Gene flow plays an important role in domestication history of domesticated species. However, little is known about the demographic history of domesticated silkworm involving gene flow with its wild relative.

Bluetongue virus (BTV) infects various ruminant species, posing significant threats to animal health and causing substantial economic losses to the livestock industry. Ovine type II alveolar epithelial cells (OAECIIs) play crucial roles in maintaining pulmonary structural integrity and modulating immune responses. Their dysfunction is closely associated with lung disease pathogenesis, making them important therapeutic targets. However, OAECIIs’ immunoregulatory functions and early response mechanisms during BTV infection remain unclear. To address this, we analyzed transcriptomic changes in OAECIIs following BTV-1 infection. RNA-seq revealed 1047 and 852 differentially expressed genes (DEGs) at 8 and 12 h post-infection (hpi), respectively, compared to uninfected controls. Bioinformatics analysis showed significant upregulation of nucleic acid-sensing receptors, interferon-stimulating factors, inflammatory mediators, and cytokines during early infection, mediated primarily through type I interferon signaling, TNF signaling, and cytosolic DNA-sensing pathways. We identified MAD5, ZNFX1, cGAS, OAS, PKR and ZBP1 as key pattern recognition receptors in OAECIIs during BTV infection. The IFN-β, MX1/2, RSAD2 and PLSCR1 pathways mediated antiviral responses, while IL-15, CXCL10, CCL2 triggered inflammatory responses, collectively causing structural alterations through AQP1/9 and tight junction protein modulation. These findings provide critical insights into early antiviral mechanisms and cellular structural changes in OAECIIs during BTV infection, establishing a foundation for understanding pneumonia pathogenesis and developing targeted BTV therapies.

To analyze the full nucleotide sequence of a null allele of major histocompatibility complex class I chain-related gene (MICA). A sequence-based typing method was used to determine the nucleotide sequence of the MICA gene. Potential alleles were identified with a computer program. The identified allele has possessed a sequence similar to that of MICA*027 except for a C→T substitution at position 184 in codon 62 (CAG→TAG) of exon 2. As a stop codon, this may result in a truncated protein. A null allele of MICA gene has been identified. The sequence has been submitted to the Genbank nucleotide sequence database (submission No. HWS10011131), which was officially named as MICA*063N by the WHO Nomenclature Committee in October 2010.

The efficient expression of recombinant proteins in aquaculture fish poses a significant challenge, partly due to the lack of dedicated bioinformatics tools for species-specific codon usage analysis and optimization. RiboScan (v1.0.0), a portable, single-file command-line tool executed in Python, was designed in this study, for mRNA codon diagnostics and optimization. RiboScan supports ten species, including five major aquaculture fish. High-risk windows that are computationally predicted to impair translational efficiency are identified based on two complementary metrics, namely, the Relative Adaptiveness Index (RAI) and estimated NN-based stability score, which are calculated using a sliding-window approach. An optimization module is used to replace the suboptimal codons in high-risk regions with host-specific synonymous codons, which are selected based on their high RAI values, leaving the encoded protein sequence unaltered. The efficacy of RiboScan was evaluated using coding sequences (CDSs) from three representative aquaculture fish genes, namely, Salmo salar growth hormone (gh; GenBank accession: M21573), Oreochromis niloticus interleukin-1 beta (il1b; GenBank accession: OR432591), and Ctenopharyngodon idella beta-actin (actb; GenBank accession: M25013). The tool identified 25–30 high-risk windows per CDS pre-optimization, whereas no high-risk windows were detected in any of the CDSs post-optimization. The mean RAI for Sal. salar gh, Or. niloticus il1b, and Ct. idella actb increased from 0.189 to 0.339, 0.126 to 0.270, and 0.140 to 0.231, respectively. RiboScan’s main analytical workflow requires no third-party dependencies, as it uses only the Python standard library. In addition, the tool yields publication-ready figures and structured comma-separated values (CSV) output files. RiboScan can be used to perform species-specific codon optimization for major aquaculture fish, and provides a practical computational framework for designing recombinant proteins, vaccines, and other engineered genetic constructs, thus contributing to aquaculture biotechnology research.