Table1_Time-series transcriptome analysis identified differentially expressed genes in broiler chicken infected with mixed Eimeria species.xlsx

Coccidiosis caused by the Eimeria species is a highly problematic disease in the chicken industry. Here, we used RNA sequencing to observe the time-dependent host responses of Eimeria-infected chickens to examine the genes and biological functions associated with immunity to the parasite. Transcriptome analysis was performed at three time points: 4, 7, and 21 days post-infection (dpi). Based on the changes in gene expression patterns, we defined three groups of genes that showed differential expression. This enabled us to capture evidence of endoplasmic reticulum stress at the initial stage of Eimeria infection. Furthermore, we found that innate immune responses against the parasite were activated at the first exposure; they then showed gradual normalization. Although the cytokine-cytokine receptor interaction pathway was significantly operative at 4 dpi, its downregulation led to an anti-inflammatory effect. Additionally, the construction of gene co-expression networks enabled identification of immunoregulation hub genes and critical pattern recognition receptors after Eimeria infection. Our results provide a detailed understanding of the host-pathogen interaction between chicken and Eimeria. The clusters of genes defined in this study can be utilized to improve chickens for coccidiosis control.

由艾美耳球虫（Eimeria）属物种引发的鸡球虫病，是家禽养殖业中极具危害性的疾病。本研究借助RNA测序技术，观察艾美耳球虫感染鸡只的时序性宿主应答反应，以此解析与该寄生虫免疫相关的基因及生物学功能。研究分别在感染后第4、7、21天（dpi）三个时间点开展转录组（transcriptome）分析。基于基因表达模式的变化特征，本研究界定了3组差异表达基因，由此得以捕捉到艾美耳球虫感染初始阶段内质网应激（endoplasmic reticulum stress）的相关证据。此外，本研究发现宿主针对该寄生虫的固有免疫应答在首次感染时即被激活，随后逐渐恢复至稳态水平。尽管细胞因子-细胞因子受体相互作用通路在感染后第4天（dpi）显著激活，但其下调可产生抗炎效应。另外，通过构建基因共表达网络，本研究鉴定出艾美耳球虫感染后的免疫调控枢纽基因（hub genes）与关键模式识别受体（pattern recognition receptors）。本研究结果为深入解析鸡与艾美耳球虫之间的宿主-病原体相互作用机制提供了详实的理论依据。本研究中界定的基因簇可用于培育抗鸡球虫病的优良鸡只品种。