The integrated analysis of RNA-seq and microRNA-seq depicts miRNA-mRNA networks involved in Japanese flounder (Paralichthys olivaceus) albinism

Na Wang; Ruoqing Wang; Renkai Wang; Yongsheng Tian; Changwei Shao; Xiaodong Jia; Songlin Chen

doi:10.1371/journal.pone.0181761

The integrated analysis of RNA-seq and microRNA-seq depicts miRNA-mRNA networks involved in Japanese flounder (Paralichthys olivaceus) albinism

PLoS One. 2017 Aug 4;12(8):e0181761. doi: 10.1371/journal.pone.0181761. eCollection 2017.

Authors

Na Wang^{1

2}, Ruoqing Wang^{1

3}, Renkai Wang^{1

3}, Yongsheng Tian^{1

2}, Changwei Shao^{1

2}, Xiaodong Jia⁴, Songlin Chen^{1

2}

Affiliations

¹ Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.
² Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
³ College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China.
⁴ Joint Laboratory for Translational Medicine Research, Beijing Institute of Genomics, Chinese Academy of Sciences & Liaocheng People's Hospital, Liaocheng, China.

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.

MeSH terms

Albinism / genetics*
Animals
Fish Proteins / genetics*
Flounder / genetics*
Flounder / growth & development
Gene Expression Profiling
Gene Regulatory Networks*
High-Throughput Nucleotide Sequencing / methods*
MicroRNAs / genetics*
RNA, Messenger / genetics*
Sequence Analysis, RNA / methods

Substances

Fish Proteins
MicroRNAs
RNA, Messenger

Grants and funding

This work was supported by grants from the National Natural Science Foundation of China (NW, 31472273; SLC, 31461163005) (http://www.nsfc.gov.cn/), and the Taishan Scholar Climb Project of Shandong Province (SLC, http://www.rcsd.gov.cn/gongcheng/shengjigongcheng/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.