Background/Objectives: In South China, Lithocarpus species dominate mixed evergreen broadleaf forests, forming symbiotic relationships with ectomycorrhizal fungi and serving as food resources for diverse fauna, including frugivorous birds and mammals. The limited understanding of chloroplast genomes in this genus restricts our insights into its species diversity. This study investigates the chloroplast genome (cp genome) sequences from seven Lithocarpus species, aims to elucidate their structural variation, evolutionary relationships, and functional gene content to provide effective support for future genetic conservation and breeding efforts. Methods: We isolated total DNA from fresh leaves and sequenced the complete cp genomes of these samples. To develop a genomic resource and clarify the evolutionary relationships within Lithocarpus species, comparative chloroplast genome studies and phylogenetic investigations were performed. Results: All studied species exhibited a conserved quadripartite chloroplast genome structure, with sizes ranging from 161,495 to 163,880 bp. Genome annotation revealed 130 functional genes and a GC content of 36.72–37.76%. Codon usage analysis showed a predominance of leucine-encoding codons. Our analysis identified 322 simple sequence repeats (SSRs), which were predominantly palindromic in structure (82.3%). All eight species exhibited the same 19 SSR categories in similar proportions. Eight highly variable regions (ndhF, ycf1, trnS-trnG-exon1, trnk(exon1)-rps16(exon2), rps16(exon2), rbcL-accD, and ccsA-ndh) have been identified, which could be valuable as molecular markers in future studies on the population genetics and phylogeography of this genus. The phylogeny tree provided critical insights into the evolutionary trajectory of Fagaceae, suggesting that Lithocarpus was strongly supported as monophyletic, while Quercus was inferred to be polyphyletic, showing a significant cytonuclear discrepancy. Conclusions: We characterized and compared the chloroplast genome features across eight Lithocarpus species, followed by comprehensive phylogenetic analyses. These findings provide critical insights for resolving taxonomic uncertainties and advancing systematic research in this genus.

The oyster Crassostrea hongkongensis is eaten raw and whole, so the endogenous peptides carried by its tissue reach the intestinal lumen unprocessed; functional work on food-derived peptides has concentrated on cationic sequences. This study asked whether the endogenous peptide population of this species is anionically skewed and whether a preparation of that population alters the cytoskeletal gene programme of human intestinal epithelial cells. The published plasma peptidome of this species (PXD025247) was re-analysed, an endogenous peptide fraction below 10 kDa was prepared from oyster soft tissues without adding any protease, and the preparation was applied to differentiated Caco-2 monolayers at 0.1–2.0 mg/mL for 6–24 h; nine transcripts were measured by quantitative PCR against vehicle, protease-digested and digestion-only controls. Of 333 peptides, 157 (47.1%) carried a net charge of −1 or lower at pH 7, 148 (44.4%) were near-neutral and 28 (8.4%) carried +2 or above, and anionic peptides outnumbered cationic peptides in all four detection strata (36.4–58.3% against 4.8–9.1%). Actin-family proteins were the largest precursor source (186 peptides, 55.9%; 68.3% coverage of actin). The preparation was recovered at 2.41 ± 0.23 mg/g of wet tissues and, at 2.0 mg/mL, increased transcription of the SRF targets CCN1 (2.91-fold), VIL1 (2.29-fold), MYH9 (2.17-fold) and ACTN1 (1.83-fold) (p < 0.01 for each) and of TMSB4X, CFL1 and PFN1 (1.90-, 1.75- and 1.55-fold; q < 0.05), whereas SRF and MRTFA transcripts were unchanged; proteinase K digestion abolished the response. An endogenous peptide preparation from oyster soft tissues therefore acts on the cytoskeletal gene programme of human intestinal epithelial cells, and the anionically skewed majority of this peptidome is the fraction that warrants direct functional characterisation.

In South China, Lithocarpus species dominate mixed evergreen broadleaf forests, forming symbiotic relationships with ectomycorrhizal fungi and serving as food resources for diverse fauna, including frugivorous birds and mammals. The limited understanding of chloroplast genomes in this genus restricts our insights into its species diversity. This study investigates the chloroplast genome (cp genome) sequences from seven Lithocarpus species, aims to elucidates their structural variation, evolutionary relationships, and functional gene content, providing a foundation for future genetic conservation and breeding efforts. Methods: We isolated total DNA from fresh leaves and sequenced the complete cp genomes of these samples. Comparative cp genome analysis and phylo-genetic analysis were conducted to develop genomic resources and elucidate the intra-specific phylogeny of Lithocarpus. Results: All studied species exhibited a conserved quadripartite chloroplast genome structure, with sizes ranging from 161,495 to 163,880 bp. Genome annotation revealed 130 functional genes and a GC content of 36.72–37.76%. Codon usage analysis showed a predominance of leucine-encoding codons. Our analysis identified 322 simple sequence repeats (SSRs), predominantly palindromic in structure (82.3%). These SSRs comprised 19 distinct categories, with similar type distributions observed across all examined species. Eight highly variable regions (ndhF, ycf1, ycf1, trnS-trnG-exon1, trnk(exon1)-rps16(exon2), rps16(exon2), rbcL-accD and ccsA-ndh) have been identified, which could serve as potential DNA markers for future population genetics or phylogeographic studies on this genus. The well-resolved plastome phy-logeny tree provided critical insights into the evolutionary trajectory of Fagaceae, sug-gested that Lithocarpus was strongly supported as monophyletic, while Quercus was in-ferred to be polyphyletic, showed a significant cytonuclear discrepancy. Conclusions: We characterized and compared the chloroplast genome features across eight Lithocarpus species, followed by comprehensive phylogenetic analyses. These findings provide critical insights for resolving taxonomic uncertainties and advancing systematic research in this genus.

Background/Objectives: Long non-coding RNA (lncRNA) was structurally similar to mRNAs, yet they could not be translated into proteins. While an increasing number of reports have systematically identified and described lncRNA in model species, information about non-model species remains scarce. Sea cucumber Holothuria leucospilota could be used for both medicinal and food purposes, which have high economic value, gradually attracting the attention of researchers. Methods: In this research, we constructed lncRNA library and compared the difference in lncRNA expression profiles between testis and ovary of sea cucumber H. leucospilota. To elucidate the molecular interactions between lncRNA and mRNA, we computationally predicted potential complementary binding sites through analysis of both cis- and trans-acting antisense mechanisms. Subsequent Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses demonstrated that the identified target genes are potentially involved in the regulatory pathways governing gonad development. Results: Quantitative reverse transcription PCR analysis showed that MSTRG.32831.1-sox9 and MSTRG.57315.1-mthfr exhibited a high expression pattern in testis; while MSTRG.11041.1-mafa and MSTRG.11074.1-macf1 showed a high expression pattern in the ovary. Conclusions: Deciphering lncRNA–mRNA expression patterns may uncover fundamental principles governing reproductive regulation in marine invertebrates. This discovery not only deepens understanding in this field but also provides valuable comparative insights for developmental biology.