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| 1 | Herbgenomics: A stepping stone for research into herbal medicine显示文摘From the prehistoric era until the publishing of the Compendium of Materia Medica and the first scientific Nobel Prize in the Chinese mainland for Tu's discovery on anti-malarial tablets,each milestone and stepping stone in the developmental history of herbal medicine involved intrepid exploration,bold hypothesis formulation,and cautious verification.After thousands of years of discovery and development,herbal research has entered a new era—the era of herbgenomics.Herbgenomics combines herbal and genomic research,bridging the gap between traditional herbal medicine and cutting-edge omics studies.Therefore,it provides a general picture of the genetic background of traditional herbs,enabling researchers to investigate the mechanisms underlying the prevention and treatment of human diseases from an omics perspective. | Haoyu Hu Xiaofeng Shen Baosheng Liao Lu Luo Jiang Xu Shilin Chen | 2019 | Science China(Life Sciences)2019，62，7： | 13 |
| 2 | Genome-wide characterization and analysis of b HLH transcription factors in Panax ginseng显示文摘Ginseng(Panax ginseng C.A. Meyer) is one of the best-selling herbal medicines, with ginsenosides as its main pharmacologically active constituents. Although extensive chemical and pharmaceutical studies of these compounds have been performed, genome-wide studies of the basic helix-loop-helix(b HLH) transcription factors of ginseng are still limited. The b HLH transcription factor family is one of the largest transcription factor families found in eukaryotic organisms, and these proteins are involved in a myriad of regulatory processes. In our study, 169 bHLH transcription factor genes were identified in the genome of P. ginseng, and phylogenetic analysis indicated that these PGb HLHs could be classified into 24 subfamilies. A total of 21 RNA-seq data sets, including two sequencing libraries for jasmonate(JA)-responsive and 19 reported libraries for organ-specific expression analyses were constructed. Through a combination of gene-specific expression patterns and chemical contents,6 PGbHLH genes from 4 subfamilies were revealed to be potentially involved in the regulation of ginsenoside biosynthesis. These 6 PGbHLHs, which had distinct target genes, were further divided into two groups depending on the absence of MYC-N structure. Our results would provide a foundation for understanding the molecular basis and regulatory mechanisms of bHLH transcription factor action in P.ginseng. | Yang Chu Shuiming Xiao He Su Baosheng Liao Jingjing Zhang Jiang Xu Shilin Chen | 2018 | Acta Pharmaceutica Sinica B2018，8，4： | 13 |
| 3 | Global Pharmacopoeia Genome Database is an integrated and mineable genomic database for traditional medicines derived from eight international pharmacopoeias显示文摘Genomic data have demonstrated considerable traction in accelerating contemporary studies in traditional medicine. However,the lack of a uniform format and dispersed storage limits the full potential of herb genomic data. In this study, we developed a Global Pharmacopoeia Genome Database(GPGD). The database contains 34,346 records for 903 herb species from eight global pharmacopoeias(Brazilian, Egyptian, European, Indian, Japanese, Korean, the Pharmacopoeia of the People’s Republic of China, and U.S. Pharmacopoeia’s Herbal Medicines Compendium). In particular, the GPGD contains 21,872 DNA barcodes from 867 species, 2,203 organelle genomes from 674 species, 55 whole genomes from 49 species, 534 genomic sequencing datasets from 366 species, and 9,682 transcriptome datasets from 350 species. Among the organelle genomes, 534 genomes from 366 species were newly generated in this study. Whole genomes, organelle genomes, genomic fragments, transcriptomes, and DNA barcodes were uniformly formatted and arranged by species. The GPGD is publicly accessible at http://gffzzf938e9d610ce4c4ahnxvkfxfocofc6kpv.ffgz.tsg.suse.edu.cn and serves as an essential resource for species identification, decomposition of biosynthetic pathways, and molecular-assisted breeding analysis. Thus, the database is an invaluable resource for future studies on herbal medicine safety, drug discovery, and the protection and rational use of herbal resources. | Baosheng Liao Haoyu Hu Shuiming Xiao Guanru Zhou Wei Sun Yang Chu Xiangxiao Meng Jianhe Wei Han Zhang Jiang Xu Shilin Chen | 2022 | Science China(Life Sciences)2022，65，4： | 11 |
| 4 | Allele-aware chromosome-level genome assembly of Artemisia annua reveals the correlation between ADS expansion and artemisinin yield显示文摘Artemisia annua is the major natural source of artemisinin,an anti-malarial medicine commonly used worldwide.Here,we present chromosome-level haploid maps for two A.annua strains with different artemisinin contents to explore the relationships between genomic organization and artemisinin production.High-fidelity sequencing,optical mapping,and chromatin conformation capture sequencing were used to assemble the heterogeneous and repetitive genome and resolve the haplotypes of A.annua.Approximately 5o,ooo genes were annotated for each haplotype genome,and a triplication event that occurred approximately 58.12million years ago was examined for the first time in this species.A total of 3,903,467-5,193,414 variants(SNPs,indels,and structural variants)were identified in the 1.5-Gb genome during pairwise comparison between haplotypes,consistent with the high heterozygosity of this species.Genomic analyses revealed a correlation between artemisinin concents and the copy number of amorpha-4,11-dienes ynthasegenes.This correlation was further confirmed by resequencing of 36A.annua samples with varied artemisinin contents.Circular consensus sequencing of transcripts facilitated the detection of paralog expression.Collectively,our study provides chromosome-level allele-aware genome assemblies for two A.annua strains and new insights into the biosynthesis of artemisinin and its regulation,which will contribute to conquering malaria worldwide. | Baosheng Liao Xiaofeng Shen Li Xiang Shuai Guo Shiyu Chen Ying Meng Yu Liang Dandan Ding Junqi Bai Dong Zhang Tomasz Czechowski Yi Li Hui Yao Tingyu Mai Caroline Howard Chao Sun Haitao Liu Jiushi Liu Jin Pei Jihai Gao Jigang Wang Xiaohui Qiu Zhihai Huang Hongyi Li Ling Yuan Jianhe Wei lan Graham Jiang Xu Boli Zhang Shilin Chen | 2022 | Molecular Plant2022，15，8： | 9 |
| 5 | BioNano Genome Map Resource for Oryza sativa ssp.japonica and indica and Its Application in Rice Genome Sequence Correction and Gap Filling显示文摘 | Ping Chen Xinyun Jing Baosheng Liao Yan Zhu Jiang Xu Renyi Liu Yinhong Zhao Xuan Li | 2017 | Molecular Plant2017，10，6： | 4 |
| 6 | Cloning and analysis of 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate reductase genes HsHDR1 and HsHDR2 in Huperzia serrate显示文摘We cloned and analyzed the two genes of the 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate reductase(HDR) gene family from Huperzia serrate.The two transcripts coding HDR,named Hs HDR1 and Hs HDR2,were discovered in the transcriptome dataset of H.serrate and were cloned by reverse transcription-polymerase chain reaction(RT-PCR).The physicochemical properties,protein domains,protein secondary structure,and 3D structure of the putative Hs HDR1 and Hs HDR2 proteins were analyzed.The full-length c DNA of the Hs HDR1 gene contained 1431 bp encoding a putative protein with 476 amino acids,whereas the Hs HDR2 gene contained 1428 bp encoding a putative protein of 475 amino acids.These two proteins contained the conserved domain of 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate reductase(PF02401),but without the transmembrane region and signal peptide.The most abundant expression of Hs HDR1 and Hs HDR2 was detected in H.serrate roots,followed by the stems and leaves.Our results provide a foundation for exploring the function of Hs HDR1 and Hs HDR2 in terpenoid and sterol biosynthesis in Huperziaceae plants. | Haizhou Lv Xin Zhang Baosheng Liao Wanjing Liu Liu He Jingyuan Song Chao Sun Hongmei Luo Shilin Chen | 2015 | Acta Pharmaceutica Sinica B2015，5，6： | 3 |
| 7 | 50th anniversary of artemisinin:From the discovery to allele-aware genome assembly of Artemisia annua显示文摘Over the past half century,the fight against malaria has been a resounding success mainlydue to thediscoveryof artemisinin.According to the World Health Organization(WHO),morbidity and mortality due to malaria have been cut by half since the promotion of artemisinin-based combination therapy(WHO,2020). | Jiang Xu Baosheng Liao Ling Yuan Xiaofeng Shen Xuejiao Liao Jigang Wang Haoyu Hu Zhihai Huang Li Xiang Shilin Chen | 2022 | Molecular Plant2022，15，8： | 1 |
| 8 | Genome-wide identification and transcriptional profiling analysis of PIN/PILS auxin transporter gene families in Panax ginseng显示文摘Objective:Plant hormones act as chemical messengers in the regulation of plant development and metabolism.The production of ginsenosides in Panax hybrid is promoted by auxins that are transported and accumulated by PIN-FORMED(PIN)and PIN-LIKES(PILS)auxin transporters.However,genome-wide studies of PIN/PILS of ginseng are still scarce.In current study,identification and transcriptional profiling of PIN/PILS gene families,as well as their potential relationship with ginsenoside biosynthesis in Panax ginseng were investigated.Methods:PIN/PILS genes in P.ginseng was identified via in silico genome-wide analysis,followed by phylogenetic relationships,gene structure,and protein profiles investigation.Moreover,previously reported RNA-sequence data from various tissues and roots after infection were utilized for PIN/PILS genes expression pattern analysis.The Pearson’s correlation analysis of specific PIN/PILS genes expression level and main ginsenoside contents were taken to reveal the potential relationship between auxin transports and ginsenoside biosynthesis in P.ginseng.Results:A genome-wide search of P.ginseng genome for homologous auxin transporter genes identified a total of 17 PIN and 11 PILS genes.Sequence alignment,putative motif organization,and sub-cellular localization indicated redundant and complementary biological functions of these PIN/PILS genes.Most PIN/PILS genes were differentially expressed in a tissue-specific manner,and showed significant correlations with ginsenoside content correspondingly.Eight auxin transporter genes,including both PIN and PILS subfamily members,were positively correlated with ginsenoside content(cor>0.60;P-value<0.05).The expression levels of eleven auxin transporter genes were increased dramatically in the early stage(0–0.5 DPI)after Cylindrocarpon destructans infection,accompanied with various overall expression patterns,implying the dynamic auxin transport in response to biotic stress.Conclusion:Based on the results,we speculate that the accumulation or depletion in temporal or spatial manner of auxin by PIN/PILS transporters involved in the regulation of HMGR activity and subsequent ginsenoside biosynthesis. | Shuiming Xiao Yang Chu Yanjun Chen Qinghe Zhao Baosheng Liao Jingjing Zhang Yuan Gao Jiang Xu Shilin Chen | 2022 | Chinese Herbal Medicines2022，14，1： | 1 |
| 9 | Genomic,transcriptomic,and epigenomic analysis of a medicinal snake,Bungarus multicinctus,to provides insights into the origin of Elapidae neurotoxins显示文摘The many-banded krait,Bungarus multicinctus,has been recorded as the animal resource of JinQianBaiHuaShe in the Chinese Pharmacopoeia.Characterization of its venoms classified chief phyla of modern animal neurotoxins.However,the evolutionary origin and diversification of its neurotoxins as well as biosynthesis of its active compounds remain largely unknown due to the lack of its high-quality genome.Here,we present the 1.58 Gbp genome of B.multicinctus assembled into 18 chromosomes with contig/scaffold N50 of 7.53 Mbp/149.8 Mbp.Major bungarotoxin-coding genes were clustered within genome by family and found to be associated with ancient local duplications.The truncation of glycosylphosphatidylinositol anchor in the 3'-terminal of a LY6E paralog released modern three-finger toxins(3FTxs)from membrane tethering before the Colubroidea divergence.Subsequent expansion and mutations diversified and recruited these 3FTxs.After the cobra/krait divergence,the modern unit-B ofβ-bungarotoxin emerged with an extra cysteine residue.A subsequent point substitution in unit-A enabled theβ-bungarotoxin covalent linkage.The B.multicinctus gene expression,chromatin topological organization,and histone modification characteristics were featured by transcriptome,proteome,chromatin conformation capture sequencing,and ChIP-seq.The results highlighted that venom production was under a sophisticated regulation.Our findings provide new insights into snake neurotoxin research,meanwhile will facilitate antivenom development,toxin-driven drug discovery and the quality control of JinQianBaiHuaShe. | Jiang Xu Shuai Guo Xianmei Yin Mingqian Li He Su Xuejiao Liao Qiushi Li Liang Le Shiyu Chen Baosheng Liao Haoyu Hu Juan Lei Yingjie Zhu Xiaohui Qiu Lu Luo Jun Chen Ruiyang Cheng Zhenzhan Chang Han Zhang Nicholas Chieh Wu Yiming Guo Dianyun Hou Jin Pei Jihai Gao Yan Hua Zhihai Huang Shilin Chen | 2023 | Acta Pharmaceutica Sinica B2023，13，5： | 0 |
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