Screening and identification of bacterium-derived horizontally transferred genes in the genomes of three Penaeus...

Horizontal gene transfer (HGT) is a major force shaping genome evolution in both prokaryotes and eukaryotes. In the past decade, numerous horizontally transferred genes from bacteria have been identified in eukaryotic lineages, with a substantial proportion found in arthropods. Shrimp, which are economically important cultured arthropods, maintain intimate associations with bacteria, providing an ideal platform for HGT research. In this study, we analyzed bacterium-derived HGT based on high-quality genomes of Penaeus monodon, Penaeus chinensis, and Penaeus japonicus via homology searches and phylogenetic analysis. Our analysis revealed 19 HGT genes, with 11 identified in P. monodon, 5 in P. chinensis, and 3 in P. japonicus. These candidates show features consistent with post-transfer assimilation in the host genome. Specifically, 84% of the candidates contain annotated introns, consistent with intron acquisition after genomic integration. In addition, most candidates exhibit GC content similar to their host genomes, consistent with post-transfer sequence amelioration. Functional annotation indicates their involvement in metabolism and catalytic activity. Notably, horizontally transferred candidates, such as chondroitinase-AC-like and lantibiotic transporter ATP-binding protein SrtF-like, can be used to test hypotheses regarding horizontally transferred genes' roles in host-microbe interfaces and shrimp immunity. The presence of glycosaminoglycan (GAG) lyase-encoding HGT genes in all three species is consistent with an early acquisition in the penaeid lineage. Collectively, our findings demonstrate that bacterium-derived horizontally transferred genes not only structurally integrate into penaeid shrimp genomes but also provide a curated resource for future comparative analyses and experimental validation relevant to shrimp-microbe interactions and aquaculture.