ArticlePloS one2017
The integrated analysis of RNA-seq and microRNA-seq depicts miRNA-mRNA networks involved in Japanese flounder (Paralichthys olivaceus) albinism.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 38 citations in OpenAlex.
- Comparative Transcriptome and Gene-Editing Analyses Reveal the Molecular Mechanism of Albinism in the Taiwanese Loach.Marine biotechnology (New York, N.Y.) · 2026Article
- Identification and Pathway Analysis of SNP Loci Affecting Abdominal Fat Deposition in Broilers.Animals : an open access journal from MDPI · 2025Article
- Comprehensive Profiling of the miRNome and Degradome Reveals Regulatory Signatures of Seed Aging and Germination.International journal of molecular sciences · 2025Article
- Transcriptomic analyses of differentially expressed human genes, micro RNAs and long-non-coding RNAs in severe, symptomatic and asymptomatic malaria infection.Scientific reports · 2024Article
- microRNA regulation of skin pigmentation in golden-back mutant of crucian carp from a rice-fish integrated farming system.BMC genomics · 2023Article
- Genome-wide identification and characterization of tissue specific long non-coding RNAs and circular RNAs in common carp (Frontiers in genetics · 2023Article
- Comparative transcriptome and miRNA analysis of skin pigmentation during embryonic development of Chinese soft-shelled turtle (Pelodiscus sinensis).BMC genomics · 2022Article
- Integrative analyses of mRNA and microRNA expression profiles reveal the innate immune mechanism for the resistance toFrontiers in immunology · 2022Article
- Best practices on the differential expression analysis of multi-species RNA-seq.Genome biology · 2021Review
- Identification and Characterization of Long Non-coding RNAs in the Intestine of Olive Flounder (Frontiers in immunology · 2021Article
- Insights Into the Albinism Mechanism for Two Distinct Color Morphs of Northern Snakehead,Frontiers in genetics · 2020Article
- RNA-seq and microRNA-seq analysis of Japanese flounder (Paralichthys olivaceus) larvae treated by thyroid hormones.Fish physiology and biochemistry · 2019Article
- Integrated Analysis of Transcriptomic, miRNA and Proteomic Changes of a Novel Hybrid Yellow Catfish Uncovers Key Roles for miRNAs in Heterosis.Molecular & cellular proteomics : MCP · 2019Article
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Authors and funding
7 authors at 3 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Albinism, a phenomenon characterized by pigmentation deficiency on the ocular side of Japanese flounder (Paralichthys olivaceus), has caused significant damage. Limited mRNA and microRNA (miRNA) information is available on fish pigmentation deficiency. In this study, a high-throughput sequencing strategy was employed to identify the mRNA and miRNAs involved in P. olivaceus albinism. Based on P. olivaceus genome, RNA-seq identified 21,787 know genes and 711 new genes by transcripts assembly. Of those, 235 genes exhibited significantly different expression pattern (fold change ≥2 or ≤0.5 and q-value≤0.05), including 194 down-regulated genes and 41 up-regulated genes in albino versus normally pigmented individuals. These genes were enriched to 81 GO terms and 9 KEGG pathways (p≤0.05). Among those, the pigmentation related pathways-Melanogenesis and tyrosine metabolism were contained. High-throughput miRNA sequencing identified a total of 475 miRNAs, including 64 novel miRNAs. Furthermore, 33 differentially expressed miRNAs containing 13 up-regulated and 20 down-regulated miRNAs were identified in albino versus normally pigmented individuals (fold change ≥1.5 or ≤0.67 and p≤0.05). The next target prediction discovered a variety of putative target genes, of which, 134 genes including Tyrosinase (TYR), Tyrosinase-related protein 1 (TYRP1), Microphthalmia-associated transcription factor (MITF) were overlapped with differentially expressed genes derived from RNA-seq. These target genes were significantly enriched to 254 GO terms and 103 KEGG pathways (p<0.001). Of those, tyrosine metabolism, lysosomes, phototransduction pathways, etc., attracted considerable attention due to their involvement in regulating skin pigmentation. Expression patterns of differentially expressed mRNA and miRNAs were validated in 10 mRNA and 10 miRNAs by qRT-PCR. With high-throughput mRNA and miRNA sequencing and analysis, a series of interested mRNA and miRNAs involved in fish pigmentation are identified. And the miRNA-mRNA regulatory network also provides a solid starting point for further elucidation of fish pigmentation deficiency.
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