A time-course transcriptome analysis of gonads from HongKong catfish (Clarias fuscus) reveals genes and pathways associated with gonadal development

Hong Kong catfish ( Clarias fuscus ) is a valuable fish species widely farmed in southern China, showing distinct differences in growth between males and females. Studying gene expression patterns during gonadal development in C. fuscus is essential for uncovering the genetic basis of sex variances and guiding breeding practices. This research presents a detailed analysis of gene expression during Phases II, III, and IV of gonadal development. A total of 11,948, 7145, and 10,672 differentially expressed genes (DEGs) were identified at these stages, with 4253 DEGs common across all three phases. Key genes related to gonadal development were pinpointed, showing significant sex-specific expression during testes or ovaries development. These genes included those involved in steroid synthesis ( cyp17a1 , cyp11a1 , hsd3b1 , cyp26a1 , hsd17b12 ), transcription factors ( sox9a , lhx9 , sox19b ), and TGF-β superfamily genes ( tgfb2 , amh , bmp15 , gdf9 ). Additionally, genes exclusively expressed during gonadal development were identified, such as dmrt1l , cyp26c1 , hsd3b1l , six2b , foxj1a , cfap65 , and cfap43 in testes, and sox2 , zp3 , mos in ovaries. KEGG enrichment analysis highlighted the importance of the Fanconi anemia pathway in oocyte meiosis and ovarian development in C. fuscus . Furthermore, weighted gene co-expression network analysis (WGCNA) emphasized the role of pathways like progesterone-mediated oocyte maturation, oocyte meiosis, and steroid hormone biosynthesis in gonadal development. This study identified crucial genes and pathways involved in the gonadal development of C. fuscus , setting the stage for a deeper understanding of the molecular mechanisms behind sex differentiation and reproductive development. • Transcriptomic analysis was performed on gonadal development in C. fuscus at three different developmental stages. • The study revealed a multitude of key genes linked to the process of gonadal development in C. fuscus . • Utilizing WGCNA, crucial pathways essential for the gonadal development of C. fuscus were pinpointed.