Identification of miRNAs, lncRNAs, circRNAs, and their ceRNA networks in the establishment of sexual size dimorphism in the olive flounder (Paralichthys olivaceus)

IF 3.9 1区农林科学 Q1 FISHERIES

Aquaculture Pub Date : 2025-04-01 DOI:10.1016/j.aquaculture.2025.742509

Yuqing Zhang , Wenying Zhang , Ao Li , Yanmin Jian , Shujing Zhang , Dongwu Liu , Xungang Tan , Feng You , Qiuxiang Pang , Shuang Jiao

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引用次数: 0

Abstract

Olive flounder (Paralichthys olivaceus), a valuable mariculture species, exhibits a significant female-biased sexual size dimorphism (SSD). Despite its economic and biological importance, the molecular mechanisms underlying this phenomenon, in particular the contribution of non-coding RNAs (ncRNAs) and their associated competitive endogenous RNA (ceRNA) regulatory mechanisms, remain unclear. In this study, we conducted whole transcriptome sequencing of the brains/pituitaries and muscles of olive flounder during the critical period for SSD establishment, identifying 23/282/85 and 25/193/82 differentially expressed (DE) miRNAs/circRNAs/lncRNAs, respectively. Based on the regulatory interactions among these DE RNAs, we constructed the lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA ceRNA networks. Our analyses revealed crucial SSD-related pathways regulated by these ncRNAs/ceRNA networks, including “ovarian steroidogenesis”, “prolactin signaling pathway”, “cell adhesion molecules”, “GABAergic synapse”, and “dopaminergic synapse” pathways in brains/pituitaries, “ECM-receptor interaction”, “PI3K-Akt signaling pathway”, “focal adhesion”, “regulation of actin cytoskeleton”, and several metabolism-related pathways in muscles. Moreover, numerous genes regulated by these ncRNAs/ceRNA networks emerged as potential candidates for SSD establishment, such as frizzled3 (fzd3), cholecystokinin A receptor (cckar), carbonic anhydrase 4 (ca4), and calcium voltage-gated channel subunit alpha1 B (cacna1b) in brains/pituitaries, and DNA (cytosine-5) methyltransferase 3A (dnmt3a), Krüppel-like factor 11 (klf11), myocyte enhancer factor 2c (mef2c), insulin receptor (insr), serum- and glucocorticoid-inducible kinase 1 (sgk1), nuclear receptor 4A1 (nr4a1), and apelin in muscles. This study provides the first preliminary insights into the ncRNAs and their ceRNA networks implicated in SSD-related growth traits in flounder, providing potential targets for selective breeding programs aimed at enhancing growth in aquaculture.

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来源期刊

Aquaculture 农林科学-海洋与淡水生物学

CiteScore

8.60

自引率

17.80%

发文量

1246

审稿时长

56 days

期刊介绍： Aquaculture is an international journal for the exploration, improvement and management of all freshwater and marine food resources. It publishes novel and innovative research of world-wide interest on farming of aquatic organisms, which includes finfish, mollusks, crustaceans and aquatic plants for human consumption. Research on ornamentals is not a focus of the Journal. Aquaculture only publishes papers with a clear relevance to improving aquaculture practices or a potential application.