Deep Transcriptomic Analysis Reveals the Dynamic Developmental Progression during Early Development of Channel Catfish (Ictalurus punctatus)

Abstract

The transition from fertilized egg to larva in fish is accompanied with various biological processes. We selected seven early developmental stages in channel catfish, <i>Ictalurus punctatus</i>, for transcriptome analysis, and covered 22,635 genes with 590 million high-quality RNA-sequencing (seq) reads. Differential expression analysis between neighboring developmental timepoints revealed significantly enriched biological categories associated with growth, development and morphogenesis, which was most evident at 2 vs. 5 days post fertilization (dpf) and 5 vs. 6 dpf. A gene co-expression network was constructed using the Weighted Gene Co-expression Network Analysis (WGCNA) approach and four critical modules were identified. Among candidate hub genes, <i>GDF10</i>, <i>FOXA2</i>, <i>HCEA</i> and <i>SYCE3</i> were involved in head formation, egg development and the transverse central element of synaptonemal complexes. <i>CK1</i>, <i>OAZ2</i>, <i>DARS1</i> and <i>UBE2V2</i> were mainly associated with regulation of cell cycle, growth, brain development, differentiation and proliferation of enterocytes. <i>IFI44L</i> and <i>ZIP10</i> were critical for the regulation of immune activity and ion transport. Additionally, <i>TCK1</i> and <i>TGFB1</i> were related to phosphate transport and regulating cell proliferation. All these genes play vital roles in embryogenesis and regulation of early development. These results serve as a rich dataset for functional genomic studies. Our work reveals new insights of the underlying mechanisms in channel catfish early development.