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Related Experiment Video

Updated: Nov 6, 2025

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Transcriptome analysis provides insights into long noncoding RNAs in medaka gonads.

Shaoyu Guo1, Ying Zhong1, Yu Zhang1

  • 1International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China.

Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
|May 7, 2021
PubMed
Summary

This study identifies novel long non-coding RNAs (lncRNAs) in medaka gonads, revealing their potential roles in reproductive development and gametogenesis. New lncRNA libraries offer insights into medaka

Keywords:
GonadsLncRNAMedakaRNA-sequencing

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Area of Science:

  • Genomics and Molecular Biology
  • Reproductive Biology
  • Aquatic Animal Models

Background:

  • Long non-coding RNAs (lncRNAs) are increasingly recognized as crucial regulators in animal sex determination and gonad development.
  • Medaka (Oryzias latipes) serves as a valuable model organism for reproductive research due to its well-characterized sex-determining genes.
  • The specific roles of gonadal lncRNAs in medaka reproductive development remain largely unexplored.

Purpose of the Study:

  • To identify and characterize lncRNAs expressed in medaka gonads (ovary and testis).
  • To predict potential target genes regulated by these lncRNAs and analyze their functional pathways.
  • To investigate the expression patterns of specific lncRNAs, including sex-biased ones, to understand their role in gametogenesis.

Main Methods:

  • High-throughput sequencing (Illumina HiSeq4000) was employed to obtain lncRNA profiles from medaka ovary and testis.
  • Bioinformatic analyses were used to identify differentially expressed lncRNAs, predict cis-regulated target genes, and perform Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses.
  • Quantitative real-time PCR (qRT-PCR) and in situ hybridization were utilized to validate sequencing data and determine the expression localization of selected lncRNAs.

Main Results:

  • A total of 5317 lncRNAs were identified in medaka gonads, with 177 up-regulated and 120 down-regulated in the testis compared to the ovary.
  • 3099 lncRNAs were predicted to regulate 6904 cis-target genes involved in key pathways such as phosphorylation, xenobiotic metabolism, insulin secretion, and GnRH signaling.
  • Sex-biased lncRNA MSTRG.14827.1 showed high expression in immature germ cells, suggesting a critical role in gametogenesis.

Conclusions:

  • This study establishes comprehensive lncRNA libraries for medaka gonads, providing a valuable resource for future research.
  • The findings highlight the significant involvement of lncRNAs in regulating gene expression networks critical for medaka reproductive development.
  • The identification of MSTRG.14827.1 offers a new target for investigating the molecular mechanisms of gametogenesis in medaka.