Alpinia oxyphylla Miq. (A. oxyphylla) is an important edible and traditional herbal medicine. In this study, the complete chloroplast genome of A. oxyphylla was sequenced, analysed, and compared to five species in the Zingiberaceae family. The size of the A. oxyphylla chloroplast genome was 161351 bp, which consisted of a large single-copy (LSC, 87248 bp) and small single-copy (SSC, 16175 bp) region separated by a pair of inverted repeats (IRa and IRb, 28964 bp each). The genome encoded 132 unique genes, including 87 protein-coding genes, 37 tRNAs and four rRNAs. The GC content of the genome was 36.17%. A total of 53 simple sequence repeats (SSRs) and 80 long repeats were identified in the A. oxyphylla chloroplast genome. The chloroplast genome of A. oxyphylla shared the highest sequence similarity of >90% with the chloroplast genome of A. zerumbet, and six chloroplast genomes in the Zingiberaceae family were compared by using CGView Comparison Tool (CCT). According to the phylogenetic tree, the Zingiberaceae family is divided into two categories, which coincide with the classification of the characteristics of sun-like and shade-like in plants. Our results reveal the phototrophic component of NADH-dehydrogenase (ndhB and ndhC), photosystem II (psbZ) and ATP synthase (atpE, atpF) exhibit adaptive evolution under different environments, and the strength of light is an important trigger for the adaptations at the chloroplast level.

The venoms of various sea anemones are rich in diverse toxins, which usually play a dual role in capturing prey and deterring predators. However, the complex components of such venoms have not been well known yet. Here, venomics of integrating transcriptomic and proteomic technologies was applied for the first time to identify putative protein and peptide toxins from different tissues of the representative sea anemone, Heteractis magnifica. The transcriptomic analysis of H. magnifica identified 728 putative toxin sequences, including 442 and 381 from the tentacles and the column, respectively, and they were assigned to 68 gene superfamilies. The proteomic analysis confirmed 101 protein and peptide toxins in the venom, including 91 in the tentacles and 39 in the column. The integrated venomics also confirmed that some toxins such as the ShK-like peptides and defensins are co-expressed in both the tentacles and the column. Meanwhile, a homology analysis was conducted to predict the three-dimensional structures and potential activity of seven representative toxins. Altogether, this venomics study revealed the venom complexity of H. magnifica, which will help deepen our understanding of cnidarian toxins, thereby supporting the in-depth development of valuable marine drugs.

Sea anemone venoms contain diverse toxins that have significant pharmacological potential, including anticancer, ecticidal, and immunotherapeutic properties. However, critically, the extraction methodology influences venom composition and bioactivity. This study characterized venom from Stichodactyla haddoni obtained via homogenization, electrical stimulation, and milking. Extraction yields varied significantly between methods: the homogenization, electrical stimulation, and milking of healthy sea anemones yielded crude venoms at rates of 17.8%, 3.4%, and 1.5%, respectively. SDS-PAGE revealed distinct protein banding patterns and concentrations, while RP-HPLC demonstrated method-dependent compositional differences. Comprehensive proteomic profiling identified 2370 proteins, encompassing both unique and shared components across extraction techniques. Label-free quantitative analysis confirmed significant variations in protein abundance that was attributable to the extraction method. Cytotoxicity assays against cancer cell lines revealed concentration-dependent inhibition, with milking-derived venom exhibiting the highest potency. Insecticidal activity against Tenebrio molitor was also method-dependent, with milking venom inducing the highest mortality rate. These findings elucidate the profound impact of extraction methodology on the protein composition and functional activities of S. haddoni venom, providing crucial insights for its optimized exploitation in pharmacological development.

Background: Maclura tricuspidata is an important medicinal and horticultural plant. However, the complete mitochondrial genome (mitogenome) of M. tricuspidata has not been reported, hindering molecular phylogenetic studies, species identification, and evolutionary research. Results: We present the first comprehensive analysis of the M. tricuspidata mitogenome. It features a multi-chromosomal structure comprising three circular-mapping chromosomes, with a total length of 416,801 bp and a GC content of 44.94%. Annotation identified 28 unique protein-coding genes (PCGs), 18 tRNA genes, and 3 rRNA genes. Codon usage analysis revealed GCU and CAA as the predominant codons for alanine and glutamine, respectively, while methionine and tryptophan, as single-codon amino acids, showed no bias. A total of 154 simple sequence repeats (SSRs) were detected: 84 on chromosome 1, 48 on chromosome 2, and 22 on chromosome 3. Analysis identified 19 homologous fragments transferred from the chloroplast genome (cpDNA), accounting for 4.31% of the mitogenome length. Using the Deepred-mt suite, 409 C-to-U RNA editing sites were predicted from the complete set of 28 mitochondrial PCGs, with the highest number in nad4 and the lowest in sdh4 . Phylogenetic analysis confirmed the placement of M. tricuspidata within the Moraceae family, showing closest relationships to Ficus carica and Morus notabilis , consistent with the APG IV system. Comparative analysis revealed extensive syntenic blocks between the M. tricuspidata mitogenome and those of related species, alongside regions lacking homology. In addition, dN/dS analysis revealed that most of the protein-coding genes in the mitogenome had undergone negative selection, and only the ccmB and sdh4 gene had undergone potential positive selection in M. tricuspidata . Conclusions: The unique structural features and complexities of the M. tricuspidata mitogenome, along with its similarities and differences compared to related species, provide valuable insights into plant mitochondrial evolution, energy metabolism, and environmental adaptation. These findings contribute significantly to the understanding of plant mitogenome diversity and biology.

Alpinia oxyphylla is a medicinal plant of the Zingiberaceae family with established neuroprotective and gastrointestinal therapeutic effects. The absence of a complete genome has hindered the elucidation of its metabolic pathways and impeded genetic improvement. Here we present the first telomere-to-telomere (T2T), gap-free genome assembly of A. oxyphylla, together with comparative genomic analyses that explore its evolutionary history and biosynthetic capacity. The 2,045.52 Mb assembly spans 24 chromosomes with a contig N50 of 91.56 Mb and exhibits high quality: 97.5% BUSCO completeness, a base-level quality value (QV) of 69.69, and a long terminal repeat assembly index (LAI) of 22.59. We annotated 38,703 protein-coding genes, 98.21% of which were functionally assigned against multiple databases. Phylogenetic analysis clarified the species’ position within Zingiberaceae and revealed extensive chromosomal conservation. This T2T gap-free genome provides a foundational resource for investigating the genetic basis and evolutionary dynamics of A. oxyphylla, supporting germplasm conservation, phytogeographic studies, and functional genomics in this pharmacologically valuable species.