Use of comparative transcriptome analysis to identify candidate genes related to albinism in channel catfish (Ictalurus punctatus)

Abstract

Transcriptome profiles of albino and wild type catfish were generated using next generation high-throughput RNA sequencing technology and compared. A total of 1106 differentially expressed genes were obtained, of which 530 were up-regulated and 576 were down-regulated in the skin tissue of albino catfish relative to wild type catfish. In total, 30,813 alternative splicing (AS) events were identified. These AS events were distributed in 15,090 genes with an average of 2.04 AS events per gene. We identified and compared a large proportion of transcripts encoding genes involved in regulation of melanogenesis, melanosome biogenesis, melanosome transport, and the tyrosine metabolism pathway in the catfish skin transcriptome dataset. Further analysis revealed that differentially expressed genes, including MART1, Cdk2, PMEL17, Tyr, Tyrp1, ADH, HGD, and TYRL, were significantly overrepresented in the melanogenesis pathway and in several biological processes associated with pigmentation. The albino catfish skin samples exhibited significantly increased expression levels of all candidate genes in the tyrosine metabolism pathway. We also identified a possible mechanism for the mutation of the catfish Hps4 gene, which affects regulation of expression of genes in the tyrosine metabolism pathway. Our findings provide a theoretical basis for further understanding of the pathogenesis of albinism in catfish.