Characterizing the Epigenetic and Transcriptomic Responses to Perkinsus marinus Infection in the Eastern Oyster Crassostrea virginica
Characterizing the Epigenetic and Transcriptomic Responses to Perkinsus marinus Infection in the Eastern Oyster Crassostrea virginica
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DOI：
10.3389/fmars.2020.00598
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发表时间：
2020-08-11
影响因子：
3.7
通讯作者：
Kelly, Morgan W.
中科院分区：
文献类型：
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作者：
Johnson, Kevin M.;Sirovy, K. A.;Kelly, Morgan W.
墨西哥湾北部的东部牡蛎经常感染原生生物寄生虫 Perkinsus marinus，这种疾病通常被称为真皮病。最近在大西洋沿岸人群中进行的实验挑战已经使用比较转录组学鉴定了抗性和易感基因型。虽然受控实验挑战是必不可少的初步评估，但将这种分析扩展到野外饲养的个体提供了一个机会来识别实验室和野外出现的感染的关键基因组特征。在这项研究中，我们将简化代表性亚硫酸氢盐测序与 30 RNA 测序 (Tag-seq) 结合起来，描述与在常见花园田地种植的牡蛎感染相关的两种分子表型。这些组合方法使我们能够检查在普通花园外植实验过程中发生感染的大量个体 (n = 40) 的 DNA 甲基化和基因表达的变化。我们对 DNA 甲基化的表观遗传学分析发现，在与免疫反应相关的基因中，与感染强度增加相关的基因体甲基化发生了显着变化。随着感染强度的增加，转录组反应较小，有 32 个基因表现出差异表达；然而，这些基因中只有 40% 也被发现存在差异甲基化。虽然差异甲基化方向和基因表达之间没有明确的模式，但甲基化百分比对逐个基因的表达水平以及处理之间基因体甲基化的变异系数有显着影响。这些结果表明，在弗吉尼亚念珠菌中，重度甲基化的基因具有高水平的基因表达和低水平的变异。将我们的差异表达结果与之前发表的实验性 P. marinus 挑战进行比较，发现与包含 C1q 结构域和 V 型质子 ATP 酶蛋白相关的基因的重叠表达模式。通过我们使用田间饲养个体的比较转录组方法和共表达网络分析，我们还能够识别出因感染而改变表达的基因网络。这些综合分析为不同感染强度下对海马感染的保守反应提供了证据，并表明 DNA 甲基化可能不是长期感染中差异基因表达的可靠预测因子。
Eastern oysters in the northern Gulf of Mexico are routinely infected with the protistan parasite Perkinsus marinus, the cause of the disease commonly known as dermo. Recent experimental challenges among Atlantic coast populations have identified both resistant and susceptible genotypes using comparative transcriptomics. While controlled experimental challenges are essential first assessments, expanding this analysis to field reared individuals provides an opportunity to identify key genomic signatures of infection that appear both in the laboratory and in the field. In this study we combined reduced representation bisulfite sequencing with 30 RNA sequencing (Tag-seq) to describe two molecular phenotypes associated with infection in oysters outplanted at a common garden field site. These combined approaches allowed us to examine changes in DNA methylation and gene expression for a large number of individuals (n = 40) that developed infections during the course of a common garden outplant experiment. Our epigenetic analysis of DNA methylation identified significant changes in gene body methylation associated with increasing infection intensity, across genes associated with immune responses. There was a smaller transcriptomic response to increasing infection intensities with 32 genes showing differential expression; however, only 40% of these genes were found to also be differentially methylated. While there was no clear pattern between direction of differential methylation and gene expression, there was a significant effect of percent methylation on gene-by-gene expression levels and the coefficient of variation in gene body methylation between treatments. These results show that in C. virginica, heavily methylated genes have high levels of gene expression with low levels of variation. Comparing our differential expression results with previously published experimental P. marinus challenges identified overlapping expression patterns for genes associated with C1q-domain-containing and V-type proton ATPase proteins. Through our comparative transcriptomic approach using field reared individuals and co-expression network analysis we have also been able to identify a network of genes that change in expression in response to infection. These combined analyses provide evidence for a conserved response to P. marinus infections across infection intensities and suggest that DNA methylation may not be a reliable predictor of differential gene expression in long-term infections.