Transcriptome profiling reveals candidate cleft palate-related genes in cultured Chinese sturgeons (Acipenser sinensis)

The Chinese sturgeon (Acipenser sinensis) is an anadromous fish distributed in the Yangtze River and the East China Sea. In this study, we report the novel finding of cleft palates in Chinese sturgeons derived from artificial fertilization. To explore the genetic basis of palate malformation in A. sinensis, Illumina RNA-seq technology was used to analyze the transcriptome data of farmed Chinese sturgeons with normal palates and cleft-palates. Raw reads were obtained and assembled into 808,612 unigenes, with an average length of 509.33 bp and an N50 of 574 bp. Sequence similarity analyses against four public databases (Nr, UniProt, KEGG, and COGs) found 158,642 unigenes that could be annotated. GABAergic synapses and TGF-β signal pathways were the two most enriched pathways with high Rich Factors in the analyses of differentially expressed genes. In these two signal pathways, six genes (GABRA4, GS, GNS, S6K, PITX2, and BMP8) were found as candidate cleft-palate genes in Chinese sturgeon. These findings contribute to our understanding of cleft palate genetics in sturgeon, while simultaneously adding to our knowledge about craniofacial development.