A species of Cardamine circaeoides Hook. f. et Thoms., 1861, which belongs to the Cardamine family (Brassicaceae), is an endemic species of the Wuling Mountains in Hunan and Hubei Provinces of China. Since there are many morphologically related species of C. circaeoides, the chloroplast (cp) genome characteristics of C. circaeoides were analyzed in order to explore the phylogenetic relationship between it and the closely related species. A cp genome totaling 154,838 base pairs exhibited a typical quadripartite structure with a pair of IRs (inverted repeats; 26,493 base pairs) separated by a small single-copy region of 17,938 base pairs and a large single-copy region of 83,914 base pairs. A total of 130 genes were found in the cp genome, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. There were 36.21%, 33.96%, 29.09%, and 42.35% GC content in the entire cp genome, LSC region, SSC region, and IR region, respectively. According to phylogenetic analysis, C. circaeoides is evolutionarily closer to Cardamine hupingshanensis.

The tribe Ampelopsideae plants are important garden plants with both medicinal and ornamental values. The study of codon usage bias (CUB) facilitates a deeper comprehension of the molecular genetic evolution of species and their adaptive strategies. The joint analysis of CUB in chloroplast genomes (cpDNA) offers valuable insights for in-depth research on molecular genetic evolution, biological resource conservation, and elite breeding within this plant family. The base composition and codon usage preferences of the eighteen chloroplast genomes were highly similar, with the GC content of bases at all positions of their codons being less than 50%. This indicates that they preferred A/T bases. Their effective codon numbers were all in the range of 35–61, which indicates that the codon preferences of the chloroplast genomes of the 18 Ampelopsideae plants were relatively weak. A series of analyses indicated that the codon preference of the chloroplast genomes of the 18 Ampelopsideae plants was influenced by a combination of multiple factors, with natural selection being the primary influence. The clustering tree generated based on the relative usage of synonymous codons is consistent with some of the results obtained from the phylogenetic tree of chloroplast genomes, which indicates that the clustering tree based on the relative usage of synonymous codons can be an important supplement to the results of the sequence-based phylogenetic analysis. Eventually, 10 shared best codons were screened on the basis of the chloroplast genomes of 18 species. The codon preferences of the chloroplast genome in Ampelopsideae plants are relatively weak and are primarily influenced by natural selection. The codon composition of the chloroplast genomes of the eighteen Ampelopsideae plants and their usage preferences were sufficiently similar to demonstrate that the chloroplast genomes of Ampelopsideae plants are highly conserved. This study provides a scientific basis for the genetic evolution of chloroplast genes in Ampelopsideae species and their suitable strategies.

Metasequoia glyptostroboides, Hu and W. C. Cheng, as the only surviving relict species of the Taxodiaceae Metasequoia genus, is a critically endangered and protected species in China. There is a risk of extinction due to the low vigor of M. glyptostroboides seeds, and the physiological mechanism of seed aging in M. glyptostroboides is not yet clear. In order to investigate the physiological and molecular mechanisms underlying the aging process of M. glyptostroboides seeds, we analyzed the antioxidant system and transcriptome at 0, 2, 4, 6, and 8 days after artificial accelerated aging treatment at 40 °C and 100% relative humidity. It was found that the germination percentage of fresh dried M. glyptostroboides seeds was 54 ± 5.29%, and significantly declined to 9.33 ± 1.88% after 6 days of aging, and then gradually decreased until the seed died on day 8. Superoxide dismutase (SOD) activity, ascorbic acid (AsA), glutathione (GSH) content and superoxide anion (O₂^·−) content and production rate significantly decreased, while malondialdehyde (MDA) and hydrogen peroxide (H₂O₂) content and glutathione peroxidase (GPX) and catalase (CAT) activity gradually increased during the aging process. A total of 42,189 unigenes were identified in the whole transcriptome, and 40,446 (95.86%) unigenes were annotated in at least one protein database. A total of 15,376 differentially expressed genes (DEGs) were obtained; KEGG enrichment analysis results revealed that seed aging may be mainly involved in the protein-processing pathways in endoplasmic reticulum, oxidative phosphorylation, and ascorbate and aldarate metabolism. Weighted gene co-expression network analysis (WGCNA) revealed that the dark magenta, orange, and medium purple modules were highly correlated with physiological indicators such as SOD, CAT, and GSH and further identified 40 hub genes such as Rboh, ACO, HSF, and CML as playing important roles in the antioxidant network of M. glyptostroboides seeds. These findings provide a broader perspective for studying the regulatory mechanism of seed aging and a large number of potential target genes for the breeding of other endangered gymnosperms.

Leonurus japonicus Houtt. (L. japonicus), as an important plant resource with both ornamental and medicinal value, has now spread worldwide and is widely studied. Currently, its chromosomal genome and chloroplast genome (cpDNA) have been reported, but the mitochondrial genome (mtDNA) has not yet been explored. In this study, we extracted DNA from fresh leaves of L. japonicus and performed sequencing and assembly of its mtDNA using both second-generation and third-generation sequencing technologies. The complete mtDNA of L. japonicus is 382,905 bp in length, with a GC content of 45.13%. This genome includes 15 tRNA genes, 32 protein-coding genes (PCGs), and 4 rRNA genes. In this mtDNA genome, we predicted a total of 480 RNA editing sites among the 32 PCGs. Subsequently, we conducted analyses on repetitive sequences, organelle genome sequence migration, and Relative Synonymous Codon Usage (RSCU). There are 28 homologous sequence fragments between the mtDNA and cpDNA of L. japonicus, which are related to the migration of 10 mtDNA genes. The RSCU analysis predicted 28 high-frequency codons, most of which prefer to end with A/U. Selection pressure analysis indicated that the Ka/Ks ratio for the majority of PCGs is less than 1, suggesting they are highly conserved during evolutionary processes. Phylogenetic results from 24 species indicate that the genera Leonurus and Scutellaria within the Lamiaceae family have the closest relationships. In summary, we have successfully assembled the complete mtDNA of L. japonicus by integrating second-generation and third-generation sequencing data for the first time. Subsequent multi-faceted analyses have allowed us to gain deeper insights into the numerous features of this genome, providing important reference data for the molecular genetics, dynamic evolution, and species identification of this plant. This work promotes the conservation and development of this important resource of medicinal and edible plants.

Eucommia ulmoides Oliv., the only member of the family Eucommiaceae, is endemic to China and has great development and utilization prospects. The seeds of E. ulmoides show dormancy but the underlying mechanism remains unknown. The aim of this study was to determine the cause of the seed dormancy and provide fundamental knowledge for the breeding, genetic improvement, and conservation of the germplasm resources of this species. According to the seed dormancy classification system developed by Jerry M. Baskin and Carol C. Baskin, we compared the germination percentage between intact seeds and isolated embryos, constructed water absorption curves, and evaluated the germination of seeds treated with scarification, cold/warm-moist stratification, after-ripening during dry storage, and gibberellic acid (GA₃). The results showed that the intact seeds germinated only at 10 °C with a low germination percentage of 13.3% whereas the isolated embryos had a high normal germination percentage among a wider range of temperatures. According to the results from the scarified seeds, half seeds, and intact seeds, the seed coat significantly restricted the embryo water absorption. The scarification, after-ripening, cold/warm-moist stratification, and GA₃ treatments promoted seed germination. Among them, cold-moist stratification was the most effective method and the temperature range of seed germination increased in both directions from 10 °C with prolonged stratification. The germination percentage increased significantly at constant temperatures with the highest germination percentage of 93.7 ± 0.3% at 10 °C and a light/dark cycle after 90 days of cold-moist stratification. Therefore, the freshly harvested E. ulmoides seeds exhibited a combinational dormancy comprising physical and Type 3 non-deep physiological dormancy, causing limited embryo water absorption by the seed coat and a low embryo growth potential. Given the unique phylogenetic characteristics and utility of E. ulmoides, our findings should promote studies of seed dormancy evolution and the development and application of E. ulmoides germplasm resources.

Herb genomics, at the forefront of traditional Chinese medicine research, combines genomics with traditional practices, facilitating the scientific validation of ancient remedies. This integration enhances public understanding of traditional Chinese medicine’s efficacy and broadens its scope in modern healthcare. Stachys species encompass annual or perennial herbs or small shrubs, exhibiting simple petiolate or sessile leaves. Despite their wide-ranging applications across various fields, molecular data have been lacking, hindering the precise identification and taxonomic elucidation of Stachys species. To address this gap, we assembled the complete chloroplast (CP) genome of Stachys geobombycis and conducted reannotation and comparative analysis of seven additional species within the Stachys genus. The findings demonstrate that the CP genomes of these species exhibit quadripartite structures, with lengths ranging from 14,523 to 150,599 bp. Overall, the genome structure remains relatively conserved, hosting 131 annotated genes, including 87 protein coding genes, 36 tRNA genes, and 8 rRNA genes. Additionally, 78 to 98 SSRs and long repeat sequences were detected , and notably, 6 highly variable regions were identified as potential molecular markers in the CP genome through sequence alignment. Phylogenetic analysis based on Bayesian inference and maximum likelihood methods strongly supported the phylogenetic position of the genus Stachys as a member of Stachydeae tribe. Overall, this comprehensive bioinformatics study of Stachys CP genomes lays the groundwork for phylogenetic classification, plant identification, genetic engineering, evolutionary studies, and breeding research concerning medicinal plants within the Stachys genus.