Abstract
The early development of fish is regulated through dynamic and complex mechanisms involving the regulation of various genes. Many genes are subjected to post-transcriptional regulation by microRNAs (miRNAs). In the Chinese aquaculture industry, the native species bighead carp (Hypophthalmichthys nobilis) is important. However, the genetic regulation related to the early development of bighead carp is unknown. Here, we generated developmental profiles by miRNA sequencing to study the dynamic regulation of miRNAs during bighead carp early development. This study identified 1 046 miRNAs, comprising 312 known miRNAs and 734 uncharacterized miRNAs. Changes in miRNA expression were identified in the six early development stages. An obviously increased expression trend was detected during the development process, with the main burst of activity occurring after the earliest stage (early blastula, DS1). Investigations revealed that several miRNAs were dominantly expressed during the development process, especially in the later stages (e.g., miR-10b-5p, miR-21, miR-92a-3p, miR-206-3p, and miR-430a-3p), suggesting that these miRNAs exerted important functions during embryonic development. The differentially expressed miRNAs (DEMs) and time-serial analysis (profiles) of DEMs were analyzed. A total of 372 miRNAs were identified as DEMs (fold-change >2, and false discovery rate <0.05), and three expression profiles of the DEMs were detected to have co-expression patterns (r > 0.7, and p < 0.05). The broad negative regulation of target genes by miRNAs was speculated, and many development-related biological processes and pathways were enriched for the targets of the DEMs, which might be associated with maternal genome degradation and embryogenesis processes. In conclusion, we revealed the repertoire of miRNAs that are active during early development of bighead carp. These findings will increase our understanding of the regulatory mechanisms of early development of fish.
Highlights
The early development of animal is a complex process, characterized by spatiotemporal changes in gene expression and morphology (Aanes et al, 2014)
After filtering out low-quality reads, and removing adaptor sequences, the clean reads were retrieved for further analyses
The sequencing data were deposited in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) repository with the accession number: PRJNA781113
Summary
The early development of animal is a complex process, characterized by spatiotemporal changes in gene expression and morphology (Aanes et al, 2014). The dynamics of gene expression and its regulation in early development have been described in model fishes, such as zebrafish (Danio rerio) (Nepal et al, 2016; Kasper et al, 2017; Shi et al, 2020) and medaka (Oryzias latipes) (Tani et al, 2010), and important aquaculture species (Rasal et al, 2016; Herkenhoff et al, 2018), such as rainbow trout (Oncorhynchus mykiss) (Ramachandra et al, 2008), turbot (Scophthalmus maximus) (Robledo et al, 2017), Nile tilapia (Oreochromis niloticus) (Pinhal et al, 2018), European sea bass (Dicentrarchus labrax) (Sarropoulou et al, 2019), and the common carp (Cyprinus carpio) (Wang et al, 2017; Wang et al, 2021)
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