution of C.goeringii.Our results provide valuable genomic resources for the improvement of orchids and other ornamental plants. | Ye Sun Gui-Zhen Chen Jie Huang Ding-Kun Liu Feng Xue Xiu-Lan Chen Shi-Qiang Chen Chun-Gui Liu Hong Liu Hui Ma Yuan Yuan Diyang Zhang Wei-Hong Sun Dong-Hui Peng Zhi-Wen Wang Siren Lan Guo-Qi Zhao Feng-Tong Li Zhong-Jian Liu | 2021 | Ornamental Plant Research2021，1，1： | 1 |
| 7 | The camphor tree genome enhances the understanding of magnoliid evolution显示文摘Magnoliids represent the third largest branch of the most diverse and species-rich angiosperms,and their phylogenetic position relative to monocots and eudicots remains uncertain(Dong et al.,2021).Here,we describe the assembly of a high-quality chromosome-level genome sequence for Cinnamomum camphora(camphor),an evergreen tree belonging to Lauraceae.Genomebased phylogenetic analysis indicated possible incomplete lineage sorting(ILS)during the rapid diversification of the early diverging branches of angiosperms,which may have led to the unstable phylogenetic position of magnoliids. | Wei-Hong Sun Shuang Xiang Qi-Gong Zhang Lin Xiao Diyang Zhang Peilan Zhang De-Qiang Chen Yang Hao, Ding-Kun Liu Le Ding Yifan Li Hui Ni Yifan Wang Xi Wu Fu-Hui Liu Guo-Rui Chen Guo-Yong Han Jin-Zhang Chen Bao-Chun Su Jin-Xing Gao Xiao-Hui Wan Zhiwen Wang Yicun Chen Yang-Dong Wang Wei Huang Bobin Liu Xiao-Xing Zou Lin Ni Zhong-Jian Liu Shuang-Quan Zou | 2022 | Journal of Genetics and Genomics2022，49，3： | 0 |
| 8 | The effect of baduanjin exercise in rehabilitation for functional ankle instability:A study protocol for a randomized controlled pilot trial显示文摘Introduction:Patients with functional ankle instability(FAI)have problems with joint control,balance,gait,and postural symmetry.Baduanjin is a type of traditional Chinese exercise that has been shown to be effective in treating many diseases and symptoms.However,to date,the effect of Baduanjin in patients with FAI has not been proved.This pilot trial is an assessor-blinded randomized controlled trial,and its objective is to study the efficacy and safety of Baduanjin on the rehabilitation of patients with FAI.Methods:Seventy-two participants,who are eligible according to specified inclusion and exclusion criteria,will be randomized(in a 1:1 ratio),using a random number table,into two groups:a Baduanjin group and a conventional treatment group.The Baduanjin group will be subjected to the Baduanjin exercise in addition to the conventional treatment therapy.Participants’exercise programs will be implemented for 4 weeks(5 days a week).All participants will be assessed at baseline,and after two and 4 weeks of treatment.The surface electromyography results of the bilateral erector spinae,tibialis anterior,and peroneus longus will be the primary outcomes,while the balance function under different conditions and the level of FAI in daily life measured using the Cumberland Ankle Instability Tool will be the secondary outcomes.Ethics and Dissemination:The trial has been approved by the Research Ethical Committee of Dongzhimen Hospital,the First Affiliated Hospital of Beijing University of Chinese Medicine(no.DZMEC-KY-2019-18),and it will follow the principles of the Consolidated Standards of Reporting Trials statements as well as the Declaration of Helsinki.The findings of this study will be submitted for publication in peer-reviewed journals.The results will also be disseminated to the participants via phone calls or e-mail. | Li ZHOU Juanjuan AI Qingwen GENG Kuangshi LI Yiting SUN Ruyu YAN Diyang LYU Zongheng LI | 2021 | Journal of Integrative Nursing2021，3，2： | 0 |
| 9 | The Melastoma dodecandrum genome and the evolution of Myrtales显示文摘Melastomataceae has abundant morphological diversity with high economic and ornamental merit in Myrtales. The phylogenetic position of Myrtales is still contested. Here, we report the chromosome-level genome assembly of Melastoma dodecandrum in Melastomataceae. The assembled genome size is299.81 Mb with a contig N50 value of 3.00 Mb. Genome evolution analysis indicated that M. dodecandrum,Eucalyptus grandis, and Punica granatum were clustered into a clade of Myrtales and formed a sister group with the ancestor of fabids and malvids. We found that M. dodecandrum experienced four whole-genome polyploidization events: the ancient event was shared with most eudicots, one event was shared with Myrtales, and the other two events were unique to M. dodecandrum. Moreover, we identified MADS-box genes and found that the AP1-like genes expanded, and AP3-like genes might have undergone subfunctionalization. The SUAR63-like genes and AG-like genes showed different expression patterns in stamens, which may be associated with heteranthery. In addition, we found that LAZY1-like genes were involved in the negative regulation of stem branching development, which may be related to its creeping features. Our study sheds new light on the evolution of Melastomataceae and Myrtales, which provides a comprehensive genetic resource for future research. | Yang Hao Yu-Zhen Zhou Bin Chen Gui-Zhen Chen Zhen-Ying Wen Diyang Zhang Wei-Hong Sun Ding-Kun Liu Jie Huang Jin-Liao Chen Xiao-Qin Zhou Wan-Lin Fan Wen-Chun Zhang Lin Luo Wen-Chao Han Yan Zheng Long Li Peng-Cheng Lu Yue Xing Shu-Ya Liu Jia-Ting Sun Ying-Hui Cao Yan-Ping Zhang Xiao-Ling Shi Sha-Sha Wu Ye Ai Jun-Wen Zhai Si-Ren Lan Zhong-Jian Liu Dong-Hui Peng | 2022 | Journal of Genetics and Genomics2022，49，2： | 0 |
| 10 | Frequent germplasm exchanges drive the high genetic diversity of Chinese-cultivated common apricot germplasm显示文摘The genetic diversity of germplasm is critical for exploring genetic and phenotypic resources and has important implications for crop-breeding sustainability and improvement.However,little is known about the factors that shape and maintain genetic diversity.Here,we assembled a high-quality chromosome-level reference of the Chinese common apricot‘Yinxiangbai’,and we resequenced 180 apricot accessions that cover four major ecogeographical groups in China and other accessions from occidental countries.We concluded that Chinese-cultivated common apricot germplasms possessed much higher genetic diversity than those cultivated in Western countries.We also detected seven migration events among different apricot groups,where 27%of the genome was identified as being introgressed.Remarkably,we demonstrated that these introgressed regions drove the current high level of germplasm diversity in Chinese-cultivated common apricots by introducing different genes related to distinct phenotypes from different cultivated groups.Our results highlight the consideration that introgressed regions may provide an important reservoir of genetic resources that can be used to sustain modern breeding programs. | Qiuping Zhang Diyang Zhang Kang Yu Jingjing Ji Ning Liu Yuping Zhang Ming Xu Yu-Jun Zhang Xiaoxue Ma Shuo Liu Wei-Hong Sun Xia Yu Wenqi Hu Si-Ren Lan Zhong-Jian Liu Weisheng Liu | 2021 | Horticulture Research2021，8，1： | 0 |
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