Transcriptome sequencing reveals the molecular mechanisms of early malformations in the critically endangered Sichuan taimen (Hucho bleekeri)

Hucho bleekeri is a Class I protected species in China. In recent years, very few records of wild H. bleekeri have been documented. Therefore, artificial breeding has become the last resort to protect this species. However, during the larvae cultivation phase, a large number of individuals exhibit abnormal morphology, which constitute the majority of dead larvae. In this study, we conducted transcriptome sequencing on normal and malformed fish at three distinct developmental stages: 4 days post-hatching (dph), 15 dph, and 31 dph, and explored the expression patterns of key differentially expressed genes (DEGs) associated with skeletal development. Transcriptomic sequencing identified a total of 3024, 2678, and 7088 DEGs in the control versus malformed groups at 4 dph, 15 dph, and 31 dph, respectively. Gene Set Enrichment Analysis showed that cell development, regulation of cytoskeleton organization, TGF-β signaling pathway, and Wnt signaling pathway, had relatively high enrichment scores. Genes involved in skeletal development, including shh, daam1, osteonectin, twist1, osteocalcin, col1a1, myod, and hox3, were significantly down-regulated in malformed fish, while mmp13 and TGFβ were significantly up-regulated. Notably, key genes in the Hedgehog signaling pathway were all inhibited in the malformed groups, indicating their crucial roles in the normal skeletal development of H. bleekeri. This study enhances our understanding of the underlying mechanisms of skeletal regulation in fish and may help reduce the incidence of malformations in H. bleekeri.