Identification of genes involved in the development of Weberian apparatus in rohu, Labeo rohita (Hamilton, 1822), as revealed by comparative transcriptome analyses.

Ostariophysi has a history of successful adaptation to freshwater environments due to the evolution of a unique morphological structure, i.e. Weberian apparatus (WA). This structure transfers sound waves from the swim bladder to the inner ear by forming a physical linkage that leads to enhanced hearing sensitivity. However, there are very few reports on genes specifically linked to this modified structure in fish. In this study, we compared Weberian ossicles, the modified vertebrae, and unmodified vertebrae transcriptomes of representative species from ostariophysi and non-ostariophysi by mRNA sequencing. A total of 21 and 25 million high-quality reads were generated from Labeo rohita and Oreochromis niloticus, respectively, and differential expression analysis identified 161 upregulated and 98 down-regulated transcripts (>2 fold change) between modified and unmodified vertebrae. Functional annotation revealed their significant involvement in biological functions such as energy metabolism, osteoblast proliferation, differentiation, and matrix mineralization related to bone development. A total of 41 miRNA target interactions were found to be associated with differentially expressed transcripts (p < 0.05). Fourteen hub genes were identified and categorized into six major GO terms: endoplasmic reticulum, large ribosomal subunit, rRNA binding, translation and metabolic process. Ontogenic expression of selected genes linked to ossification showed elevated expression till 3 days post-hatch (dph). A novel gene, LrOSSP1 (Ossicle Secretory Signal Protein 1), reported for the first time, exclusively found in ostariophysi, demonstrated significant up-regulation in the earliest stages of larval development in this study. This is the first report of its kind in Labeo rohita and will be helpful in understanding the molecular underplay of modified vertebrae in ostariophysans.