Combined Illumina and Pacbio sequencing technology on transcriptome analysis reveals several key regulations during the early development of American shad (Alosa sapidissima)

Abstract

This study was conducted to examine the early developmental processes and mechanisms in American shad (Alosa sapidissima). Both Illumina and Pacific Biosciences (PacBio) sequencing were employed to analyze the transcriptome at embryonic, larval, and fingerling stages. Moreover, quantitative reverse transcription PCR (qRT-PCR) analysis was performed to validate the reproducibility and repeatability of identified differentially expressed genes (DEGs). 88.91 G of clean data from Illumina sequencing were retained, and 57.0 G of subreads were obtained from PacBio RS II sequencing. It was observed that compared to embryonic samples, 6070 DEGs were screened in larval. These DEGs were mainly enriched in Gene Ontology (GO) terms of cell or organ differentiation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of protein digestion and absorption, pancreatic secretion, and phototransduction. There were 2897 DEGs found in the fingerling_vs_larva. These DEGs primarily participated in KEGG pathways related to the carbon metabolism, microbial metabolism, and amino acid metabolism. In conclusion, the molecular developmental profile showed that the larva existed as a very different organism from the embryo and fingerling during a short period of its early life history. The development related to organ formation and the visual system was more pronounced from embryo to larva development. At the same time, the function of digestion and stress response were activated, thereby generating from the larval to fingerling.