Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou North Avenue No.1838, Guangzhou, 510515, Guangdong, China.
Department of Bioinformatics, School of Basic Medicine School of Basic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China.
Parasit Vectors. 2018 Jul 11;11(1):402. doi: 10.1186/s13071-018-2983-5.
Toxoplasma gondii is one of the most important apicomplexan parasites and infects one-third of the human population worldwide. Transformation between the tachyzoite and bradyzoite stages in the intermediate host is central to chronic infection and life-long risk. There have been some transcriptome studies on T. gondii; however, we are still early in our understanding of the kinds and levels of gene expression that occur during the conversion between stages.
We used high-throughput RNA-sequencing data to assemble transcripts using genome-based and de novo strategies. The expression-level analysis of 6996 T. gondii genes showed that over half (3986) were significantly differentially expressed during stage conversion, whereas 2205 genes were upregulated, and 1778 genes were downregulated in tachyzoites compared with bradyzoites. Several important gene families were expressed at relatively high levels. Comprehensive functional annotation and gene ontology analysis revealed that stress response-related genes are important for survival of bradyzoites in immune-competent hosts. We compared Trinity-based de novo and genome-based strategies, and found that the de novo assembly strategy compensated for the defects of the genome-based strategy by filtering out several transcripts with low expression or those unannotated on the genome. We also found some inaccuracies in the ToxoDB gene models. In addition, our analysis revealed that alternative splicing can be differentially regulated in response to life-cycle change. In depth analysis revealed a 20-nt, AG-rich sequence, alternative splicing locus from alt_acceptor motif search in tachyzoite.
This study represents the first large-scale effort to sequence the transcriptome of bradyzoites from T. gondii tissue cysts. Our data provide a comparative view of the tachyzoite and bradyzoite transcriptomes to allow a more complete dissection of all the molecular regulation mechanisms during stage conversions. A better understanding of the processes regulating stage conversion may guide targeted interventions to disrupt the transmission of T. gondii.
刚地弓形虫是最重要的顶复门寄生虫之一，全球有三分之一的人口受到感染。中间宿主中的速殖子和缓殖子阶段之间的转化是慢性感染和终身风险的核心。已经有一些关于刚地弓形虫的转录组研究；然而，我们对于在阶段转换过程中发生的基因表达的种类和水平还处于早期理解阶段。
我们使用高通量 RNA 测序数据，通过基于基因组和从头组装的策略来组装转录本。对 6996 个刚地弓形虫基因的表达水平分析表明，超过一半（3986 个）在速殖子和缓殖子之间的阶段转换过程中差异表达显著，而与缓殖子相比，速殖子中有 2205 个基因上调，1778 个基因下调。几个重要的基因家族表达水平较高。全面的功能注释和基因本体分析表明，应激反应相关基因对于免疫功能正常宿主中的缓殖子存活至关重要。我们比较了基于 Trinity 的从头组装和基于基因组的策略，发现从头组装策略通过过滤掉一些低表达或在基因组上未注释的转录本来弥补基于基因组的策略的缺陷。我们还发现了一些 ToxoDB 基因模型中的不准确之处。此外，我们的分析表明，可变剪接可以在应对生命周期变化时受到差异调控。深入分析显示，在速殖子中从 alt_acceptor 基序搜索发现了一个 20nt 的 AG 丰富的可变剪接位点。
本研究代表了首次大规模测序刚地弓形虫组织包囊中的缓殖子转录组。我们的数据提供了速殖子和缓殖子转录组的比较视图，以更完整地剖析阶段转换过程中的所有分子调控机制。更好地理解调节阶段转换的过程可能会指导针对破坏刚地弓形虫传播的靶向干预。
