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

Affiliation

Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, People's Republic of China. [Email]

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,