Ya Wu’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.

Stephania japonica, a popular indoor ornamental and medicinal plant widely found in southern China, contains many natural compounds with potential medicinal value. S. japonica is also favored by researchers for its ability to produce catharanthine. Energy metabolism functions in plant development, and the composition of mitochondrial genome is regarded as the foundation for understanding energy metabolism and getting insights into plant environmental adaptation. In present investigation, the whole mitochondrial genome of S. japonica was assembled from both second- and third-generation sequencing data. The mitochondrial genome size of S. japonica is 555,117 bp. It is depicted as a complex polycyclic structure. In addition, we conducted an in-depth study of the cytochrome c oxidase (cox) gene, of which expression levels in different tissues of S. japonica were measured by real-time quantification PCR. Two phylogenetic trees were established in the light of sequences concerning 19 conserved mitochondrial protein-coding genes and cox gene, respectively. Both phylogenetic trees show that S. japonica is more closely related to Aconitum kusnezoffii. The result showed that the cox genes were the most highly expressed in the roots. A high-quality mitochondrial genome exhibits potential application value for the progress of molecular markers, identification of species as super DNA barcoding, and resolve mitochondrial energy metabolism mechanisms in response to the environment using genomic information. With the recognition of the medicinal value of Stephania plants, the genomic information of S. japonica has been thoroughly studied and the comprehensive analysis of its mitochondrial genome in this investigation can offer valuable insights for the breeding of new plant varieties.

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.

Mentha is a commonly used spice worldwide, which possesses medicinal properties and fragrance. These characteristics are conferred, at least partially, by essential oils such as menthol. In this study, a gap-free assembly with a genome size of 414.3 Mb and 31,251 coding genes was obtained for Mentha suaveolens ‘Variegata’. Based on its high heterozygosity (1.5%), two complete haplotypic assemblies were resolved, with genome sizes of 401.9 Mb and 405.7 Mb, respectively. The telomeres and centromeres of each haplotype were almost fully annotated. In addition, we detected a total of 41,135 structural variations. Enrichment analysis demonstrated that genes involved in terpenoid biosynthesis were affected by these structural variations. Analysis of volatile metabolites showed that Mentha suaveolens mainly produces piperitenone oxide rather than menthol. We identified three genes in the Mentha suaveolens genome which encode isopiperitenone reductase (ISPR), a key rate-limiting enzyme in menthol biosynthesis. However, the transcription levels of ISPR were low. Given that other terpenoid biosynthesis genes were expressed, Mentha suaveolens ISPRs may account for the accumulation of piperitenone oxide in this species. The findings of this study may provide a valuable resource for improving the detection rate and accuracy of genetic variants, thereby enhancing our understanding of their impact on gene function and expression. Moreover, our haplotype-resolved gap-free genome assembly offers novel insights into molecular marker-assisted breeding of Mentha.

Prunella vulgaris (Lamiaceae) is widely distributed in Eurasia. Former studies have demonstrated that P. vulgaris has a wide range of pharmacological effects. Nevertheless, no complete P. vulgaris mitochondrial genome has been reported, which limits further understanding of the biology of P. vulgaris. Here, we assembled the first complete mitochondrial genome of P. vulgaris using a hybrid assembly strategy based on sequencing data from both Nanopore and Illumina platforms. Then, the mitochondrial genome of P. vulgaris was analyzed comprehensively in terms of gene content, codon preference, intercellular gene transfer, phylogeny, and RNA editing. The mitochondrial genome of P. vulgaris has two circular structures. It has a total length of 297, 777 bp, a GC content of 43.92%, and 29 unique protein-coding genes (PCGs). There are 76 simple sequence repeats (SSRs) in the mitochondrial genome, of which tetrameric accounts for a large percentage (43.4%). A comparative analysis between the mitochondrial and chloroplast genomes revealed that 36 homologous fragments exist in them, with a total length of 28, 895 bp. The phylogenetic analysis showed that P. vulgaris belongs to the Lamiales family Lamiaceae and P. vulgaris is closely related to Salvia miltiorrhiza. In addition, the mitochondrial genome sequences of seven species of Lamiaceae are unconservative in their alignments and undergo frequent genome reorganization. This work reports for the first time the complete mitochondrial genome of P. vulgaris, which provides useful genetic information for further Prunella studies.