中国农业科学 ›› 2019, Vol. 52 ›› Issue (1): 166-180.doi: 10.3864/j.issn.0578-1752.2019.01.015
郭睿(),杜宇(
),童新宇,熊翠玲,郑燕珍,徐国钧,王海朋,耿四海,周丁丁,郭意龙,吴素珍,陈大福(
)
收稿日期:
2018-08-02
接受日期:
2018-10-01
出版日期:
2019-01-01
发布日期:
2019-01-12
通讯作者:
陈大福
基金资助:
GUO Rui(),DU Yu(
),TONG XinYu,XIONG CuiLing,ZHENG YanZhen,XU GuoJun,WANG HaiPeng,GENG SiHai,ZHOU DingDing,GUO YiLong,WU SuZhen,CHEN DaFu(
)
Received:
2018-08-02
Accepted:
2018-10-01
Online:
2019-01-01
Published:
2019-01-12
Contact:
DaFu CHEN
摘要:
【目的】 微小RNA(microRNA,miRNA)是一类重要的基因表达调控因子,可影响宿主与病原间的互作过程。蜜蜂球囊菌(Ascosphaera apis)是一种特异性侵染蜜蜂幼虫的致死性真菌病原。本研究旨在对意大利蜜蜂(Apis mellifera ligustica,简称意蜂)幼虫肠道在球囊菌胁迫前期的差异表达miRNA(differentially expressed miRNA,DEmiRNA)及其靶基因进行深入分析,在miRNA组学水平探究意蜂幼虫在球囊菌侵染前期的胁迫应答,并通过构建显著DEmiRNA的调控网络筛选出与宿主应答相关的关键miRNA。【方法】 利用small RNA-seq(sRNA-seq)技术对正常及球囊菌侵染的意蜂4日龄幼虫肠道(AmCK和AmT)进行高通量测序,首先对原始数据进行质控和评估,随后将过滤后的数据与西方蜜蜂(Apis mellifera)参考基因组进行比对;将比对上的序列标签(tags)注释到miRBase数据库,得出已知miRNA的表达量;通过TPM(tags per million)算法对各样本中miRNA的表达量进行归一化处理,以|log2 fold change|≥1且P≤0.05作为标准筛选得到显著DEmiRNA;利用TargetFinder 软件预测显著DEmiRNA的靶基因,并对其进行GO和KEGG代谢通路(pathway)富集分析。利用Cytoscape软件对miRNA-mRNA调控网络进行可视化。最后,利用茎环反转录PCR(Stem-loop RT-PCR)和荧光定量PCR(qPCR)验证测序数据的可靠性。【结果】 AmCK和AmT样品的测序分别得到13 553 302和10 777 534条原始读段(raw reads),经严格过滤后得到的有效读段(clean reads)数分别为13 186 921和10 480 913条。各样品的生物学重复间的Pearson相关性系数分别在0.9822和0.9508以上。共有10个显著DEmiRNA,包括4个上调miRNA和6个下调miRNA。显著DEmiRNA在AmT的整体表达水平低于AmCK。10个显著DEmiRNA可靶向结合3 788个靶基因,其中上调miRNA的1 240个靶基因可注释到GO数据库中的39个GO条目,主要富集在结合、细胞进程、代谢进程和应激反应等;下调miRNA的749个靶基因可注释到34个GO条目,主要富集在细胞进程、结合、代谢进程和应激反应等。KEGG数据库注释结果显示,上调miRNA和下调miRNA的靶基因分别注释到95和66条代谢通路,富集基因数最多的分别是Wnt信号通路、Hippo信号通路、光传导以及内吞作用、磷脂酰肌醇信号系统、嘌呤代谢。对于上调和下调miRNA,分别有31和52个靶基因注释到内吞作用,15和7个靶基因注释到泛素介导的蛋白水解,11和5个靶基因注释到Jak-STAT信号通路,1和3个靶基因注释到MAPK信号通路。显著DEmiRNA与靶mRNA之间形成复杂的调控网络,7个显著DEmiRNA靶向结合96个与Wnt信号通路相关的mRNA,8个显著DEmiRNA靶向结合55个与内吞作用相关的mRNA。Stem-loop RT-PCR和qPCR结果验证了测序数据的可靠性。【结论】 对意蜂幼虫肠道在球囊菌侵染前期的DEmiRNA及其靶基因进行预测和分析,并构建和分析了DEmiRNA-mRNA调控网络,研究结果提供了宿主miRNA的表达谱和差异表达信息,揭示了DEmiRNA通过调控细胞生命活动、新陈代谢以及部分细胞和体液免疫等生物学过程参与宿主的胁迫应答。miR-4331-y、miR-4968-y、miR-8440-y、novel-m0023-5p和novel-m0025-3p共同参与了宿主的Wnt信号通路和内吞作用的调控,可作为白垩病治疗的潜在分子靶标。
郭睿,杜宇,童新宇,熊翠玲,郑燕珍,徐国钧,王海朋,耿四海,周丁丁,郭意龙,吴素珍,陈大福. 意大利蜜蜂幼虫肠道在球囊菌侵染前期的 差异表达microRNA及其调控网络[J]. 中国农业科学, 2019, 52(1): 166-180.
GUO Rui,DU Yu,TONG XinYu,XIONG CuiLing,ZHENG YanZhen,XU GuoJun,WANG HaiPeng,GENG SiHai,ZHOU DingDing,GUO YiLong,WU SuZhen,CHEN DaFu. Differentially Expressed MicroRNAs and Their Regulation Networks in Apis mellifera ligustica Larval Gut During the Early Stage of Ascosphaera apis Infection[J]. Scientia Agricultura Sinica, 2019, 52(1): 166-180.
表1
本研究使用的引物"
引物名称 Primer name | 引物序列 Primer sequence |
---|---|
LOOP-miR-3793-x | CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGTGGCCAGG |
LOOP-ame-miR-6000a-5p | CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGATAGAGAC |
LOOP-novel-m0031-3p | CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGTCCTGCTT |
LOOP-novel-m0034-5p | CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGATATCACA |
F-miR-3793-x | ACACTCCAGCTGGGAGCGTGTTTTC |
F-ame-miR-6000a-5p | ACACTCCAGCTGGGCAGCAGCAGCAG |
F-novel-m0031-3p | GCATCCTCTTGAAT |
F-novel-m0034-5p | CAGGTAACTACTGC |
R | CTCAACTGGTGTCGTGGA |
U6-F | GTTAGGCTTTGACGATTTCG |
U6-R | GGCATTTCTCCACCAGGTA |
表3
AmCK vs AmT 中DEmiRNA的信息统计"
差异表达miRNA ID DEmiRNA ID | AmCK中的表达量 Expression in AmCK | AmT中的表达量 Expression in AmT | 以2为底miRNA的相对变化倍数的对数值 log2 fold change | 靶基因数 Number of target genes |
---|---|---|---|---|
miR-7085-x | 0.01 | 8.40 | 9.71 | 129 |
miR-8440-y | 0.01 | 5.29 | 9.05 | 2265 |
novel-m0023-5p | 0.01 | 1.79 | 7.48 | 334 |
miR-3793-x | 33.72 | 89.76 | 1.41 | 398 |
novel-m0034-3p | 4.06 | 1.95 | -1.05 | 768 |
miR-4331-y | 74.07 | 27.70 | -1.42 | 77 |
ame-miR-6000a-5p | 19.06 | 4.14 | -2.20 | 77 |
miR-971-y | 3.25 | 0.31 | -3.37 | 100 |
novel-m0025-3p | 0.88 | 0.01 | -6.46 | 294 |
miR-4968-y | 11.61 | 0.01 | -10.18 | 279 |
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