中华蜜蜂幼虫肠道中微小RNA的鉴定及分析

doi:10.3864/j.issn.0578-1752.2022.01.017

中国农业科学 ›› 2022, Vol. 55 ›› Issue (1): 208-218.doi: 10.3864/j.issn.0578-1752.2022.01.017

• 畜牧·兽医·资源昆虫 • 上一篇下一篇

中华蜜蜂幼虫肠道中微小RNA的鉴定及分析

冯睿蓉¹(),付中民^1,²(),杜宇¹,张文德¹,范小雪¹,王海朋¹,万洁琦¹,周紫彧¹,康育欣¹,陈大福^1,²,郭睿^1,²(),史培颖¹()

¹福建农林大学动物科学学院（蜂学学院）,福州 350002
²福建农林大学蜂疗研究所,福州 350002

收稿日期:2021-04-28 接受日期:2021-06-07 出版日期:2022-01-01 发布日期:2022-01-07
通讯作者: 郭睿,史培颖
作者简介:冯睿蓉,E-mail： frr18705911634@163.com。|付中民,E-mail： 369699776@qq.com。
基金资助:
国家现代农业产业技术体系建设专项(CARS-44-KXJ7);福建农林大学杰出青年科研人才计划(xjq201814);福建农林大学硕士生导师团队项目(郭睿);福建省大学生创新创业训练计划(202010389012);福建省大学生创新创业训练计划(202010389016)

Identification and Analysis of MicroRNAs in the Larval Gut of Apis cerana cerana

FENG RuiRong¹(),FU ZhongMin^1,²(),DU Yu¹,ZHANG WenDe¹,FAN XiaoXue¹,WANG HaiPeng¹,WAN JieQi¹,ZHOU ZiYu¹,KANG YuXin¹,CHEN DaFu^1,²,GUO Rui^1,²(),SHI PeiYing¹()

¹College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002
²Apitherapy Research Institute, Fujian Agriculture and Forestry University, Fuzhou 350002

Received:2021-04-28 Accepted:2021-06-07 Online:2022-01-01 Published:2022-01-07
Contact: Rui GUO,PeiYing SHI

摘要/Abstract

摘要：

【目的】利用small RNA-seq（sRNA-seq）技术和生物信息学方法对中华蜜蜂（Apis cerana cerana,简称中蜂）幼虫肠道的微小RNA（microRNA,miRNA）进行全转录组鉴定和分析,旨在丰富中蜂的miRNA信息,并为深入研究miRNA调控中蜂幼虫肠道发育的分子机理提供依据。【方法】利用sRNA-seq技术对中蜂4、5和6日龄幼虫肠道样品（Ac1、Ac2和Ac3）进行测序,通过数据质控获得有效标签序列（clean tags）。采用Blast工具将clean tags连续比对东方蜜蜂（Apis cerana）基因组和miRBase数据库,以鉴定保守miRNA和新miRNA。采用TPM法对miRNA的表达量进行归一化处理。通过GraphPad Prism 7软件统计各组肠道样品中sRNA占比、miRNA长度分布及首位碱基偏向性。利用相关软件预测上述miRNA靶向的mRNA并进行GO和KEGG数据库注释。进一步根据靶向结合关系构建和分析注释到发育和免疫相关通路的基因及其靶向miRNA的调控网络,并利用Cytoscape软件进行可视化。利用茎环反转录PCR（Stem-loop RT-PCR）、分子克隆和Sanger测序验证miRNA的表达和序列的真实性。【结果】共鉴定到中蜂的371个保守miRNA和64个新miRNA;这些miRNA的长度介于18—25 nt且首位碱基主要偏向于U;上述miRNA共靶向14 750条mRNA,涉及离子结合、金属离子结合、细胞膜、细胞膜组件和单一有机体进程等2 270个GO条目,以及内吞作用、细胞凋亡、mTOR信号通路、RNA转运和昆虫激素的生物合成等332条KEGG通路。进一步分析结果显示156个miRNA与注释到Wnt、Hippo、Notch和mTOR等生长发育相关通路的67个靶基因存在调控关系,145个miRNA与注释到Toll、Imd/JNK、Jak-STAT和抗菌效应因子等免疫相关途径的21个靶基因存在调控关系。Stem-loop RT-PCR 结果显示miR-8-y、miR-9-z、miR-14-y、miR-281-y、miR-283-x和miR-306-x均能扩增出预期的特异性片段;Sanger测序结果显示上述6个miRNA的序列与深度测序结果一致。【结论】提供了中蜂miRNA的数量、结构特征和表达谱;揭示中蜂幼虫肠道miRNA潜在调控诸多生命进程与细胞活动;中蜂幼虫肠道的部分miRNA可通过靶向结合相应的mRNA参与调节发育和免疫相关途径。

关键词: 东方蜜蜂, 中华蜜蜂, 幼虫, 肠道, 微小RNA, 调控网络

Abstract:

【Objective】 In this study, transcriptome-wide identification and analysis of miRNAs in the larval guts of Apis cerana cerana was conducted using a combination of small RNA-seq (sRNA-seq) technology and bioinformatic method, aiming to enrich the information of A. c. cerana miRNAs and offer a basis for further investigation of miRNA-regulated molecular mechanism underlying A. c. cerana larval gut development.【Method】 Gut samples of A. c. cerana 4-, 5-, and 6-day-old larvae (Ac1, Ac2, and Ac3 ) were sequenced using sRNA-seq technology, and clean tags were obtained after quality control. By using Blast tool, clean tags were continuously mapped to Apis cerana genome and miRBase database to identify known miRNAs and novel miRNAs. TPM method was used to perform normalization of miRNAs’ expression. The ratio of sRNAs, length distribution of miRNAs and first base bias were calculated with GraphPad Prism 7 software. Using related software, target mRNAs of above-mentioned miRNAs were predicted followed by GO and KEGG database annotation. Further, regulatory networks between genes associated with development and immune-related pathways and corresponding target miRNAs were constructed and analyzed, followed by visualization of regulatory networks with Cytoscape software. The authenticity of miRNA expression and sequence was verified by using Stem-loop RT-PCR, molecular cloning and Sanger sequencing.【Result】 In total, 371 known miRNAs and 64 novel ones of A. c. cerana were identified; their length was distributed among 18-25 nt, and the first base had an U bias. The aforementioned miRNAs could target 14 750 mRNAs, involving 2 270 GO terms such as ion binding, metal ion binding, membrane, membrane part and single-organism process, as well as 332 KEGG pathways including endocytosis, apoptosis, mTOR signaling pathway, RNA transport and insect hormone biosynthesis. Further investigation suggested that 156 miRNAs could target 67 genes relative to development-associated pathways such as Wnt, Hippo, Notch and mTOR signaling pathways, while 145 miRNAs could target 21 genes relevant to immune-associated pathways such as Toll, Imd/JNK, Jak-STAT signaling pathways and antimicrobial effectors. Stem-loop RT-PCR result indicated that specific fragments with expected sizes could be amplified from miR-8-y, miR-9-z, miR-14-y, miR-281-y, miR-283-x and miR-306-x; Sanger sequencing result demonstrated that sequences of above-mentioned six miRNAs were in accordance with those in deep sequencing result.【Conclusion】 Our findings provide number, structural characteristics and expression profile of A. c. cerana miRNAs, and unraveled that miRNAs in A. c. cerana larval gut potentially regulate a lot of life processes and cellular activities, part of miRNAs can participate in regulation of development-related and immune-related pathways by targeting corresponding mRNAs.

Key words: Apis cerana, Apis cerana cerana, larva, gut, microRNA, regulatory network

冯睿蓉,付中民,杜宇,张文德,范小雪,王海朋,万洁琦,周紫彧,康育欣,陈大福,郭睿,史培颖. 中华蜜蜂幼虫肠道中微小RNA的鉴定及分析[J]. 中国农业科学, 2022, 55(1): 208-218.

FENG RuiRong,FU ZhongMin,DU Yu,ZHANG WenDe,FAN XiaoXue,WANG HaiPeng,WAN JieQi,ZHOU ZiYu,KANG YuXin,CHEN DaFu,GUO Rui,SHI PeiYing. Identification and Analysis of MicroRNAs in the Larval Gut of Apis cerana cerana[J]. Scientia Agricultura Sinica, 2022, 55(1): 208-218.

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样品 Sample	高质量读段 High quality reads	有效序列标签 Clean tags	占比 Ratio (%)
Ac1-1	11231070	9761109	86.91
Ac1-2	11994516	10566352	88.09
Ac1-3	10594332	9048317	85.41
Ac2-1	13057999	10932504	83.72
Ac2-2	10718330	8834247	82.42
Ac2-3	10273562	8440841	82.16
Ac3-1	10611126	8828377	83.20
Ac3-2	9932874	8401872	84.59
Ac3-3	12822276	10953694	85.43

中华蜜蜂幼虫肠道中微小RNA的鉴定及分析

Identification and Analysis of MicroRNAs in the Larval Gut of Apis cerana cerana

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