Identification and characterization of salt-tolerance relative miRNAs in Procambarus clarkii by high-throughput sequencing

ExRNA - Tập 1 Số 1 - 2019
Fangfang Jin1, Yanchun Sun2
1State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Road, Nanjing, Jiangsu 210046, China
2Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing 210023, China

Tóm tắt

Abstract Procambarus clarkii is one of the important economic species in China and has been served as tasty food in recent years after being introduced to Nanjing. Significant problems of environment factors, such as salinity, pH and temperature, especially salinity, has the potential to result in significant economic losses in many crayfish-producing farms in China. miRNAs are a kind of ~ 22 nucleotide small non coding RNAs which were encoded by plants, animals and some viruses with functions in RNA silencing or post-transcription regulation. We constructed four sRNA library of P. clarkia from different tissues and treatments by using high-throughput sequencing technology. A total of 101 conserved miRNAs and two novel pre-miRNAs were identified and RT-qPCR were further performed to confirm existence of part of identified miRNAs. A genome wide expression profile of salt-tolerance miRNAs was proved and three miRNAs were further validated by RT-qPCR with dynamic response to different salinity stages. The study of miRNAs in P. clarkia can help us better understanding the role of miRNAs in salt-tolerance in P. clarkia.

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Tài liệu tham khảo

Sanchez Lopez FJ, Gil Garcia MD, Martinez Vidal JL, Aguilera PA, Garrido Frenich A. Assessment of metal contamination in Donana National Park (Spain) using crayfish (Procamburus clarkii). Environ Monit Assess. 2004;93:17–29.

Yue GH, Li JL, Bai ZY, Wang CM, Feng FLC. Genetic diversity and population structure of the invasive alien red swamp crayfish. Biol Invasions. 2010;12:2697–706.

Gherardi F. Crayfish invading Europe: the case study of Procambarus clarkii. Mar Freshw Behav Phy. 2006;39:175–91.

Ambros V. The functions of animal microRNAs. Nature. 2004;431:350–5.

Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004;116:281–97.

Bartel DP. Metazoan MicroRNAs. Cell. 2018;173:20–51.

Bartel DP. MicroRNAs: target recognition and regulatory functions. Cell. 2009;136:215–33.

Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB, Bartel DP. The microRNAs of Caenorhabditis elegans. Genes Dev. 2003;17:991–1008.

Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T. Identification of tissue-specific microRNAs from mouse. Curr Biol. 2002;12:735–9.

Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell. 2005;120:15–20.

Friedman RC, Farh KK, Burge CB, Bartel DP. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 2009;19:92–105.

S. Griffiths-Jones, miRBase: microRNA sequences and annotation, Curr Protoc Bioinformatics, Chapter 12 (2010) Unit 12 19 11–10.

Wang K, Shen X-l, Jia J-s, Yu X-d, Du J, Lin S-h, Du Z-q. High-throughput sequencing analysis of microRNAs in gills of red swamp crayfish, Procambarus clarkii infected with white spot syndrome virus. Fish Shellfish Immunol. 2018;83:18–25.

Du Z-q, Wang K, Shen X-l, Jin Y-h, Jin H-x, Li X-c. Identification and characterization of intestine microRNAs and targets in red swamp crayfish, Procambarus clarkii infected with white spot syndrome virus. PLoS One. 2017;12(11).

Du ZQ, Leng XY, Shen XL, Jin YH, Li XC. Identification and characterization of lymph organ microRNAs in red swamp crayfish, Procambarus clarkii infected with white spot syndrome virus. Fish Shellfish Immunol. 2017;69:78–84.

Ou J, Li Y, Ding Z, Xiu Y, Wu T, Du J, Li W, Zhu H, Ren Q, Gu W, Wang W. Transcriptome-wide identification and characterization of the Procambarus clarkii microRNAs potentially related to immunity against Spiroplasma eriocheiris infection. Fish Shellfish Immunol. 2013;35:607–17.

Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank. Nucleic Acids Res. 2008;36:D25–30.

Jiang P, Wu H, Wang W, Ma W, Sun X, Lu Z. MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features. Nucleic Acids Res. 2007;35:W339–44.

Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics. 2008;24:713–4.

Li R, Yu C, Li Y, Lam T-W, Yiu S-M, Kristiansen K, Wang J. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics. 2009;25:1966–7.

Horiuchi S. Characterization of gill Na,K-ATPase in the freshwater crayfish, Procambarus clarki (Girard). Comp Biochem Physiol B. 1977;56:135–8.

Serrano L, Towle DW, Charmantier G, Spanings-Pierrot C. Expression of Na(+)/K(+)-ATPase alpha-subunit mRNA during embryonic development of the crayfish Astacus leptodactylus. Comp Biochem Physiol Part D Genomics Proteomics. 2007;2:126–34.

Xu WN, Liu WB, Yang WW, Zhang DD, Jiang GZ. Identification and differential expression of hepatopancreas microRNAs in red swamp crayfish fed with emodin diet. Fish Shellfish Immunol. 2014;39:1–7.

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