Baimei Liu’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.

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.

Cepharanthine, a secondary metabolite isolated from Stephania, has garnered attention for its reported effectiveness against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). To discover more cepharanthine analogs with anti-coronavirus properties, we assembled three Stephania genomes, proposed the cepharanthine biosynthetic pathway, and assessed the antiviral potential of compounds involved in the pathway. Nearly perfect telomere-to-telomere assembly with one remaining gap has been obtained for the S. japonica genome. Genome-guided cepharanthine analogs mining in Stephania was performed to identify cepharanthine-related metabolites with anti-coronavirus properties, and seven cepharanthine analogs can broad-spectrum inhibit coronavirus including SARS-CoV-2, GX_P2V, SADS-CoV and PEDV infection. Two other genera that produce cepharanthine analogs, Nelumbo and Thalictrum, are also believed to have potential for antiviral compound discovery. Here, we have systematically assessed anti-coronavirus activity of a series of cepharanthine metabolites from the viewpoint of biosynthesis pathway, our study will provide an opportunity to accelerate broad-spectrum anti-coronavirus drug discovery.