Dataset Information

Comparative microRNA-seq Analysis Depicts Candidate miRNAs Involved in Skin Color Differentiation in Red Tilapia.

ABSTRACT: Differentiation and variation in body color has been a growing limitation to the commercial value of red tilapia. Limited microRNA (miRNA) information is available on skin color differentiation and variation in fish so far. In this study, a high-throughput Illumina sequencing of sRNAs was conducted on three color varieties of red tilapia and 81,394,491 raw reads were generated. A total of 158 differentially expressed miRNAs (|log?(fold change)| ≥ 1 and q-value ≤ 0.001) were identified. Target prediction and functional analysis of color-related miRNAs showed that a variety of putative target genes—including slc7a11, mc1r and asip—played potential roles in pigmentation. Moreover; the miRNA-mRNA regulatory network was illustrated to elucidate the pigmentation differentiation, in which miR-138-5p and miR-722 were predicted to play important roles in regulating the pigmentation process. These results advance our understanding of the molecular mechanisms of skin pigmentation differentiation in red tilapia.

SUBMITTER: Wang L

PROVIDER: S-EPMC5979384 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

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Comparative microRNA-seq Analysis Depicts Candidate miRNAs Involved in Skin Color Differentiation in Red Tilapia.

Wang Lanmei L Zhu Wenbin W Dong Zaijie Z Song Feibiao F Dong Juanjuan J Fu Jianjun J

International journal of molecular sciences 20180416 4

Differentiation and variation in body color has been a growing limitation to the commercial value of red tilapia. Limited microRNA (miRNA) information is available on skin color differentiation and variation in fish so far. In this study, a high-throughput Illumina sequencing of sRNAs was conducted on three color varieties of red tilapia and 81,394,491 raw reads were generated. A total of 158 differentially expressed miRNAs (|log₂(fold change)| ≥ 1 and <i>q</i>-value ≤ 0.001) were identifi ...[more]

PMID: 29659520

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Project description: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.

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Dataset Information

Comparative microRNA-seq Analysis Depicts Candidate miRNAs Involved in Skin Color Differentiation in Red Tilapia.

Publications

Comparative microRNA-seq Analysis Depicts Candidate miRNAs Involved in Skin Color Differentiation in Red Tilapia.

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