Hirudinaria manillensis is an ephemeral, blood-sucking ectoparasite, possessing anticoagulant capacities with potential medical applications. Analysis of codon usage patterns would contribute to our understanding of the evolutionary mechanisms and genetic architecture of H. manillensis, which in turn would provide insight into the characteristics of other leeches. We analysed codon usage and related indices using 18,000 coding sequences (CDSs) retrieved from H. manillensis RNA-Seq data. We identified four highly preferred codons in H. manillensis that have G/C-endings. Points generated in an effective number of codons (ENC) plot distributed below the standard curve and the slope of a neutrality plot was less than 1. Highly expressed CDSs had lower ENC content and higher GC content than weakly expressed CDSs. Principal component analysis conducted on relative synonymous codon usage (RSCU) values divided CDSs according to GC content and divided codons according to ending bases. Moreover, by determining codon usage, we found that the majority of blood-diet related genes have undergone less adaptive evolution in H. manillensis, except for those with homologous sequences in the host species. Codon usage in H. manillensis had an overall preference toward C-endings and indicated that codon usage patterns are mediated by differential expression, GC content, and biological function. Although mutation pressure effects were also notable, the majority of genetic evolution in H. manillensis was driven by natural selection.

The genus Lespedeza (tribe: Desmodieae) consists of about 40 species that have high medicinal and economic value. However, in this genus, using morphological characters, the species identification is quite complicated, which can be solved by the analysis of the complete chloroplast genomes. As primary organelle genomes, the complete genome sequences of chloroplasts (cp) provide unique molecular information to study the divergence of species, RNA editing, and phylogeny. Therefore, to the best of our knowledge, for the first time, we sequenced the complete cp genomes of two representative Lespedeza species: Lespedeza davurica and Lespedeza cuneata. The cp genomes of both the species were found to be 149,010 bp in length, exhibiting the typical angiosperm chloroplast structure containing four regions. The Lespedeza cp genomes showed similar conserved gene contents, order, and orientations with a total GC content of 35.0%. A total of 128 genes, including 83 protein-coding genes, 37 tRNAs, and eight rRNAs, were identified from each genome. Unique molecular features of the two Lespedeza cp genome sequences were obtained by performing the analysis of repeats, sequence divergence, codon usage, and predicting the RNA editing sites in addition to phylogenetic analysis with other key genera in tribe Desmodieae. Using the two datasets, the phylogenetic relationship of Lespedeza species among Deasmodieae was discovered, suggesting that whole cp genomes provided useful information for phylogenetic studies of these species.

Mitochondrial genomes offer pragmatic genetic markers to reconstruct evolutionary relationships and inform taxonomic classifications. Here, we present complete mitochondrial sequences for four Chinese pygmy grasshoppers (Tetrigidae), aiming to reevaluate phylogenetic patterns and morphological taxonomy. Our 17,643 bp, 16,274 bp, 15,086 bp, and 15,398 bp mitogenomes of Exothotettix guangxiensis, Formosatettix longwangshanensis, Euparatettix sinufemoralis and Systolederus zhengi, respectively, exhibit archetypal Tetrigidae architecture. We constructed phylogenies using 13 protein-coding loci from 39 Tetrigidae mitogenomes, revealing several genus-level clusters with statistically solid support, conflicts regarding Ex. guangxiensis, F. longwangshanensis merging into Tetrix, and two subclades of Systolederus. The dated divergence analysis indicates over 150 Mya of Tetrigidae ancestry, tracing the Systolederus generic group splits up to ~75 million years ago. Moreover, the Tetrix generic group radiated over 14 Mya across vast distributions, consistent with rapid adaptive dispersals. Our mitochondrial reconstructions suggest that Synstolederus is taxonomically overextended for a single genus, while the distinctiveness of Ex. guangxiensis and F. longwangshanensis from Tetrix appears questionable, and the Tetrix generic group comprises a potential tRNA-Ile coding region. Our integrative mitogenomic approaches will help resolve issues stemming from morphological taxonomy that is reliant on traits that are prone to convergence. This investigation enhances comprehension of Tetrigidae phylogeny and accentuates molecular systematics.

Cadmium (Cd)-containing chemicals can cause serious damage to biological systems. In animals and plants, Cd exposure can lead to metabolic disorders or death. However, for the most part the effects of Cd on specific biological processes are not known. DNA methylation is an important mechanism for the regulation of gene expression. In this study we examined the effects of Cd exposure on global DNA methylation in a living organism by whole-genome bisulfite sequencing (WGBS) using Drosophila melanogaster as model. A total of 71 differentially methylated regions and 63 differentially methylated genes (DMGs) were identified by WGBS. A total of 39 genes were demethylated in the Cd treatment group but not in the control group, whereas 24 showed increased methylation in the former relative to the latter. In most cases, demethylation activated gene expression: genes such as Cdc42 and Mekk1 were upregulated as a result of demethylation. There were 37 DMGs that overlapped with differentially expressed genes from the digital expression library including baz, Act5C, and ss, which are associated with development, reproduction, and energy metabolism. DNA methylation actively regulates the physiological response to heavy metal stress in Drosophila in part via activation of apoptosis.

The gut microbiome significantly influences the health and productivity of silkworms (Bombyx mori), the cornerstone of sericulture. With the increasing use of cost-effective artificial diets in sericulture, it is crucial to understand how these diets impact the silkworm gut microbiomes. Here we employed 16S rRNA sequencing to delineate the impact of three distinct dietary regimens on the silkworm gut microbiomes: exclusive mulberry leaf diet (SY), exclusive artificial feed diet (SL), and a sequential transition from artificial feed to mulberry leaves (ZS). Our results unveiled stark differences in microbial diversity across the groups, with the ZS group displaying an intermediary complexity. LefSe and random forest analyses identified Methylobacteriaceae, Microbacterium, and Rhodococcus as significantly enriched in the ZS group, suggesting their potential to facilitate silkworms’ adaptation to dietary transitions. Functional profiling revealed differential pathway regulation, indicating a metabolic reconfiguration in response to dietary modulations. Notably, the enrichment of Lactobacillus and Weissella in both the SL and ZS groups highlights their potential as probiotics in artificial diets. Our findings provide insights into the diet adaptation mechanisms of silkworm gut microbiota, paving the way for harnessing the intestinal bacteria to enhance silkworm health and silk production through targeted microbial interventions in sericulture practices.

Ferns represent the second-largest group of vascular plants, yet their genomic resources lag far behind. Here, we present a chromosome-scale genome assembly of Cibotium barometz (L.) J. Sm., a medicinally important fern species. The 3.49 Gb genome, assembled into 66 chromosomes with 99.41% sequence anchorage, revealed an exceptionally high proportion (83.93%) of repetitive elements, dominated by recently expanded LTR retrotransposons. We identified 30,616 protein-coding genes, providing insights into fern-specific gene families. Genomic analyses uncover the evolutionary dynamics of 513 key biosynthetic genes, particularly those involved in terpenoid and flavonoid production. Expression profiling across tissues revealed tissue-specific regulation of these pathways, with notable upregulation of chalcone synthase genes in roots. Our structural analysis of 1-deoxy-d-xylulose-5-phosphate synthase, a key enzyme in terpenoid biosynthesis, demonstrated high conservation across land plants while highlighting fern-specific adaptations. The identification of multiple isoforms for key enzymes points to potential gene-duplication events or the evolution of fern-specific variants. This genome provides a foundation for understanding fern biology, evolution, and the molecular basis of their medicinal properties. It also offers valuable resources for conservation efforts and pharmacological research, paving the way for sustainable utilization of this valuable medicinal plant and advancing our understanding of plant diversity and natural product biosynthesis.