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

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.

Identification and Characterization of Long Non-coding RNAs in the Intestine of Olive Flounder (Paralichthys olivaceus) During Edwardsiella tarda Infection

“…Furthermore, at least 84% of the clean reads from each library were mapped on to the genome of the olive flounder, which is higher than what has been previously reported. Previous reports have shown that the mapping rates were only 67.32, 74, and 79.13% ( 18 , 27 ), which are relatively low. It has been speculated that the low mapping rates of olive flounders may be due to their imperfect reference genome ( 18 ).…”

“…In recent years, ceRNA regulatory networks have been widely investigated in types of diseases (11,37). Moreover, Chu et al (27,38) confirmed the hypothesis that ceRNA regulatory networks also exist in teleosts. In this study, the lncRNA-miRNA-mRNA networks were constructed by using a combination of lncRNA-miRNA and miRNA-mRNA pairs.…”

“…The lncRNA MARL functions as a ceRNA for miR-122 to control the abundance of mitochondrial antiviral signaling proteins (MAVS), thereby inhibiting Siniperca chuatsi rhabdovirus (SCRV) replication and promoting antiviral responses ( 38 ). In addition, the lncRNA AANCR functions as a ceRNA for miR-210 to control the protein abundance of MITA, thereby inhibiting SCRV replication and promoting antiviral responses ( 27 ). To the best of our knowledge, the present study is the first to identify two potential ceRNA regulatory networks, LNC_001979-novel_171-Potusc2 and LNC_001979-novel_171-Podad1, from the intestine of olive flounder.…”

Best practices on the differential expression analysis of multi-species RNA-seq

“…By assessing mRNA profiles, it is possible to interrogate the specific genetic processes underlying, and giving rise to, specific phenotypes of interest. The use of transcriptomics has expanded to evaluate the transcriptional profile of other RNA populations [ 4 ], such as rRNAs [ 5 ], miRNAs [ 6 – 8 ], tRNAs [ 9 , 10 ], and other small RNAs [ 11 – 14 ]. Traditional transcriptomics analyses usually identify transcriptional alterations in a single organism.…”

Comparative analysis of distinctive transcriptome profiles with biochemical evidence in bisphenol S- and benzo[a]pyrene-exposed liver tissues of the olive flounder Paralichthys olivaceus

“…Genomic platforms have been successfully applied to understand diverse molecular and physiological characteristics of P . olivaceus [ 11 – 14 ]. The recently published whole genome sequence of P .…”