Transcriptomic profiling to unravel the underlying causes of early gonadal development of hilsa (Tenualosa ilisha) in Bangladesh.

Hilsa (Tenualosa ilisha) is crucial to Bangladesh's economy and ecology, but recent trends show early maturation in small-sized hilsa, with unclear causes. This study aimed to identify differentially expressed genes (DEGs) between the ovaries of large and small hilsa using RNA-sequencing. Samples from both sizes were collected from the Meghna River in Chandpur District, and four ovary libraries were sequenced via the Illumina platform. A total of 908 DEGs were detected, of which 453 were up-regulated and 455 were down-regulated. Transcriptome analysis revealed significant differences in Gene Ontology terms such as extracellular region (GO:0005576), innate immune response (GO:0045087), and protein ubiquitination (GO:0016567), peptide antigen binding (GO:0042605), KEGG pathways including MAPK signaling pathway (ko04010), endocytosis (ko04144), and spliceosome (ko03040), as well as COG terms like signal transduction, between the ovary of large and small hilsa shad. These findings suggest that differentially expressed genes may play a role in regulating the ovarian development of T. ilisha. However, the entire process, from sampling to final annotation, is described here, along with the workflow. This study will offer a valuable resource for current and upcoming Hilsa transcriptome-based expression profiling studies.