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Sponsored Artificial Intelligence: A Modern Approach, Global Edition Artificial Intelligence: A Modern Approach, Global Edition

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Mengqiang Wang

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Jul 2026

Transcriptomic analysis revealed the potential regulatory mechanism of extracellular vesicles on the innate immunity in Chlamys farreri.

Extracellular vesicles (EVs), as antimicrobial factors, load a variety of immune-related molecules, play a complex and critical role in host-pathogen interactions. The regulatory mechanism of how EVs respond to external stimuli by regulating immune regulatory elements in the innate immune response of marine invertebrates remains unresolved. To address this, we conducted a global transcriptomic analysis of hemocytes in Chlamys farreri stimulated by EVs derived from different sources. Transcriptomic analysis identified 892 specifically upregulated and 246 specifically downregulated genes in the group of scallops injected with EVs obtained after LPS stimulation (group S) relative to the group of scallops injected with PBS buffer (group P). Functional annotation analysis revealed that the differentially expressed genes (DEGs) participate in critical immune signaling pathways, including the NOD-like receptor, RIG-I-like receptor, and HIF-1 signaling pathways. Among the DEGs unique to the group S, we identified canonical genes linked to autophagy, apoptosis, and immune responses, such as cell division control protein 42 homolog (CDC42), dual specificity protein phosphatase 1 (DUSP1), TNF receptor-associated factor 3 (TRAF3), Caspase 3 (CASP3), serine/threonine-protein kinase ULK3 (ULK3), and Myeloid differentiation primary response protein MyD88-3 (MyD88-3). Protein-protein interaction (PPI) network analysis pointed to ADP-ribosylation factor (CDKN2A), phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase (PTEN), CDC42, CASP3, and the downregulated protein heat shock protein 90 (HSP90) as prominent hub DEGs involved in the regulation of innate immunity. Temporal analysis of selected immune DEGs further demonstrated the immunomodulatory role of EVs in Chlamys farreri. Our study establishes that EVs are essential for regulating innate immunity in marine invertebrates, offering novel insights for shellfish disease prevention and control.

Shengwen Li, Dianli Zhao, Yansong Hou et al. · 0 citations
Open access Aug 2026

Genome Wide Structural Variants Provide Insights Into Population Structure and Genetic Divergence in Pacific White Shrimp ( Penaeus vannamei ) Breeding Populations

Structural variants (SVs) are a major yet underused source of adaptive variation in aquaculture. We built a genome‐wide SV atlas for 180 Penaeus vannamei from six commercial breeding populations and discovered 1,159,046 SVs, with uneven chromosomal distributions and multi‐type hotspots. Over 63.53% of SVs overlapped repeats—especially simple sequence repeats, DNA transposons, and LINEs. SV and SNP densities were highly correlated. Across populations, 482 k SVs were shared and 145,623 were singletons; the fraction of deletions increased from shared to singleton classes. BMK and KH harbored more singletons than SIS, RH, and CP, indicating greater divergence. PCA and ADMIXTURE recovered three major clusters and revealed the substructure in RH, mirroring SNP analyses. Selection scans identified 78–193 sweep windows per population encompassing 38–161 candidate genes. These genes were predominantly enriched in population‐specific processes such as chromatin regulation, meiotic recombination, membrane‐associated functions, suggesting that structural variants may contribute to divergence in reproductive, metabolic, and structural pathways across breeding programs. Nevertheless, 10 genes showed parallel signals in over 3 populations; many carry short deletions likely affecting regulatory or coding elements. Together, these results show that genome architecture and domestication jointly shape the shrimp SV landscape; that SVs alone robustly resolve population history; and that a small set of recurrent, deletion‐bearing regulatory genes may underpin convergent improvement. The SV map and candidate loci provide diagnostic markers for germplasm tracing and candidate loci for marker‐assisted or genomic selection in P. vannamei breeding.

Ming-Yang Zhao, Hao Wang, Mingxuan Teng et al. · 0 citations