Albinism, a phenomenon characterized by pigmentation deficiency on the ocular side of Japanese flounder (Paralichthys olivaceus), has caused significant damage and limited mRNA and microRNA (miRNA) information is available on fish pigmentation deficiency. In a recent study, a team led by scientists from the Qingdao National Laboratory for Marine Science and Technology employed RNA sequencing to identify the mRNA and miRNAs involved in Polivaceusalbinism.

Based on Polivaceus 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). 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.

Through high-throughput mRNA and miRNA sequencing and analysis, a series of interesting mRNA and miRNAs involved in fish pigmentation were identified in this study. The miRNA-mRNA regulatory networks also provide a solid starting point for further elucidation of fish pigmentation deficiency.

The volcanoplot of differentially expressed genes in RNA-seq


The differentially expressed genes including 41 up-regulated genes and 194 down-regulated genes in PO_alb vs PO_con were illustrated in a volcanoplot (fold change≥2 and q-value≤0.05)


N. Wang , R. Wang, R Wang, Y. Tian, C. Shao, X. Jia, S. Chen (2017) The integrated analysis of RNA-seq and microRNA-seq depicts miRNA-mRNA networks involved in Japanese flounder (Paralichthys olivaceus) albinism PLOS ONE doi: 10.1371/journal.pone.0181761 [article]

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