Integrated analysis of RNA-seq and microRNA-seq depicts miRNA-mRNA networks involved in stripe patterns of Botia superciliaris skin [miRNA-seq]

Purpose:In order to elucidate the molecular mechanism of the stripe patterns in B. superciliaris skin.These results will enhance understanding of molecular mechanisms underlying skin pigmentation and facilitate molecular-assisted selection of highly valued skin colors. Methods:In this study, Illumina sequencing was employed to identify the mRNAs and miRNAs involved in stripe pattern formation in B. superciliaris skin. target prediction revealed a variety of putative target genes; differentially expressed mRNAs and miRNAs patterns were observed in 5 mRNAs and mir-217 by qRT-PCR. Results:Based on the zebrafish genome, a total of 44,206,176 and 46,941,318 high-quality transcriptome reads were generated, which resulted in 134,586 unigenes that were used as reference sequences. A total of 24,113 genes exhibited significantly different expression patterns (fold-change = 2 or = 0.5 and q = 0.05), including 15,117 up-regulated genes and 8,996 down-regulated genes associated with black and yellow stripes.These genes were enriched in 65 GO terms and 7 KEGG pathways (q = 0.05), which included melanogenesis, and contained 32 up-regulated genes and 12 down-regulated genes. High-throughput miRNA sequencing identified a total of 355 miRNAs, which included 38 novel miRNAs. Furthermore, 87 differentially expressed miRNAs that contained 50 up-regulated and 37 down-regulated miRNAs were identified in different color skin Conclusions:This study provides novel insight into the mechanism that produces different color stripes in B. superciliaris by combining RNA-seq with small RNA-seq. 5 genes and 1 miRNAs were selected arbitrarily for verification . Compared with previous fish studies, revealed that these DE mRNAs and miRNAs are likely involved in melanin synthesis, and the quantitative mRNA/miRNA data and pathway information presented here provide a strong basis for elucidation of the detailed functions of mRNAs and miRNAs associated with black and yellow stripe formation in aquarium fish. Overall design: Black and yellow skin tissue samples were collected from 6 individuals . and mRNA and miRNA library construction and sequencing