Genes

Background: The subtribe Pleurothallidinae is a diverse group within Orchidaceae with a complex taxonomic history. Comparative plastome analysis can provide insights into genome evolution and facilitate phylogenetic reconstruction. Methods: Here we analyzed 25 complete chloroplast genomes representing 15 genera, including 14 newly assembled genomes, to investigate plastome evolution in this subtribe. Results: All genomes exhibited the typical quadripartite structure (148, 246–158, 138 bp) with conserved gene content (128–134 genes). While most protein-coding genes were under purifying selection, we detected signatures of positive selection in specific lineages. Notably, ndhF in Lepanthes tachirensis showed a markedly elevated Ka/Ks ratio (3.65), which may be associated with adaptation to an extensive distributional range. ENC-plot analysis indicated that natural selection, rather than mutation pressure alone, shapes codon usage bias, with patterns varying among species from different geographic regions. Nucleotide diversity analysis identified eight hypervariable intergenic regions (psbK-psbI, atpI-rps2, petN-psbM, psbB-psbT, petD-rpoA, rpoA-rps11, rps3-rpl22, ccsA-ndhD) suitable as candidate molecular markers. Phylogenetic analysis confirmed that Lepanthes and Pleurothallis are non-monophyletic as traditionally defined. Conclusions: These findings expand plastome resources for Pleurothallidinae, reveal lineage-specific patterns of selection, and provide molecular markers for future taxonomic and evolutionary studies.

Background: This study determined the complete mitochondrial genome sequence of the marine crab to elucidate its phylogenetic position within Heterotremata, specifically the superfamily Goneplacoidea, and to explore the biological significance of its genetic composition and arrangement. Methods: The complete mitochondrial genome of Eucrate alcocki was sequenced using the Illumina platform and de novo assembled. Genome annotation and structural analysis were performed using MITOS2 and PhyloSuite. Phylogenetic relationships were reconstructed based on 13 protein-coding genes from 59 heterotrematan species using both Bayesian inference and maximum likelihood methods. Results: The mitochondrial genome of E. alcocki is a circular molecule of 15,720 bp with 72.2% AT content and a unique F-H-ND5 → H-F-ND5 gene rearrangement. Phylogenetic analysis robustly places E. alcocki in a distinct clade with Entricoplax vestita (BI = 1.00, ML = 100%), separate from the congeneric species Eucrate crenata and E. solaris, suggesting potential paraphyly within the genus Eucrate. Conclusions: This discovery provides preliminary evidence suggesting existing crab classification systems and molecular evidence for further understanding the evolutionary history of crabs. Our findings demonstrate that genomic characteristics hold significant value in revealing evolutionary pathways and can serve as a foundation for more comprehensive taxonomic and evolutionary research in the future.

Background/Objectives: The elongated egg is a morphological mutant of silkworm (Bombyx mori) eggs, yet the biochemical processes and molecular mechanisms underlying this trait remain unclear. Methods: In this study, we performed transcriptome sequencing on the ovaries of female pupae from the Nistari silkworm strain (comparing normal and elongated eggs) during the first three days post-pupation using high-throughput sequencing. Results: A total of 153.56 Gb of filtered data was obtained, identifying 23,366 genes and 35,798 mRNAs. Comparative analysis across three control groups revealed 374 differentially expressed genes (DEGs), with 131 upregulated and 243 downregulated genes in the elongated egg group. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that these DEGs were primarily associated with protein hydrolysis, DNA metabolic processes, and euchromatin/heterochromatin organization. Trend expression analysis revealed that transcriptional activity in elongated eggs was significantly higher than in normal eggs, particularly on day 3 of the pupal stage. Conclusions: Weighted gene co-expression network analysis (WGCNA) classified gene expression patterns into twelve modules, with two modules showing specificity. Thirteen hub genes were identified, which are functionally linked to translation initiation, protein density regulation, post-translational modification, and protein turnover. These findings provide foundational insights into the molecular mechanisms driving the formation of the elongated egg in silkworms.