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Background <p>Caridean shrimps remain under-studied despite their economic value. <i>Lebbeus groenlandicus</i> (<i>L. groenlandicus</i>) lacks foundational molecular resources, limiting management and aquaculture applications. MicroRNAs (miRNAs) regulate immunity and metabolism and offer biomarker potential, yet no miRNAome has been reported for this species.</p> Objective <p>To generate the first miRNAome for <i>L. groenlandicus</i>, characterize orthologous and novel miRNAs, and assess tissue-specific expression.</p> Method <p>Small RNA-seq libraries (15–35 nt) were prepared from the hepatopancreas and muscle of three individuals (six libraries). Reads were aligned to human, mouse, and zebrafish miRNA references; miRDeep2 was used for discovery/quantification, with BLASTN, intersection, and MFE analyses for validation. Differential expression was tested with DESeq2; qRT-PCR evaluated species specificity of candidates.</p> Results <p>On average, 25.17% of reads mapped to known miRNAs, yielding average 117 known miRNAs per tissue and average 25 novel candidates per tissue. Cross-species alignment and intersection defined 61 orthologous miRNAs. Hepatopancreas showed strong up-regulation of several novel miRNAs and orthologs miR-1260a, miR-184, miR-7a-1; down-regulated sets included novel miRNAs and orthologs miR-1a-2, miR-133a-2, miR-10a, miR-5004. miR-10a was evolutionarily conserved. Candidate NM00003 exhibited a stable stem-loop structure and species-specific expression.</p> Conclusion <p>We deliver the first miRNAome for <i>L. groenlandicus</i>, revealing conserved regulators of immunity and metabolism, and identify novel miRNAs as practical biomarker candidates for aquaculture monitoring and stock management.</p>

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De novo identification and differential expression of MicroRNA in the Lebbeus groenlandicus

  • 期刊论文

  • 发表日期：

    2025年12月8日

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  • Du Hyeong Lee,
  • Hae Jin Shin,
  • Woo Ryung Kim,
  • Eun Gyung Park,
  • Yun Ju Lee,
  • Hyeon-su Jeong,
  • Hyun-Young Roh,
  • Ga-ram Jeong,
  • Tae Hwan Shin,
  • Heui-Soo Kim

摘要

Background

Caridean shrimps remain under-studied despite their economic value. Lebbeus groenlandicus (L. groenlandicus) lacks foundational molecular resources, limiting management and aquaculture applications. MicroRNAs (miRNAs) regulate immunity and metabolism and offer biomarker potential, yet no miRNAome has been reported for this species.

Objective

To generate the first miRNAome for L. groenlandicus, characterize orthologous and novel miRNAs, and assess tissue-specific expression.

Method

Small RNA-seq libraries (15–35 nt) were prepared from the hepatopancreas and muscle of three individuals (six libraries). Reads were aligned to human, mouse, and zebrafish miRNA references; miRDeep2 was used for discovery/quantification, with BLASTN, intersection, and MFE analyses for validation. Differential expression was tested with DESeq2; qRT-PCR evaluated species specificity of candidates.

Results

On average, 25.17% of reads mapped to known miRNAs, yielding average 117 known miRNAs per tissue and average 25 novel candidates per tissue. Cross-species alignment and intersection defined 61 orthologous miRNAs. Hepatopancreas showed strong up-regulation of several novel miRNAs and orthologs miR-1260a, miR-184, miR-7a-1; down-regulated sets included novel miRNAs and orthologs miR-1a-2, miR-133a-2, miR-10a, miR-5004. miR-10a was evolutionarily conserved. Candidate NM00003 exhibited a stable stem-loop structure and species-specific expression.

Conclusion

We deliver the first miRNAome for L. groenlandicus, revealing conserved regulators of immunity and metabolism, and identify novel miRNAs as practical biomarker candidates for aquaculture monitoring and stock management.