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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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摘要
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R2D2、Argonaute-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Dicer、Argonaute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.
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Received: 11 August 2020
Accepted: 10 October 2020
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| 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: xiaoshan9401@126.com; Correspondence YE Gong-yin, Tel: +86-571-88982696, E-mail: chu@zju.edu.cn |
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.
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