Abstract
The Penaeus monodon genome has been widely used as a reference for transcriptomic analyses of gene expression underlying development, immunity, stress responses, and reproductive maturation. In this study, we evaluated the impact of transcriptome assembly strategies and mapping methods on downstream differential gene expression (DGE) analyses. Transcriptomes were generated from the hepatopancreas and ovaries of wild-caught female broodstock at two ovarian maturation stages (stage I and stage IV) using genome-guided (GG) and de novo (DN) assembly strategies. Assembly performance was first assessed based on transcript recovery and functional annotation. DN assembly produced the highest number of unigenes, of which 49% matched proteins in the NCBI non-redundant (nr) database, and 69% of annotated unigenes were assigned to Gene Ontology terms. We next evaluated the effects of three mapping methods (reference-based (RB), GG-based, and DN-based) on the detection of differentially expressed genes (DEGs) between maturation stages. The DN mapping method identified the greatest number of DEGs across tissues (820) exceeding GG (488) and RB (117) mapping methods. Overall, these findings demonstrate that different assembly strategies and mapping methods substantially influence DEG recovery in P. monodon. The DN assembly recovered a greater number of transcripts and DEGs, while the GG assembly is better suited for identifying reproduction-related benchmark genes of interest. Based on these findings, we suggest that integrating DN and GG assemblies can improve the robustness of differential gene expression analyses in non-model organisms.