Chi Song’s research while affiliated with Chengdu University of Traditional Chinese Medicine and other places

Background Karyotype and genome size are critical genetic characteristics with significant value for cytogenetics, taxonomy, phylogenetics, evolution, and molecular biology. The Lycosidae family, known for its diverse spiders with varying ecological habits and behavioral traits, has seen limited exploration of its karyotype and genome size. Methods We utilized an improved tissue drop technique to prepare chromosome slides and compare the features of male and female karyotypes for two wolf spiders with different habits of Lycosidae. Furthermore, we predicted their genome sizes using flow cytometry (FCM) and K-mer analysis. Results The karyotypes of female and male Hippasa lycosina were 2n♀ = 26 = 14 m + 12 sm and 2n♂ = 24 = 10 m + 14 sm, respectively, and were composed of metacentric (m) and submetacentric (sm) chromosomes. In contrast, the karyotypes of Lycosa grahami consisted of telocentric (t) and subtelocentric (st) chromosomes (2n♀ = 20 = 20th and 2n♂ = 18 = 12th + 6t, for females and males). The sex chromosomes were both X 1 X 2 O. The estimated sizes of the H. lycosina and L. grahami genomes were 1966.54–2099.89 Mb and 3692.81–4012.56 Mb, respectively. Flow cytometry yielded slightly smaller estimates for genome size compared to k-mer analysis. K-mer analysis revealed a genome heterozygosity of 0.42% for H. lycosina and 0.80% for L. grahami , along with duplication ratios of 21.39% and 54.91%, respectively. Conclusion This study describes the first analysis of the genome sizes and karyotypes of two spiders from the Lycosidae that exhibit differential habits and provides essential data for future phylogenetic, cytogenetic, and genomic studies.

Asparagus cochinchinensis has been recognized as an edible and medicinal herb in China, which has resulted in high market demand. Therefore, optimizing its cultivation practice is essential to maintain and enhance production levels. In this study, we simultaneously employed amplicon sequencing and transcriptomic sequencing technology to analyze the rhizosphere bacterial community structure and gene expression level in A. cochinchinensis collected from the main production areas. Results showed that a total of 50 phyla, 138 classes, 343 orders, 490 families, and 875 genera were identified, of which Proteobacteria and RB41 were the most abundant at the phylum and genus level, respectively. Transcriptomics results showed that the gene expression was related to biotic stress resistance, plant growth and development, and polysaccharide metabolism, which was supported by qPCR results. These findings offer valuable insights into the utilization safety and quality improvement of A. cochinchinensis.

Traditional medicines serve not only as an integral part of medical treatments prescribed by healthcare providers but also as a fundamental reservoir for novel molecular scaffolds. However, gaps remain in our understanding of the mechanisms underlying their activity. A superfamily of membrane proteins, G protein-coupled receptors (GPCRs), have been demonstrated to be potential targets for several compounds isolated from traditional medicines. Given that GPCRs serve as targets for approximately one-third of all marketed drugs, they may be compelling targets for repurposing traditional medicines. Despite this potential, research investigating their activity or potential ligands across GPCRome, the library of human GPCRs, is scarce. Drawing on the functional and structural knowledge presently available, this review contemplates prospective trends in GPCR drug discovery, proposes innovative strategies for investigating traditional medicines, and highlights ligand screening approaches for identifying novel drug-like molecules. To discover bioactive molecules from traditional medicines that either directly bind to GPCRs or indirectly modify their function, a genome-wide pan-GPCR drug discovery platform was designed for the identification of bioactive components and targets, and the evaluation of their pharmacological profiles. This platform aims to aid the exploration of all-sided relations between traditional medicines and GPCRome using advanced high-throughput screening techniques. We present various approaches used by many, including ourselves, to illuminate the previously unexplored aspects of traditional medicines and GPCRs.

Asparagus cochinchinensis is a medicinal plant in China, which has gained attention owing its protective effect in human health. However, there are seldom studies to systematically reveal the rhizosphere bacterial community of A. cochinchinensis. In this study, we employed metagenomics and culturomics to analyze the bacterial community composition and diversity in continuous rhizosphere soil of A. cochinchinensis. Meanwhile, we assessed the effect of soil physicochemical properties on the bacterial community. Results showed that the most abundant TAXA is a taxon belonging to the family Streptomycetaceae, the genus Mycobacterium and the species Oligotropha carboxidovorans. The bacterial communities across various areas were similar. Significant differences of exchangeable magnesium and available phosphorus level were observed between three groups. Furthermore, bacterial community structure correlated closely with soil physicochemical properties. Additionally, a total of 103 strains were isolated and identified, representing 28 species. Based on this study, the rhizosphere bacterial community of A. cochinchinensis might influence its growth and development. The rhizosphere strains were isolated and their function request further investigation. This study firstly revealed the bacterial community in the A. cochinchinensis rhizosphere soil, providing valuable references for its quality improvement in practical cultivation process.

The dysfunction of gut microbiome and bile acid metabolism might cause the incidence and relapse of ulcerative colitis (UC). Thus, natural products have been considered effective for UC through the regulation of gut microbiome and bile acid. In this study, we evaluated the regulatory effect of berberine on gut microbiome and bile acid metabolism in UC. Results showed that the relative abundances of beneficial bacteria showed a decreasing trend in the UC model, and the taurine conjugated bile acids increased from the liver tissue to the colon tissue. Berberine inhibited the colonization of harmful bacteria and promoted the primary bile acid metabolism. Moreover, we used multi-omics technology (metagenomics, metabolomics, and transcriptomics technology) to reveal that berberine restored the intestinal barrier function through bile acid/S1PR2/RhoA/ROCK pathway. The result of transmission electron microscopy directly showed that the damaged intestinal mucosal barrier was repaired through the berberine treatment. This study revealed the treatment influence on UC through multi-omics technology in vitro and in vivo models, which provides references for explaining the mechanism of berberine on UC.

Introduction Cepharanthine (CEP), a bisbenzylisoquinoline alkaloid (bisBIA) extracted from Stephania japonica, has received significant attention for its anti-coronavirus properties. While ethylene response factors (ERFs) have been reported to regulate the biosynthesis of various alkaloids, their role in regulating CEP biosynthesis remains unexplored. Methods Genome-wide analysis of the ERF genes was performed with bioinformatics technology, and the expression patterns of different tissues, were analyzed by transcriptome sequencing analysis and real-time quantitative PCR verification. The nuclear-localized ERF gene cluster was shown to directly bind to the promoters of several CEP-associated genes, as demonstrated by yeast one-hybrid assays and subcellular localization assays. Results In this work, 59 SjERF genes were identified in the S. japonica genome and further categorized into ten subfamilies. Notably, a SjERF gene cluster containing three SjERF genes was found on chromosome 2. Yeast one-hybrid assays confirmed that the SjERF gene cluster can directly bind to the promoters of several CEP-associated genes, suggesting their crucial role in CEP metabolism. The SjERFs cluster-YFP fusion proteins were observed exclusively in the nuclei of Nicotiana benthamiana leaves. Tissue expression profiling revealed that 13 SjERFs exhibit high expression levels in the root, and the qRT-PCR results of six SjERFs were consistent with the RNA-Seq data. Furthermore, a co-expression network analysis demonstrated that 24 SjERFs were highly positively correlated with the contents of various alkaloids and expression levels of CEP biosynthetic genes. Conclusion This study provides the first systematic identification and analysis of ERF transcription factors in the S.japonica genome, laying the foundation for the future functional research of SjERFs transcription factors.

Asteraceae, the largest family of angiosperms, has attracted widespread attention for its exceptional medicinal, horticultural, and ornamental value. However, researches on Asteraceae plants face challenges due to their intricate genetic background. With the continuous advancement of sequencing technology, a vast number of genomes and genetic resources from Asteraceae species have been accumulated. This has spurred a demand for comprehensive genomic analysis within this diverse plant group. To meet this need, we developed the Asteraceae Genomics Database (AGD; http://cbcb.cdutcm.edu.cn/AGD/). The AGD serves as a centralized and systematic resource, empowering researchers in various fields such as gene annotation, gene family analysis, evolutionary biology, and genetic breeding. AGD not only encompasses high-quality genomic sequences, and organelle genome data, but also provides a wide range of analytical tools, including BLAST, JBrowse, SSR Finder, HmmSearch, Heatmap, Primer3, PlantiSMASH, and CRISPRCasFinder. These tools enable users to conveniently query, analyze, and compare genomic information across various Asteraceae species. The establishment of AGD holds great significance in advancing Asteraceae genomics, promoting genetic breeding, and safeguarding biodiversity by providing researchers with a comprehensive and user-friendly genomics resource platform.

Background Terpenes are important components of plant aromas, and terpene synthases (TPSs) are the key enzymes driving terpene diversification. In this study, we characterized the volatile terpenes in five different Chrysanthemum nankingense tissues. In addition, genome-wide identification and expression analysis of TPS genes was conducted utilizing an improved chromosome-scale genome assembly and tissue-specific transcriptomes. The biochemical functions of three representative TPSs were also investigated. Results We identified tissue-specific volatile organic compound (VOC) and volatile terpene profiles. The improved Chrysanthemum nankingense genome assembly was high-quality, including a larger assembled size (3.26 Gb) and a better contig N50 length (3.18 Mb) compared to the old version. A total of 140 CnTPS genes were identified, with the majority representing the TPS-a and TPS-b subfamilies. The chromosomal distribution of these TPS genes was uneven, and 26 genes were included in biosynthetic gene clusters. Closely-related Chrysanthemum taxa were also found to contain diverse TPS genes, and the expression profiles of most CnTPSs were tissue-specific. The three investigated CnTPS enzymes exhibited versatile activities, suggesting multifunctionality. Conclusions We systematically characterized the structure and diversity of TPS genes across the Chrysanthemum nankingense genome, as well as the potential biochemical functions of representative genes. Our results provide a basis for future studies of terpene biosynthesis in chrysanthemums, as well as for the breeding of improved chrysanthemum varieties.