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. 2019 Jul;24(4):689-695.
doi: 10.1007/s12192-019-00989-x. Epub 2019 Jun 17.

Genome-wide identification of Chinese shrimp (Fenneropenaeus chinensis) microRNA responsive to low pH stress by deep sequencing

Yuying He  1   2 , Zhaoxia Li  3 , Haien Zhang  4 , Shuo Hu  4 , Qingyin Wang  1 , Jian Li  5   6
Affiliations

Genome-wide identification of Chinese shrimp (Fenneropenaeus chinensis) microRNA responsive to low pH stress by deep sequencing

Yuying He et al. Cell Stress Chaperones. 2019 Jul.

Abstract

pH has a great impact on the distribution, growth, behavior, and physiology in many aquatic animals. Here, we analyzed miRNA expression profiles of Chinese shrimp (Fenneropenaeus chinensis) from control pH (8.2) and low pH (6.5)-treated shrimp. Expression analysis identified 6 known miRNAs and 23 novel miRNAs with significantly different expression between control pH 8.2 and low pH 6.5; the predicted target genes of differentially expressed miRNAs were significantly enriched in organic acid metabolic process, oxidoreductase activity, coenzyme binding, cofactor binding, and collagen trimer. Moreover, target genes were significantly enriched in several Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways including citrate cycle, pyruvate metabolism, cytokine-cytokine receptor interaction, tight junction, carbon metabolism, etc. Our survey expanded the number of known shrimp miRNAs and provided comprehensive information about miRNA response to low pH stress.

Keywords: Fenneropenaeus chinensis; HiSeq sequencing; Low pH stress; microRNA.

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Figures

Fig. 1
Fig. 1
Small RNA library sequencing and annotation. a Length distribution of small RNA reads. b Annotation of small RNAs. The percentages of each type of sRNAs are indicated in brackets
Fig. 2
Fig. 2
GO enrichment analysis of predicted target genes for differentially expressed miRNAs
Fig. 3
Fig. 3
Pathway enrichment analysis of predicted target genes for differentially expressed miRNAs
Fig. 4
Fig. 4
Selected miRNAs were experimentally tested by qRT-PCR confirming expression patterns of deep sequencing. a Most miRNAs were consistent with the expression patterns of deep sequencing. b Regression analysis between sequencing and qRT-PCR
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