Parasite presence induces gene expression changes in an ant host related to immunity and longevity

Most species are either parasites or exploited by parasites, making parasite-host interactions a driver of evolution. Parasites with complex life cycles often evolve strategies to facilitate transmission to the definitive host by manipulating their intermediate host. Such manipulations could explain phenotypic changes in the ant Temnothorax nylanderi, the intermediate host of the cestode Anomotaenia brevis. In addition to behavioral and morphological alterations, infected workers exhibit increased survival, comparable to that of queens, which live up to two decades. We used transcriptomic data from cestodes and ants of different castes and infection status to investigate the molecular underpinnings of phenotypic alterations in infected workers, and whether the extended lifespan of queens and infected workers has a common molecular basis. To this end we sequenced the abdominal RNA of infected and uninfected ants of parasitized nests and queens and workers from unparasitized nests and assembled a transcriptome using StringTie. After filtering the transcriptome for those transcripts with an ORF greater or equal than 150 bp and filtering the gene count matrix for only those genes that had at least 5 counts in at least 3 samples, we first conducted a Principal Component Analysis. We tested each PC for its association with infection status and for the significant PCs we extracted the loadings of each gene (dataset S1). Moreover, we analyzed gene expression using DESeq2, comparing infected workers with their uninfected nestmates and on the other hand queens and their workers from unparasitized nests. The significant upregulated genes in each group can be found in the dataset S2. GO enrichment was performed using topGO on both the genes and their loadings on PC2 using a Kolomogorov-Smirnov test and the upregulated genes compared to the whole transcriptome using Fisher's exact tests (dataset S3). Afterward, we analyzed the overlap between genes upregulated in infected workers and in queens. Infected workers and queens commonly upregulated only six genes, one of them with a known anti-aging function. Our text-mining approach revealed that both groups overexpressed immune genes, although not the same ones. Our findings suggest that the lifespan extension of infected workers is not achieved via the expression of queen-specific genes. To be able to filter the abdominal RNA sequences of infected workers from cestode RNA, we additionally sequenced RNA of 320 cysticercoids and de novo assembled a transcriptome of A. brevis. The analysis of the cestodes’ transcriptome revealed dominant expression of genes of the mitochondrial respiratory transport chain indicating an active metabolism and shedding light on the physiology of the parasite in its cysticercoid stage (dataset S4).绝大多数物种均为寄生物，或被寄生物寄生，这使得寄生物-宿主相互作用成为演化的驱动力之一。拥有复杂生活史的寄生物往往演化出多种策略，通过操控中间宿主来实现向终宿主的传播。此类宿主操控现象可解释中间宿主——蚁类Temnothorax nylanderi的表型变化：该蚁是绦虫Anomotaenia brevis的中间宿主。除行为与形态改变外，受感染的工蚁存活率显著提升，可与寿命长达二十年之久的蚁后相媲美。本研究使用来自不同品级、不同感染状态的绦虫与蚂蚁的转录组（transcriptome）数据，探究受感染工蚁表型改变的分子基础，以及蚁后与受感染工蚁的寿命延长是否共享共同的分子机制。为此，我们对寄生蚁巢内受感染与未受感染的蚂蚁，以及未寄生蚁巢内的蚁后与工蚁的腹部RNA进行测序，并通过StringTie组装转录组。随后对转录组进行过滤，保留开放阅读框（Open Reading Frame, ORF）长度≥150 bp的转录本；同时对基因计数矩阵进行筛选，仅保留在至少3个样本中计数≥5的基因。首先开展主成分分析（Principal Component Analysis, PCA），检验各主成分与感染状态的相关性，针对显著相关的主成分提取各基因的载荷值（数据集S1）。此外，我们使用DESeq2分析基因表达水平：一方面比较受感染工蚁与其未受感染的同巢同伴，另一方面比较未寄生蚁巢内的蚁后与其工蚁。各组中显著上调的基因详见数据集S2。我们使用topGO分别针对PC2的基因载荷值，通过柯尔莫哥洛夫-斯米尔诺夫检验（Kolomogorov-Smirnov test）进行基因本体（GO）富集分析；同时针对上调基因集，以全转录组为背景通过费希尔精确检验（Fisher's exact tests）进行GO富集分析（数据集S3）。后续我们分析了受感染工蚁与蚁后上调基因的重叠区域。结果显示，受感染工蚁与蚁后仅共有6个上调基因，其中1个具备已知的抗衰老功能。文本挖掘分析表明，两组均存在免疫基因的过表达，但二者并非同一类免疫基因。本研究结果提示，受感染工蚁的寿命延长并非通过蚁后特异性基因的表达实现。为了从受感染工蚁的腹部RNA中分离出绦虫RNA序列，我们额外对320个囊尾蚴（cysticercoids）的RNA进行测序，并从头组装了A. brevis的转录组。对绦虫转录组的分析显示，线粒体呼吸链相关基因的表达占主导，这表明该寄生虫处于活跃代谢状态，并为其囊尾蚴阶段的生理特征提供了参考依据（数据集S4）。