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, Ictalurus punctatus, 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, GDF10, FOXA2, HCEA and SYCE3 were involved in head formation, egg development and the transverse central element of synaptonemal complexes. CK1, OAZ2, DARS1 and UBE2V2 were mainly associated with regulation of cell cycle, growth, brain development, differentiation and proliferation of enterocytes. IFI44L and ZIP10 were critical for the regulation of immune activity and ion transport. Additionally, TCK1 and TGFB1 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.

Comparative Transcriptome Analysis During the Seven Developmental Stages of Channel Catfish (Ictalurus punctatus) and Tra Catfish (Pangasianodon hypophthalmus) Provides Novel Insights for Terrestrial Adaptation

“…At each time point, two replicates (pooled from four embryos/larvae) were taken for RNA isolation and Illumina sequencing. Sample collection, processing, and total RNA extraction were described in our previous study ( Ma et al, 2020 ). RNA concentration and integrity of each sample were initially measured on a NanoDrop 2000 Spectrophotometer (NanoDrop Technologies).…”

Whole-Genome Sequencing Analyses Reveal the Evolution Mechanisms of Typical Biological Features of Decapterus maruadsi

“…Of note, BMP3-knockout mice show an increase in bone mass [102]. BMP-3b functions predominantly in bone and cartilage development and can inhibit osteoblast differentiation by antagonizing BMP-2 and -4-mediated osteogenesis [103][104][105]. BMP-3b injected into Xenopus embryos triggers secondary head formation autonomously, whereas the depletion of BMP-3b caused headless Xenopus embryos [106].…”

Conserved and specific gene expression patterns in the embryonic development of tardigrades

“…Most studies report that the phylotypic stages have the lowest TAI or the most conserved embryonic stage, while early and late stages have higher TAI (Cridge et al, 2019; Drost et al, 2015). Therefore, it is necessary to employ the method of phylotranscriptomics, combined with the embryonic developmental status, to comprehensively understand the gene expression patterns and potential biological implications during embryonic development (Ma et al, 2020).…”