Cite this paper:
SONG Wei, ZHU Yefei, WANG Lumin, JIANG Keji, ZHANG Fengying, MA Chunyan, MA Lingbo. Identification and profiling of microRNAs of Euphausia superba using Illumina deep sequencing[J]. HaiyangYuHuZhao, 2018, 36(6): 2278-2287

Identification and profiling of microRNAs of Euphausia superba using Illumina deep sequencing

SONG Wei1, ZHU Yefei1, WANG Lumin2, JIANG Keji1, ZHANG Fengying1, MA Chunyan1, MA Lingbo1
1 Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China;
2 Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China
MicroRNAs (miRNAs) are an abundant class of conserved, non-coding small RNAs that play important role in gene regulation at post translational level. There have been no reports on the miRNAs of the Antarctic krill Euphausia superba despite the species' crucial position in Antarctic food webs. Two small RNA libraries were constructed from eyestalk and muscle, subsequently, and deep sequencing analysis was performed to investigate and profile E. superba miRNAs. A total of 19 304 586 and 23 005 104 unique sequences were obtained from the eyestalk and muscle, respectively. After compared the small RNA sequences with the Rfam database, 12 342 039 and 7 907 477 reads in eyestalk and muscle were matched to the transcriptome sequence of E. superba. A total of 236 distinct miRNAs were identified after annotation to known animal miRNAs registered in miRBase 21. In both libraries, the most abundant known miRNA were miR-750 with 92 583 reads in muscle and miR-1304-3p with 56 386 reads in eyestalk while the average value was less than 106, revealing a wide range of different expression levels. In addition, miR-277a enriched in both libraries and may be involved in modulating Krebs cycle by targeting to Vimar. Differential expression analysis showed that 56 mature miRNAs were significantly up/down regulated according to expression fold change. It appeared that the expression of several abundant miRNAs maybe tissue-specific or tissue-bias. Notably, the expression pattern of miR-750 and miR-1 family, which was suggested as the crucial candidates, involved in muscle development. Taken together, this study provides the first miRNA profile of E. superba and some of these miRNAs were expected to play important role in immune response, reproduction, energy metabolism, and muscle development and so on. Thus, the results provides a reference for functional studies of miRNAs in E. superba.
Key words:    microRNA|Antarctic krill|Illumina deep-sequencing|eyestalk|muscle   
Received: 2017-08-04   Revised:
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Atkinson A, Siegel V, Pakhomov E, Rothery P. 2004. Longterm decline in krill stock and increase in salps within the southern Ocean. Nature, 432(7013):100-103,
Begemann G. 2008. MicroRNAs and RNA interference in zebrafish development. Zebrafish, 5(2):111-119,
Bos J L. 2005. Linking Rap to cell adhesion. Current Opinion in Cell Biology, 17(2):123-128,
Brown B D, Gentner B, Cantore A, Colleoni S, Amendola M, Zingale A, Baccarini A, Lazzari G, Galli C, Naldini L. 2007. Endogenous microRNA can be broadly exploited to regulate transgene expression according to tissue, lineage and differentiation state. Nature Biotechnology, 25(12):1 457-1 467,
Bruce C R, Kriketos A D, Cooney G J, Hawley J A. 2004. Disassociation of muscle triglyceride content and insulin sensitivity after exercise training in patients with Type 2 diabetes. Diabetologia, 47(1):23-30, 1007/s00125-003-1265-7.
Cai X Z, Hagedorn C H, Cullen B R. 2004. Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA, 10(12):1 957-1 966,
Calin G A, Dumitru C D, Shimizu M, Bichi R, Zupo S, Noch E, Aldler H, Rattan S, Keating M, Rai K, Rassenti L, Kipps T, Negrini M, Bullrich F, Croce C M. 2002.Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proceedings of the National Academy of Sciences of the United States of America, 99(24):15 524-15 529,
Cascella K, Jollivet D, Papot C, Léger N, Corre E, Ravaux J, Clark M S, Toullec J Y. 2015. Diversification, evolution and sub-functionalization of 70kDa heat-shock proteins in two sister species of antarctic krill:differences in thermal habitats, responses and implications under climate change. PLoS One, 10(4):e0121642, 1371/journal.pone.0121642.
Cortez M A, Bueso-Ramos C, Ferdin J, Lopez-Berestein G, Sood A K, Calin G A. 2011. MicroRNAs in body fluidsthe mix of hormones and biomarkers. Nature Reviews Clinical Oncology, 8(8):467-477,
Courteau L A, Storey K B, Morin P Jr. 2012. Differential expression of microRNA species in a freeze tolerant insect, Eurosta solidaginis. Cryobiology, 65(3):210-214,
De Souza Gomes M, Muniyappa M K, Carvalho S G, GuerraSá, R, Spillane C. 2011. Genome-wide identification of novel microRNAs and their target genes in the human parasite Schistosoma mansoni. Genomics, 98(2):96-111,
Fricke C, Green D, Smith D, Dalmay T, Chapman T. 2014.MicroRNAs influence reproductive responses by females to male sex peptide in Drosophila melanogaster. Genetics, 198(4):1 603-1 619,
Hafner M, Landgraf P, Ludwig J, Rice A, Ojo T, Lin C, Holoch D, Lim C, Tuschl T. 2008. Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing. Methods, 44(1):3-12,
Harrington W F, Rodgers M E. 1984. Myosin. Annual Review of Biochemistry, 53:35-73,
He L, Hannon G J. 2004. MicroRNAs:small RNAs with a big role in gene regulation. Nature Reviews Genetics, 5(7):522-531,
Huang T Z, Cui Y L, Zhang X B. 2014. Involvement of viral microRNA in the regulation of antiviral apoptosis in shrimp. Journal of Virology, 88(5):2 544-2 554,
Ikeda K T, Hirose Y, Hiraoka K, Noro E, Fujishima K, Tomita M, Kanai A. 2015. Identification, expression, and molecular evolution of microRNAs in the "living fossil" Triops cancriformis (tadpole shrimp). RNA, 21(2):230-242,
Jopling C L, Yi M, Lancaster A M, Lemon S M, Sarnow P. 2005. Modulation of hepatitis C virus RNA abundance by a liver-specific MicroRNA. Science, 309(5740):1 577-1 581,
Katayama H. 2016. Structure-activity relationship of crustacean peptide hormones. Bioscience, Biotechnology, and Biochemistry, 80(4):633-641, 1080/09168451.2015.1116932.
Kozomara A, Griffiths-Jones S. 2014. miRBase:annotating high confidence microRNAs using deep sequencing data.Nucleic Acids Research, 42(Database issue):D68-D73,
Kwon C, Han Z, Olson E N, Srivastava D. 2005. MicroRNA1influences cardiac differentiation in Drosophila and regulates Notch signaling. Proceedings of the National Academy of Sciences of the United States of America, 102(52):18 986-18 991,
Langmead B, Salzberg S L. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods, 9(4):357-359,
Legeai F, Rizk G, Walsh T, Edwards O, Gordon K, Lavenier D, Leterme N, Méreau A, Nicolas J, Tagu D, JaubertPossamai S. 2010. Bioinformatic prediction, deep sequencing of microRNAs and expression analysis during phenotypic plasticity in the pea aphid, Acyrthosiphon pisum. BMC Genomics, 11:281,
Li S K, Zhu S, Li C B, Zhang Z, Zhou L Z, Wang S J, Wang S Q, Zhang Y L, Wen X B. 2013. Characterization of microRNAs in mud crab Scylla paramamosain under Vibrio parahaemolyticus infection. PLoS One, 8(8):e73392,
Lv J J, Liu P, Gao B Q, Li J. 2016. The identification and characteristics of salinity-related microRNAs in gills of Portunus trituberculatus. Cell Stress and Chaperones, 21(1):63-74,
Marco A, Hooks K, Griffiths-Jones S. 2012. Evolution and function of the extended miR-2 microRNA family. RNA Biology, 9(3):242-248,
Melton C, Judson R L, Blelloch R. 2010. Opposing microRNA families regulate self-renewal in mouse embryonic stem cells. Nature, 463(7281):621-626, 1038/nature08725.
Mishima Y, Abreu-Goodger C, Staton A A, Stahlhut C, Shou C, Cheng C, Gerstein M, Enright A J, Giraldez A J. 2009.Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization.Genes & Development, 23(5):619-632, 1101/gad.1760209.
Morin R D, O'Connor M D, Griffith M, Kuchenbauer F, Delaney A, Prabhu A L, Zhao Y J, McDonald H, Zeng T, Hirst M, Eaves C J, Marra M A. 2008. Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Research, 18(4):610-621,
O'Connell R M, Chaudhuri A A, Rao D S, Baltimore D. 2009.Inositol phosphatase SHIP1 is a primary target of miR-155. Proceedings of the National Academy of Sciences of the United States of America, 106(17):7 113-7 118,
O'Rourke J R, Georges S A, Seay H R, Tapscott S J, McManus M T, Goldhamer D J, Swanson M S, Harfe B D. 2007.Essential role for Dicer during skeletal muscle development. Developmental Biology, 311(2):359-368,
Ou J T, Li Y, Ding Z F, Xiu Y J, Wu T, Du J, Li W J, Zhu H X, Ren Q, Gu W, Wang W. 2013. Transcriptome-wide identification and characterization of the Procambarus clarkii microRNAs potentially related to immunity against Spiroplasma eriocheiris infection. Fish & Shellfish Immunology, 35(2):607-617,
Pauli A, Rinn J L, Schier A F. 2011. Non-coding RNAs as regulators of embryogenesis. Nature Reviews Genetics, 12(2):136-149,
Pushpavalli S N C V L, Sarkar A, Bag I, Hunt C R, Ramaiah M J, Pandita T K, Bhadra U, Pal-Bhadra M. 2014.Argonaute-1 functions as a mitotic regulator by controlling Cyclin B during Drosophila early embryogenesis. The FASEB Journal, 28(2):655-666,
Ren X Y, Cui Y T, Gao B Q, Liu P, Li J. 2016. Identification and profiling of growth-related microRNAs of the swimming crab Portunus trituberculatus by using Solexa deep sequencing. Marine Genomics, 28:113-120,
Ruby J G, Stark A, Johnston W K, Kellis M, Bartel D P, Lai E C. 2007. Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Research, 17(12):1 850-1 864,
Ryan B M, Robles A I, Harris C C. 2010. Genetic variation in microRNA networks:the implications for cancer research.Nature Reviews Cancer, 10(6):389-402,
Shao P, Liao J Y, Guan D G, Yang J H, Zheng L L, Jing Q, Zhou H, Qu L H. 2012. Drastic expression change of transposon-derived piRNA-like RNAs and microRNAs in early stages of chicken embryos implies a role in gastrulation. RNA Biology, 9(2):212-227,
Sokol N S, Ambros V. 2005. Mesodermally expressed Drosophila microRNA-1 is regulated by Twist and is required in muscles during larval growth. Genes & Development, 19(19):2 343-2 354, 1101/gad.1356105.
Song Y N, Shi L L, Liu Z Q, Qiu G F. 2014. Global analysis of the ovarian microRNA transcriptome:implication for miR-2 and miR-133 regulation of oocyte meiosis in the Chinese mitten crab, Eriocheir sinensis (Crustacea:Decapoda). BMC Genomics, 15:547,
Tan T T, Chen M, Harikrishna J A, Khairuddin N, Mohd Shamsudin M I, Zhang G J, Bhassu S. 2013. Deep parallel sequencing reveals conserved and novel miRNAs in gill and hepatopancreas of giant freshwater prawn. Fish & Shellfish Immunology, 35(4):1 061-1 069,
Tay Y, Zhang J Q, Thomson A M, Lim B, Rigoutsos I. 2008.MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation. Nature, 455(7216):1 124-1 128,
Turner L M, Webster S G, Morris S. 2013. Roles of crustacean hyperglycaemic hormone in ionic and metabolic homeostasis in the Christmas Island blue crab, Discoplax celeste. Journal of Experimental Biology, 216(Pt 7):1 191-1 201,
Vasudevan S, Tong Y C, Steitz J A. 2007. Switching from repression to activation:microRNAs can up-regulate translation. Science, 318(5858):1 931-1 934,
Xi Q Y, Xiong Y Y, Wang Y M, Cheng X, Qi Q E, Shu G, Wang S B, Wang L N, Gao P, Zhu X T, Jiang Q Y, Zhang Y L, Liu L. 2015. Genome-wide discovery of novel and conserved microRNAs in white shrimp (Litopenaeus vannamei). Molecular Biology Reports, 42(1):61-69,
Xiao M, Li J, Li W, Wang Y, Wu F Z, Xi Y P, Zhang L, Ding C, Luo H B, Li Y, Peng L N, Zhao L P, Peng S L, Xiao Y, Dong S, Cao J, Yu W. 2017. MicroRNAs activate gene transcription epigenetically as an enhancer trigger. RNA Biology, 14(10):1 326-1 334,
Yan X C, Ding L, Li Y C, Zhang X F, Liang Y, Sun X W, Teng C B. 2012. Identification and profiling of microRNAs from skeletal muscle of the common carp. PLoS One, 7(1):e30925, 0030925.
Yao X M, Wang L L, Song L S, Zhang H, Dong C H, Zhang Y, Qiu L M, Shi Y H, Zhao J M, Bi Y K. 2010. A Dicer-1 gene from white shrimp Litopenaeus vannamei:expression pattern in the processes of immune response and larval development. Fish & Shellfish Immunology, 29(4):565-570,