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Identification and comparative analysis of the oriental river prawn (Macrobrachium nipponense) microRNA expression profile during hypoxia using a deep sequencing approach

文献类型： 外文期刊

作者： Sun, Shengming 1 ; Fu, Hongtuo 1 ; Ge, Xianping 1 ; Zhu, Jian 1 ; Gu, Zhimin 2 ; Xuan, Fujun 3 ;

作者机构： 1.Chinese Acad Fishery Sci, Freshwater Fisheries Res Ctr, Minist Agr, Key Lab Genet Breeding & Aquaculture Biol Freshwa, Wuxi 214081, Peoples R China

2.Zhejiang Inst Freshwater Fisheries, Minist Agr, Key Lab Hlth Freshwater Aquaculture, Huzhou 313001, Peoples R China

3.Yancheng Teachers Univ, Jiangsu Prov Key Lab Coastal Wetland Bioresources, Yancheng 224051, Peoples R China

关键词： Hypoxia;Macrobrachium nipponense;MicroRNA;Solexa deep sequencing;mRNA

期刊名称：COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS （ 影响因子：2.674； 五年影响因子：2.941 ）

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收录情况： SCI

摘要： Hypoxia refers to a state of oxygen deficiency, which is observed frequently in aquaculture ponds. MicroRNAs (miRNAs) are small non-coding RNAs that are important effectors in regulating gene expression through post transcriptional mechanisms. They are key elements in the response to hypoxia. The oriental river prawn (Macrobrachium nipponense) is an important commercial aquaculture species, and is sensitive to hypoxia. To date, there are no reports describing M. nipponense miRNAs. In this study, Solexa deep sequencing technology was used for high-throughput analysis of miRNAs in a small RNA library isolated from four M. nipponense tissues (gill, hepatopancreas, muscle and hemocytes). In total, 9,227,356 reads were obtained, 4,293,155 of which were related to 267 unique miRNAs, including 203 conserved and 64 prawn-specific miRNAs. Furthermore, miRNA features including length distribution and end variations were characterized. Annotation of targets revealed a broad range of biological processes and signal transduction pathways regulated by M. nipponense miRNAs. In addition, 880 co-expressed and 39 specific (25 normoxia-specific and 14 hypoxia-specific) miRNAs that may be involved in the response to hypoxia were confirmed using miRNA microarray analysis from the four prawn tissues combined. Real-time quantitative PCR (qPCR) analysis of eight miRNAs in the normoxia and hypoxia groups showed good concordance between the sequencing and qPCR data. This study provides the first large-scale identification and characterization of M. nipponense miRNAs and their potential targets, and represents a foundation for further characterization of their roles in the regulation of the diversity of hypoxia processes. (C) 2016 Elsevier Inc. All rights reserved.

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[1]Identification of differentially expressed genes in hepatopancreas of oriental river prawn, Macrobrachium nipponense exposed to environmental hypoxia. Sun, Shengming,Ge, Xianping,Fu, Hongtuo,Zhu, Jian,Xuan, Fujun,Zhang, Shiyong.

[2]Molecular Cloning and Functional Characterization of a Hexokinase from the Oriental River Prawn Macrobrachium nipponense in Response to Hypoxia. Sun, Shengming,Fu, Hongtuo,Zhu, Jian,Ge, Xianping,Xuan, Fujun. 2017

[3]Transciptomic and histological analysis of hepatopancreas, muscle and gill tissues of oriental river prawn (Macrobrachium nipponense) in response to chronic hypoxia. Sun, Shengming,Fu, Hongtuo,Zhu, Jian,Ge, Xianping,Xuan, Fujun,Gu, Zhimin. 2015

[4]Molecular characterization and mRNA expression of hypoxia inducible factor-1 and cognate inhibiting factor in Macrobrachium nipponense in response to hypoxia. Sun, Shengming,Fu, Hongtuo,Ge, Xianping,Zhu, Jian,Qiao, Hui,Jin, Shubo,Zhang, Wenyi,Xuan, Fujun.

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[6]Molecular cloning, characterization, and expression analysis of p53 from the oriental river prawn, Macrobrachium nipponense, in response to hypoxia. Sun, Shengming,Fu, Hongtuo,Zhu, Jian,Ge, Xianping,Gu, Zhimin,Xuan, Fujun.

[7]THE METALLOTHIONEIN GENE FROM THE ORIENTAL RIVER PRAWN MACROBRACHIUM NIPPONENSE (DE HAAN, 1849): CHARACTERIZATION AND EXPRESSION IN RESPONSE TO HYPDXIA AND REOXYGENATION. Sun, Shengming,Gu, Zhimin,Fu, Hongtuo,Zhu, Jian.

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