Transcriptome Sequencing Analysis Reveals Dynamic Changes in Major Biological Functions during the Early Development of Clearhead Icefish, Protosalanx chinensis

• Published in: Fishes Vol. 7; no. 3; p. 115
• Main Authors: Tang, Xuemei, Jiang, Shulun, Wang, Henglin, Zhou, Yanfeng, Peng, Fei, Zhang, Xizhao, Zhou, Yifan, Guo, Shiyue, You, Yang
• Format: Journal Article
• Language: English
• Published: Basel MDPI AG 01.06.2022
• Subjects: Amino acids; Analysis; Bile; biological function; Cell differentiation; Cell proliferation; Critical period; early development; Eggs; Embryogenesis; Fatty acids; Fish; G protein-coupled receptors; Gene expression; Genomes; Hatching; Heart; Jaw; Ligands; Metabolism; Modules; Peptidase; Proliferation; Protosalanx chinensis; Sea surface; Sequence analysis; Sequencing; Serine; Software; Teeth; transcriptome; Transcriptomes; Umami; Visual perception; WGCNA; United States > US; China
• ISSN: 2410-3888; 2410-3888
• DOI: 10.3390/fishes7030115

Early development, when many important developmental events occur, is a critical period for fish. However, research on the early development of clearhead icefish is very limited, especially in molecular research. In this study, we aimed to explore the dynamic changes in the biological functions of five key periods in clearhead icefish early development, namely the YL (embryonic), PM (first day after hatching), KK (fourth day after hatching), LC (seventh day after hatching), and SL (tenth day after hatching) stages, through transcriptome sequencing and different analysis strategies. A trend expression analysis and an enrichment analysis revealed that the expression ofgenes encoding G protein-coupled receptors and their ligands, i.e., prss1_2_3, pomc, npy, npb, sst, rln3, crh, gh, and prl that are associated with digestion and feeding regulation gradually increased during early development. In addition, a weighted gene co-expression network analysis (WGCNA) showed that eleven modules were significantly associated with early development, among which nine modules were significantly positively correlated. Through the enrichment analysis and hub gene identification results of these nine modules, it was found that the pathways related to eye, bone, and heart development were significantly enriched in the YL stage, and the ccnd2, seh1l, kdm6a, arf4, and ankrd28 genes that are associated with cell proliferation and differentiation played important roles in these developmental processes; the pak3, dlx3, dgat2, and tas1r1 genes that are associated with jaw and tooth development, TG (triacylglycerol) synthesis, and umami amino acid receptors were identified as hub genes for the PM stage; the pathways associated with aerobic metabolism and unsaturated fatty acid synthesis were significantly enriched in the KK stage, with the foxk, slc13a2_3_5, ndufa5, and lsc2 genes playing important roles; the pathways related to visual perception were significantly enriched in the LC stage; and the bile acid biosynthetic and serine-type peptidase activity pathways were significantly enriched in the SL stage. These results provide a more detailed understanding of the processes of early development of clearhead icefish.