DNA Methylation and Demethylation Are Regulated by Functional DNA Methyltransferases and DnTET Enzymes inDiuraphis noxia
DNA Methylation and Demethylation Are Regulated by Functional DNA Methyltransferases and DnTET Enzymes inDiuraphis noxia
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DOI：
10.3389/fgene.2020.00452
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发表时间：
2020-06-23
影响因子：
3.7
通讯作者：
Botha, Anna-Maria
中科院分区：
文献类型：
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作者：
du Preez, Pieter H.;Breeds, Kelly;Botha, Anna-Maria
蚜虫是全世界农作物的重要经济害虫。尽管存在抗性品种，但抗性不断受到挑战并最终被打破，对粮食安全构成威胁。在当前的研究中，研究了毒力不同的两种相关的俄罗斯小麦蚜虫（Diuraphis noxia，Kurdjumov）生物型（即SA1和SAM）的表观基因组，以阐明其在该物种毒力中的作用。全基因组亚硫酸氢盐测序分别覆盖了SA1的6,846,597,083个胞嘧啶碱基和SAM的7,397,965,699个胞嘧啶碱基，其中总共70,861,462个碱基（SA1）和74,073,939个碱基（SAM）被甲基化，代表1.126+/-其基因组中有 0.321% (SA1) 和 1.105 +/- 0.295% (SAM) 甲基化。对序列读数进行 DNA 甲基化背景分析，结果显示 RWA 在所有背景（CpG、CHG 和 CHH）中都存在甲基化，其中大部分甲基化在 CpG 背景内（+/- 5.19%），而其他背景显示出低得多的甲基化水平（CHG - +/- 0.27%；CHH - +/- 0.34%）。顶部链的甲基化程度比底部链稍高（0.02%）。在绘制的 35,493 个基因中，我们还分析了每个基因的甲基化背景，发现基因区域的 CpG 甲基化比基因间区域高得多。 CHG 和 CHH 水平在基因和基因间区域之间没有差异。基因的外显子区域比内含子区域甲基化程度更高（+/- 0.56%）。我们还测量了蚜虫生物型之间的 5mC 和 5hmC 水平，发现生物型之间的 5mC 水平几乎没有差异，但剧毒 SAM 中的 5hmC 水平要高得多。 RWA 的 DNA 甲基转移酶 1（DNMT1a 和 DNMT1b）和 DNMT3（DNMT3a 和 DNMT3b）各有两个同源物，但只有一个 DNMT2，只有 DNMT3 的表达在两种 RWA 生物型之间存在显着差异。 RWA 在基因组中具有 10-11 易位酶 (DnTET) 的单一直向同源物。喂养研究表明，毒性更强的 RWA 生物型 SAM 上调 DnDNMT3 和 DnTET 对表达抗生素和抗异种的小麦的反应。
Aphids are economically important insect pests of crops worldwide. Despite resistant varieties being available, resistance is continuously challenged and eventually broken down, posing a threat to food security. In the current study, the epigenome of two related Russian wheat aphid (Diuraphis noxia, Kurdjumov) biotypes (i.e., SA1 and SAM) that differ in virulence was investigated to elucidate its role in virulence in this species. Whole genome bisulfite sequencing covered a total of 6,846,597,083 cytosine bases for SA1 and 7,397,965,699 cytosine bases for SAM, respectively, of which a total of 70,861,462 bases (SA1) and 74, 073,939 bases (SAM) were methylated, representing 1.126 +/- 0.321% (SA1) and 1.105 +/- 0.295% (SAM) methylation in their genomes. The sequence reads were analyzed for contexts of DNA methylation and the results revealed that RWA has methylation in all contexts (CpG, CHG and CHH), with the majority of methylation within the CpG context (+/- 5.19%), while the other contexts show much lower levels of methylation (CHG - +/- 0.27%; CHH - +/- 0.34%). The top strand was slightly (0.02%) more methylated than the bottom strand. Of the 35,493 genes that mapped, we also analyzed the contexts of methylation of each of these and found that the CpG methylation was much higher in genic regions than in intergenic regions. The CHG and CHH levels did not differ between genic and intergenic regions. The exonic regions of genes were more methylated (+/- 0.56%) than the intronic regions. We also measured the 5mC and 5hmC levels between the aphid biotypes, and found little difference in 5mC levels between the biotypes, but much higher levels of 5hmC in the virulent SAM. RWA had two homologs of each of theDNA methyltransferases 1(DNMT1aandDNMT1b) andDNMT3s(DNMT3aandDNMT3b), but only a singleDNMT2, with only the expression ofDNMT3that differed significantly between the two RWA biotypes. RWA has a single ortholog of Ten eleven translocase (DnTET) in the genome. Feeding studies show that the more virulent RWA biotype SAM upregulateDnDNMT3andDnTETin response to wheat expressing antibiosis and antixenosis.