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.
Highlights
Albinism, characterized by pigmentation deficiency in the skin, hair and eyes of mammals, has been extensively studied since the early 19th century [1, 2]
There have been five enzymes identified as being required for human melanin pigmentation, namely tyrosinase (TYR), tyrosinase-related protein-1 (TYRP1), P (OCA2), solute carrier family 45 member 2 (SLC45A2), and G-protein coupled receptor 143 (GPR143), and defects in any of these enzymes could result in albinism [7]
Further genome mapping analysis revealed that over 79.13% of reads were mapped with P. olivaceus genome
Summary
Albinism, characterized by pigmentation deficiency in the skin, hair and eyes of mammals, has been extensively studied since the early 19th century [1, 2]. MicroRNAs (miRNAs), a type of non-coding RNA with a length between 22–24 nt, could act as post-transcriptional negative regulators of mRNA stability or translation [11, 12]. Since their initial discovery in the 1990s, miRNAs have been proven to extensively regulate cell differentiation, development and diseases [13,14,15]. Over 60% of mRNAs are thought to be regulated by miRNAs [16]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
