Comparative transcriptome analysis reveals ncRNA-mediated regulatory networks associated with muscle crispiness in grass carp.

Wenwen Zhu; Xitong Xiao; Yujie Yan; Chuan Yu; Di Fei; Zhiyuan Cao; Yixiang Wan; Mohammad Mehdi Ommati; Yong Huang

doi:10.1016/j.cbd.2026.101942

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Comparative transcriptome analysis reveals ncRNA-mediated regulatory networks associated with muscle crispiness in grass carp.

Wenwen Zhu·Xitong Xiao·Yujie Yan·Chuan Yu·Di Fei·Zhiyuan Cao·Yixiang Wan·Mohammad Mehdi Ommati·Yong Huang

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Abstract

Non-coding RNAs (ncRNAs) have been demonstrated to be involved in muscle development and to function as key regulators. However, the molecular mechanism underlying muscle crispiness in grass carp (GC) remains poorly understood, and whether these ncRNAs are involved in its regulation is still unknown. In the current investigation, differentially expressed (DE) RNAs (including lncRNAs, circRNAs, miRNAs, and mRNAs) were identified; concomitantly, target genes prediction was conducted, and functional and signaling pathway enrichment analyses were performed. Pathways related to muscle crispiness were identified, and the competitive endogenous RNA (ceRNA) (lncRNA/circRNA-miRNA-mRNA) regulatory network was further constructed. The results showed that a total of 126 DE-lncRNAs, 17 DE-circRNAs, 329 DE-miRNAs, and 442 DE-mRNAs were identified in muscle tissues of both the GC and crisp grass carp (CGC). GO and KEGG enrichment analyses revealed that target genes of DE-ncRNAs were significantly enriched in signaling pathways, including structural constituents of muscle, apoptosis, oxidative phosphorylation, and regulation of actin cytoskeleton, suggesting that these pathways may be involved in muscle texture remodeling. Subsequently, DE-RNAs enriched in related pathways were identified, and a core ceRNA regulation network comprising 3 lncRNAs, 4 circRNAs, 3 miRNAs, and 17 mRNAs was constructed. Additionally, 10 DE-RNAs from randomly selected groups were validated by qRT-PCR. Our findings not only provide scientific evidence elucidating the molecular mechanisms underlying muscle crispiness in GC but also establish a foundation for studying changes in muscle textural qualities across other fish species.

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Animals Carps Gene Regulatory Networks Gene Expression Profiling RNA, Untranslated RNA, Competitive Endogenous Muscles MicroRNAs Transcriptome RNA, Circular RNA, Messenger Crisp grass carp Muscle crispiness ceRNA circRNA lncRNA miRNA Journal Article Comparative Study

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Wenwen Zhu, Xitong Xiao, Yujie Yan, Chuan Yu, Di Fei, Zhiyuan Cao, Yixiang Wan, Mohammad Mehdi Ommati, Yong Huang. 2026-07-18. Comparative transcriptome analysis reveals ncRNA-mediated regulatory networks associated with muscle crispiness in grass carp.. https://doi.org/10.1016/j.cbd.2026.101942

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Journal Article; Comparative Study resource Animals subject Carps subject Comparative Study subject Crisp grass carp subject Gene Expression Profiling subject Gene Regulatory Networks subject Journal Article subject MicroRNAs subject Muscle crispiness subject Muscles subject ceRNA subject circRNA subject lncRNA subject miRNA subject

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