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Journal of Integrative Agriculture  2022, Vol. 21 Issue (4): 1106-1115    DOI: 10.1016/S2095-3119(20)63465-7
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Genome-wide characterization of miRNA and siRNA pathways in the parasitoid wasp Pteromalus puparum
XIAO Shan1, FANG Qi1, LIU Ming-ming1, ZHANG Jiao1, WANG Bei-bei1, YAN Zhi-chao1, WANG Fang1, David W. STANLEY2, YE Gong-yin1
1 State Key Laboratory of Rice Biology/Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, P.R.China
2 Biological Control of Insects Research Laboratory, USDA Agricultural Research Service, Columbia, Missouri 65203, USA
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微RNA (microRNAs,miRNA)、小干扰RNA (small interfering RNA,siRNA) 是真核生物体内触发RNA干扰 (RNA interference,RNAi) 的两种非编码小RNA。两种非编码RNA生物合成通路在黑腹果蝇、埃及伊蚊、家蚕以及其他昆虫中具有广泛研究,但在膜翅目昆虫尤其是寄生蜂中少见。蝶蛹金小蜂是蝴蝶蛹期寄生蜂。本研究通过蝶蛹金小蜂基因组对miRNA、siRNA合成通路鉴定并分析。结果表明除siRNA通路中R2D2Argonaute-2基因在基因组中分别具有2、3个拷贝,两个通路其他关键基因均只有1个拷贝。结构域保守性分析表明蝶蛹金小蜂相关蛋白与其他物种同源蛋白具有相似结构。对膜翅目昆虫DicerArgonaute基因进化分析表明siRNA通路相关基因进化速率更快。但与其他膜翅目昆虫相反,蝶蛹金小蜂中Dicer-2基因进化速率比Dicer-1基因更低。表达分析显示miRNA通路基因在蝶蛹金小蜂成虫中表达量更高而siRNA通路基因表达模式各不相同。本研究为了解寄生蜂miRNA、siRNA生物合成通路及其作用机制提供新的认识。

Abstract  microRNAs (miRNAs) and small interfering RNAs (siRNAs) are small non-coding RNAs (ncRNAs) that trigger RNA interference (RNAi) in eukaryotic organisms.  The biogenesis pathways for these ncRNAs are well established in Drosophila melanogaster, Aedes aegypti, Bombyx mori and other insects, but lacking in hymenopteran species, particularly in parasitoid wasps.  Pteromalus puparum is a parasitoid of pupal butterflies.  This study identified and analyzed two pathways by interrogating the P. puparum genome.  All core genes of the two pathways are present in the genome as a single copy, except for two genes in the siRNA pathway, R2D2 (two copies) and Argonaute-2 (three).  Conserved domain analyses showed the protein structures in P. puparum were similar to cognate proteins in other insect species.  Phylogenetic analyses of hymenopteran Dicer and Argonaute genes suggested that the siRNA pathway-related genes evolved faster than those in the miRNA pathway.  The study found a decelerated evolution rate of P. puparum Dicer-2 with respect to Dicer-1, which was contrary to other hymenopterans.  Expression analyses revealed high mRNA levels for all miRNA pathway genes in P. puparum adults and the siRNA related genes were expressed in different patterns.  The findings add valuable new knowledge of the miRNA and siRNA pathways and their regulatory actions in parasitoid wasps.
Keywords:  miRNA pathway       siRNA pathway        annotation        Pteromalus puparum  
Received: 11 August 2020   Accepted: 10 October 2020
Fund: The study was funded by the Key Program of National Natural Science Foundation of China (31830074), the Program for Chinese Outstanding Talents in Agricultural Scientific Research of the Ministry of Agriculture and Rural Affairs of China, the Program for Chinese Innovation Team in Key Areas of Science and Technology (2016RA4008).
About author:  XIAO Shan, E-mail:; Correspondence YE Gong-yin, Tel: +86-571-88982696, E-mail:

Cite this article: 

XIAO Shan, FANG Qi, LIU Ming-ming, ZHANG Jiao, WANG Bei-bei, YAN Zhi-chao, WANG Fang, David W. STANLEY, YE Gong-yin. 2022. Genome-wide characterization of miRNA and siRNA pathways in the parasitoid wasp Pteromalus puparum. Journal of Integrative Agriculture, 21(4): 1106-1115.

Baum J A, Bogaert T, Clinton W, Heck G R, Feldmann P, Ilagan O, Johnson S, Plaetinck G, Munyikwa T, Pleau M, Vaughn T, Roberts J. 2007. Control of coleopteran insect pests through RNA interference. Nature Biotechnology, 25, 1322–1326.
Belles X. 2017. MicroRNAs and the evolution of insect metamorphosis. Annual Review of Entomology, 62, 111–125.
Bernhardt S A, Simmons M P, Olson K E, Beaty B J, Blair C D, Black W C. 2012. Rapid intraspecific evolution of miRNA and siRNA genes in the mosquito Aedes aegypti. PLoS ONE, 7, e44198.
Bernstein E, Caudy A A, Hammond S M, Hannon G J. 2001. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature, 409, 363–366.
Bustin S A, Benes V, Garson J A, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl M W, Shipley G L, Vandesompele J, Wittwer C T. 2009. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clinical Chemistry, 55, 611–622.
Cai J, Ye G Y, Hu C. 2004. Parasitism of Pieris rapae (Lepidoptera: Pieridae) by a pupal endoparasitoid, Pteromalus puparum (Hymenoptera: Pteromalidae): Effects of parasitization and venom on host hemocytes. Journal of Insect Physiology, 50, 315–322.
Capella-Gutierrez S, Silla-Martinez J M, Gabaldon T. 2009. trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics, 25, 1972–1973.
Carthew R W, Sontheimer E J. 2009. Origins and mechanisms of miRNAs and siRNAs. Cell, 136, 642–655.
Costa D F, Torchilin V P. 2018. Micelle-like nanoparticles as siRNA and miRNA carriers for cancer therapy. Biomedical Microdevices, 20, 59.
Davuluri G R, van Tuinen A, Fraser P D, Manfredonia A, Newman R, Burgess D, Brummell D A, King S R, Palys J, Uhlig J, Bramley P M, Pennings H M, Bowler C. 2005. Fruit-specific RNAi-mediated suppression of DET1 enhances carotenoid and flavonoid content in tomatoes. Nature Biotechnology, 23, 890–895.
Denli A M, Tops B B, Plasterk R H, Ketting R F, Hannon G J. 2004. Processing of primary microRNAs by the microprocessor complex. Nature, 432, 231–235.
Dowling D, Pauli T, Donath A, Meusemann K, Podsiadlowski L, Petersen M, Peters R S, Mayer C, Liu S, Zhou X, Misof B, Niehuis O. 2016. Phylogenetic origin and diversification of RNAi pathway genes in insects. Genome Biology and Evolution, 8, 3784–3793.
Forstemann K, Horwich M D, Wee L, Tomari Y, Zamore P D. 2007. Drosophila microRNAs are sorted into functionally distinct argonaute complexes after production by Dicer-1. Cell, 130, 287–297.
Ghildiyal M, Seitz H, Horwich M D, Li C, Du T, Lee S, Xu J, Kittler E L, Zapp M L, Weng Z, Zamore P D. 2008. Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells. Science, 320, 1077–1081.
Guo W C, Fu K Y, Yang S, Li X X, Li G Q. 2015. Instar-dependent systemic RNA interference response in Leptinotarsa decemlineata larvae. Pesticide Biochemistry and Physiology, 123, 64–73.
Hussain M, Asgari S. 2014. MicroRNAs as mediators of insect host-pathogen interactions and immunity. Journal of Insect Physiology, 70, 151–158.
Iovino N, Pane A, Gaul U. 2009. miR-184 has multiple roles in Drosophila female germline development. Developmental Cell, 17, 123–133.
Jaubert-Possamai S, Rispe C, Tanguy S, Gordon K, Walsh T, Edwards O, Tagu D. 2010. Expansion of the miRNA pathway in the hemipteran insect Acyrthosiphon pisum. Molecular Biology and Evolution, 27, 979–987.
Jiang F, Ye X, Liu X, Fincher L, McKearin D, Liu Q. 2005. Dicer-1 and R3D1-L catalyze microRNA maturation in Drosophila. Genes & Development, 19, 1674–1679.
Jones P, Binns D, Chang H Y, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn A F, Sangrador-Vegas A, Scheremetjew M, Yong S Y, Lopez R, Hunter S. 2014. InterProScan 5: Genome-scale protein function classification. Bioinformatics, 30, 1236–1240.
Kalyaanamoorthy S, Minh B Q, Wong T K F, von Haeseler A, Jermiin L S. 2017. ModelFinder: Fast model selection for accurate phylogenetic estimates. Nature Methods, 14, 587–589.
Katoh K, Standley D M. 2013. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Molecular Biology and Evolution, 30, 772–780.
Ketting R F, Fischer S E, Bernstein E, Sijen T, Hannon G J, Plasterk R H. 2001. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes & Development, 15, 2654–2659.
Kiriakidou M, Tan G S, Lamprinaki S, De Planell-Saguer M, Nelson P T, Mourelatos Z. 2007. An mRNA m7G cap binding-like motif within human Ago2 represses translation. Cell, 129, 1141–1151.
Krogh A, Larsson B, von Heijne G, Sonnhammer E L. 2001. Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. Journal of Molecular Biology, 305, 567–580.
Lee R C, Feinbaum R L, Ambros V. 1993. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 75, 843–854.
Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, Lee J, Provost P, Radmark O, Kim S, Kim V N. 2003. The nuclear RNase III Drosha initiates microRNA processing. Nature, 425, 415–419.
Lee Y, Kim M, Han J, Yeom K H, Lee S, Baek S H, Kim V N. 2004. MicroRNA genes are transcribed by RNA polymerase II. 
EMBO Journal, 23, 4051–4060.
Leggewie M, Schnettler E. 2018. RNAi-mediated antiviral immunity in insects and their possible application. Current Opinion in Virology, 32, 108–114.
Letunic I, Bork P. 2018. 20 years of the SMART protein domain annotation resource. Nucleic Acids Research, 46, D493–D496.
Ling L, Kokoza V A, Zhang C, Aksoy E, Raikhel A S. 2017. MicroRNA-277 targets insulin-like peptides 7 and 8 to control lipid metabolism and reproduction in Aedes aegypti mosquitoes. Proceedings of the National Academy of Sciences of the United States of America, 114, E8017–E8024.
Liu Q, Rand T A, Kalidas S, Du F, Kim H E, Smith D P, Wang X. 2003. R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway. Science, 301, 1921–1925.
Liu W, Xie Y, Ma J, Luo X, Nie P, Zuo Z, Lahrmann U, Zhao Q, Zheng Y, Zhao Y, Xue Y, Ren J. 2015. IBS: An illustrator for the presentation and visualization of biological sequences. Bioinformatics, 31, 3359–3361.
Livak K J, Schmittgen T D. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2–∆∆CT method. Methods, 25, 402–408.
Lucas K, Raikhel A S. 2013. Insect MicroRNAs: Biogenesis, expression profiling and biological functions. Insect Biochemistry and Molecular Biology, 43, 24–38.
Ma X, Zuo Z, Shao W, Jin Y, Meng Y. 2018. The expanding roles of Argonautes: RNA interference, splicing and beyond. Briefings in Functional Genomics, 17, 191–197.
Marques J T, Kim K, Wu P H, Alleyne T M, Jafari N, Carthew R W. 2010. Loqs and R2D2 act sequentially in the siRNA pathway in Drosophila. Nature Structural & Molecular Biology, 17, 24–30.
Matranga C, Tomari Y, Shin C, Bartel D P, Zamore P D. 2005. Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes. Cell, 123, 607–620.
Mendell J T. 2008. miRiad roles for the miR-17-92 cluster in development and disease. Cell, 133, 217–222.
Mongelli V, Saleh M C. 2016. Bugs are not to be silenced: Small RNA pathways and antiviral responses in insects. Annual Review of Virology, 3, 573–589.
Nguyen L T, Schmidt H A, von Haeseler A, Minh B Q. 2015. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution, 32, 268–274.
Obbard D J, Jiggins F M, Halligan D L, Little T J. 2006. Natural selection drives extremely rapid evolution in antiviral RNAi genes. Current Biology, 16, 580–585.
Okamura K, Chung W J, Ruby J G, Guo H, Bartel D P, Lai E C. 2008. The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs. Nature, 453, 803–806.
Ortiz-Rivas B, Jaubert-Possamai S, Tanguy S, Gauthier J P, Tagu D, Claude R. 2012. Evolutionary study of duplications of the miRNA machinery in aphids associated with striking rate acceleration and changes in expression profiles. BMC Evolutionary Biology, 12, 216.
Piatek M J, Werner A. 2014. Endogenous siRNAs: Regulators of internal affairs. Biochemical Society Transactions, 42, 1174–1179.
Rehwinkel J, Behm-Ansmant I, Gatfield D, Izaurralde E. 2005. A crucial role for GW182 and the DCP1:DCP2 decapping complex in miRNA-mediated gene silencing. RNA, 11, 1640–1647.
Solovyev V, Kosarev P, Seledsov I, Vorobyev D. 2006. Automatic annotation of eukaryotic genes, pseudogenes and promoters. Genome Biology, 7, 1–12.
Suyama M, Torrents D, Bork P. 2006. PAL2NAL: Robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Research, 34, W609–W612.
Tang Q Y, Zhang C X. 2013. Data Processing System (DPS) software with experimental design, statistical analysis and data mining developed for use in entomological research. Insect Science, 20, 254–260.
Tian L, Zeng Y, Xie W, Wu Q, Wang S, Zhou X, Zhang Y. 2019. Genome-wide identification and analysis of genes associated with RNA interference in Bemisia tabaci. Pest Management Science, 75, 3005–3014.
Tomoyasu Y, Miller S C, Tomita S, Schoppmeier M, Grossmann D, Bucher G. 2008. Exploring systemic RNA interference in insects: A genome-wide survey for RNAi genes in Tribolium. Genome Biology, 9, R10.
Wang L, Fang Q, Qian C, Wang F, Yu X Q, Ye G. 2013. Inhibition of host cell encapsulation through inhibiting immune gene expression by the parasitic wasp venom calreticulin. Insect Biochemistry and Molecular Biology, 43, 936–946.
Werren J H, Loehlin D W. 2009. The parasitoid wasp Nasonia: an emerging model system with haploid male genetics. Cold Spring Harbor Protocols, doi: 10.1101/pdb.emo134.
Yang Z. 2007. PAML 4: Phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution, 24, 1586–1591.
Yi R, Qin Y, Macara I G, Cullen B R. 2003. Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes & Development, 17, 3011–3016.
Zhang Y, Zhao B, Roy S, Saha T T, Kokoza V A, Li M, Raikhel A S. 2016. microRNA-309 targets the Homeobox gene SIX4 and controls ovarian development in the mosquito Aedes aegypti. Proceedings of the National Academy of Sciences of the United States of America, 113, E4828–E4836.
Zhu K Y, Palli S R. 2020. Mechanisms, applications, and challenges of insect RNA interference. Annual Review of Entomology, 65, 293–311.
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