中国农业科学 ›› 2020, Vol. 53 ›› Issue (15): 3187-3204.doi: 10.3864/j.issn.0578-1752.2020.15.018
• 畜牧·兽医·资源昆虫 • 上一篇
耿四海(),石彩云(
),范小雪,王杰,祝智威,蒋海宾,范元婵,陈华枝,杜宇,王心蕊,熊翠玲,郑燕珍,付中民,陈大福,郭睿(
)
收稿日期:
2019-12-02
接受日期:
2019-12-28
出版日期:
2020-08-01
发布日期:
2020-08-06
通讯作者:
郭睿
作者简介:
耿四海,E-mail: 基金资助:
GENG SiHai(),SHI CaiYun(
),FAN XiaoXue,WANG Jie,ZHU ZhiWei,JIANG HaiBin,FAN YuanChan,CHEN HuaZhi,DU Yu,WANG XinRui,XIONG CuiLing,ZHENG YanZhen,FU ZhongMin,CHEN DaFu,GUO Rui(
)
Received:
2019-12-02
Accepted:
2019-12-28
Online:
2020-08-01
Published:
2020-08-06
Contact:
Rui GUO
摘要:
【目的】通过对东方蜜蜂微孢子虫(Nosema ceranae)纯化孢子与侵染意大利蜜蜂(Apis mellifera ligustica,简称意蜂)工蜂的东方蜜蜂微孢子虫的差异表达miRNA(DEmiRNA)及其靶mRNA进行系统分析,筛选、分析和探讨病原毒力因子和侵染因子相关的DEmiRNA及调控网络,在miRNA组学层面揭示东方蜜蜂微孢子虫对意蜂的侵染机制。【方法】利用small RNA-seq(sRNA-seq)技术对东方蜜蜂微孢子虫感染7 d和10 d的意蜂工蜂中肠和东方蜜蜂微孢子虫纯化孢子(NcCK)进行深度测序,通过连续比对rRNA数据库、西方蜜蜂(Apis mellifera)基因组和东方蜜蜂微孢子虫基因组筛滤出处于侵染过程的东方蜜蜂微孢子虫(NcT1和NcT2)数据和东方蜜蜂微孢子虫孢子的测序数据。根据P≤0.05,|log2 fold change|≥1的标准,通过比较分析筛选出各比较组中的差异表达miRNA(differentially expressed miRNA,DEmiRNA)。通过相关生物信息学软件对DEmiRNA进行表达谱分析,靶mRNA预测及功能和代谢通路注释,以及调控网络的构建与分析。通过Stem-loop RT-qPCR验证DEmiRNA的差异表达趋势及测序数据的可靠性。【结果】NcCK vs NcT1、NcCK vs NcT2和NcT1 vs NcT2比较组分别包含164、122和60个DEmiRNA。Venn分析结果显示,3个比较组共有的上调和下调miRNA分别为5和6个。上述DEmiRNA分别预测出1 885、1 733和1 524个靶mRNA。这些靶mRNA分别注释到27、25和26个功能条目,其中注释数量最多的是新陈代谢进程、催化活性、细胞进程、结合和细胞。上述靶mRNA可分别注释到84、84和84条代谢通路,其中注释数量最多的是代谢途径、核糖体和次级代谢产物生物合成。此外,对于NcCK vs NcT1、NcCK vs NcT2和NcT1 vs NcT2中的DEmiRNA,分别有35、26和12个靶向结合MAPK信号通路相关靶mRNA,分别有49、40和17个DEmiRNA靶向结合糖酵解/糖异生通路相关靶mRNA。进一步分析发现,东方蜜蜂微孢子虫的DEmiRNA参与调控蓖麻毒素B凝集素、细胞凋亡抑制因子、极管蛋白和孢壁蛋白等病原毒力因子的基因表达,以及己糖激酶、ATP/ADP移位酶、ABC转运蛋白和转录因子ste12等侵染因子的基因表达。【结论】通过对东方蜜蜂微孢子虫纯化孢子与侵染意蜂工蜂的东方蜜蜂微孢子虫进行深入细致的miRNA组学分析和探讨,解析了病原侵染过程的miRNA差异表达谱,揭示了东方蜜蜂微孢子虫可能通过调节相应miRNA的表达水平对蓖麻毒素B凝集素、细胞凋亡抑制因子、极管蛋白和孢壁蛋白等毒力因子及己糖激酶、ATP/ADP移位酶、ABC转运蛋白和转录因子ste12等侵染因子基因表达进行调控,从而适应宿主细胞内的环境并促进自身的增殖与侵染。
耿四海,石彩云,范小雪,王杰,祝智威,蒋海宾,范元婵,陈华枝,杜宇,王心蕊,熊翠玲,郑燕珍,付中民,陈大福,郭睿. 微小RNA介导东方蜜蜂微孢子虫侵染意大利蜜蜂工蜂的分子机制[J]. 中国农业科学, 2020, 53(15): 3187-3204.
GENG SiHai,SHI CaiYun,FAN XiaoXue,WANG Jie,ZHU ZhiWei,JIANG HaiBin,FAN YuanChan,CHEN HuaZhi,DU Yu,WANG XinRui,XIONG CuiLing,ZHENG YanZhen,FU ZhongMin,CHEN DaFu,GUO Rui. The Mechanism Underlying MicroRNAs-Mediated Nosema ceranae Infection to Apis mellifera ligustica Worker[J]. Scientia Agricultura Sinica, 2020, 53(15): 3187-3204.
表1
本研究使用的引物"
引物ID Primer ID | 引物序列 Primer sequence |
---|---|
miR-2478-y | Loop: GTCGTATCCAGTGCGTGTCGTGGAGTCGGCAATTGCACTGGATACGACTGGTGTC F: GCGCGCGTCGAATCCCACT |
novel-m0017-5p | Loop: GTCGTATCCAGTGCGTGTCGTGGAGTCGGCAATTGCACTGGATACGACGGGCATA F: GCGCGCGTGGACCAGTGGC |
novel-m0010-5p | Loop: GTCGTATCCAGTGCGTGTCGTGGAGTCGGCAATTGCACTGGATACGACGCTCGCT F: GCGCGCGTTTAGTTTGGCT |
miR-3968-y | Loop: GTCGTATCCAGTGCGTGTCGTGGAGTCGGCAATTGCACTGGATACGACTGGTGTC F: GCGCGCGTCGAATCCCACT |
miR-146-x | Loop: GTCGTATCCAGTGCGTGTCGTGGAGTCGGCAATTGCACTGGATACGACAACCCAT R: GCGCGCGTGAGAACTGAAT |
miR-24-y | Loop: GTCGTATCCAGTGCGTGTCGTGGAGTCGGCAATTGCACTGGATACGACGTTCCTG F: GCGCGCGTGGCTCAGTTCA |
miR-2965-y | Loop: GTCGTATCCAGTGCGTGTCGTGGAGTCGGCAATTGCACTGGATACGACTGCTCTC F: GCGCCGGAGGACTGCT |
miR-318-y | Loop: GTCGTATCCAGTGCGTGTCGTGGAGTCGGCAATTGCACTGGATACGACGACCAAC F: CGGCCGCTCACTGGGC |
R: CAGTGCGTGTCGTGGAGT | |
5S rRNA | F: CGAGCGGTTTCCCATCTCAGTA R: AAAACACCGGAACTCGTCAGCT |
表2
sRNA-seq 数据总览"
样品Sample | 原始读段Raw reads | 有效标签Clean tags | 映射读段Mapped reads | 映射率Mapping ratio (%) |
---|---|---|---|---|
NcCK1 | 16506662 | 13466818 | 7560765 | 56.14 |
NcCK2 | 15368310 | 11938692 | 7655068 | 64.12 |
NcCK3 | 12180663 | 10160918 | 6349388 | 62.49 |
NcT1-1 | 13345686 | 6950844 | 1865571 | 26.84 |
NcT1-2 | 12837034 | 7324633 | 2510215 | 34.27 |
NcT1-3 | 13943680 | 7249967 | 1934012 | 26.68 |
NcT2-1 | 13820326 | 10605224 | 5503089 | 51.89 |
NcT2-2 | 14311818 | 9988951 | 4763103 | 47.68 |
NcT2-3 | 14013040 | 9722581 | 4513943 | 46.43 |
图3
各个比较组中DEmiRNA靶基因的GO数据库注释 A:NcCK vs NcT1靶向的mRNA Target mRNA in NcCK vs NcT1;B:NcCK vs NcT2靶向的mRNA Target mRNA in NcCK vs NcT2;C:NcT1 vs NcT2靶向的mRNA Target mRNA in NcT1 vs NcT2。1:代谢进程Metabolic process;2:细胞进程Cellular process;3:单一有机体进程Single-organism process;4:定位Localization;5:生物学调控Biological regulation;6:生物进程调控Regulation of biological process;7:细胞成分组织或生物合成Cellular component organization or biogenesis;8:应激反应Response to stimulus;9:信号Signaling;10:复制Reproduction;11:生长Growth;12:细胞Cell;13:细胞组分Cell part;14:细胞器Organelle;15:大分子复合物Macromolecular complex;16:细胞膜Membrane;17:细胞膜组分Membrane part;18:细胞器组分Organelle part;19:膜封闭腔Membrane-enclosed lumen;20:病毒Virion;21:病毒组分Virion part;22:催化活性Catalytic activity;23:结合Binding;24:运输活性Transporter activity;25:分子结构活性Structural molecule activity;26:核苷酸结合转录因子活性Nucleic acid binding transcription factor activity;27:分子功能调节Molecular function regulator"
表3
各比较组中DEmiRNA的靶mRNA富集的前15条通路"
通路 Pathway | NcCK vs NcT1比较组 NcCK vs NcT1 group | NcCK vs NcT2比较组 NcCK vs NcT2 group | NcT1 vs NcT2比较组 NcT1 vs NcT2 group |
---|---|---|---|
新陈代谢途径 Metabolic pathways | 119 | 113 | 103 |
核糖体 Ribosome | 56 | 50 | 41 |
次生代谢产物合成 Biosynthesis of secondary metabolites | 48 | 47 | 42 |
真菌生物核糖体的生物合成 Ribosome biogenesis in eukaryotes | 37 | 38 | 29 |
抗生素的生物合成 Biosynthesis of antibiotics | 36 | 35 | 31 |
内质网蛋白质加工 Protein processing in endoplasmic reticulum | 35 | 32 | 29 |
嘌呤代谢 Purine metabolism | 33 | 28 | 26 |
嘧啶代谢 Pyrimidine metabolism | 32 | 28 | 25 |
细胞周期 Cell cycle | 31 | 30 | 28 |
RNA转运 RNA transport | 30 | 26 | 24 |
蛋白酶体 Proteasome | 28 | 25 | 24 |
减数分裂 Meiosis | 26 | 24 | 24 |
mRNA监督通路 mRNA surveillance pathway | 24 | 21 | 22 |
DNA复制 DNA replication | 24 | 24 | 22 |
泛素蛋白水解 Ubiquitin mediated proteolysis | 24 | 24 | 20 |
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