Schistosoma mansoni Egg, Adult Male and Female Comparative Gene Expression Analysis and Identification of Novel Genes by RNA-Seq.
Schistosoma mansoni Egg, Adult Male and Female Comparative Gene Expression Analysis and Identification of Novel Genes by RNA-Seq.
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DOI：
10.1371/journal.pntd.0004334
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发表时间：
2015-12
影响因子：
3.8
通讯作者：
Verjovski-Almeida S
中科院分区：
文献类型：
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作者：
Anderson L;Amaral MS;Beckedorff F;Silva LF;Dazzani B;Oliveira KC;Almeida GT;Gomes MR;Pires DS;Setubal JC;DeMarco R;Verjovski-Almeida S
血吸虫病是世界上最流行的寄生虫病之一，是一个公共卫生问题。曼氏血吸虫是导致美洲、中东和非洲血吸虫病的最广泛的种类。成年雌虫（与雄虫交配）在肝门静脉血管中产卵，是发病的主要原因。以前使用微阵列和基因表达序列分析（SAGE）对雌性和雄性成虫的比较单独转录组进行了评估，从而限制了发现新基因的可能性。此外，仅用有限的细菌克隆cDNA文库分析了一次卵子转录组。为了比较mansoni卵、雌虫和雄虫的基因表达，我们使用454/Roche技术对这三种寄生虫形式进行了RNA-Seq分析，并使用Trinity de novo组装方法重建了转录组。所得到的序列被定位到基因组中，并与预测的Smp基因和H3K4me3 ChIP-Seq公共数据进行交叉参考。我们首次获得了mansoni s.m ansoni卵、雌虫和雄虫成虫的独立、无偏的基因表达谱，确定了这三种寄生虫各自丰富的生物学过程和特定的丰富功能。与预测基因不匹配的转录本分析了它们的蛋白质编码潜力和编码保守蛋白结构域的存在。检测到232个新的蛋白质编码基因，这些基因可能与生殖、代谢和细胞生物发生有关，有助于对寄生虫生物学的理解。大规模RNA-Seq分析使用从头组装与基因模型附近组蛋白标记的全基因组信息相关联，构成了一种尚未在血吸虫中探索的转录组分析新方法。重要的是，所有数据都已整合到UCSC基因组浏览器搜索和下载工具（http://schistosoma.usp.br/）中。该数据库为探索血吸虫基因组和转录组提供了新的途径，并将促进对这种重要寄生虫的分子研究。血吸虫病是由血吸虫属寄生虫引起的公共卫生问题，其中曼氏血吸虫是主要病原体。寄生虫有一个复杂的生命周期；它们的性繁殖阶段依赖于雌虫和雄虫成虫在人类宿主的肠系膜循环内交配，雌虫每天释放数百个卵。生命周期的这一阶段负责病理的发展，这与人类宿主肝脏和肠道中积累的卵子数量成正比。该寄生虫的基因组和转录组测序代表了血吸虫研究的重要进展，但仍需要进行综合分析以更好地了解该寄生虫的生物学。在这项研究中，我们首次描述了虫卵、雌性和雄性成虫的大规模转录组，这些寄生虫形式主要负责血吸虫病的病理。我们可以将基因转录区与启动子区进行交叉比对，从而改进基因注释。此外，我们还鉴定了目前基因组注释中尚未描述的新蛋白质编码基因的表达，从而提高了对该寄生虫的生物学知识。
Schistosomiasis is one of the most prevalent parasitic diseases worldwide and is a public health problem. Schistosoma mansoni is the most widespread species responsible for schistosomiasis in the Americas, Middle East and Africa. Adult female worms (mated to males) release eggs in the hepatic portal vasculature and are the principal cause of morbidity. Comparative separate transcriptomes of female and male adult worms were previously assessed with using microarrays and Serial Analysis of Gene Expression (SAGE), thus limiting the possibility of finding novel genes. Moreover, the egg transcriptome was analyzed only once with limited bacterially cloned cDNA libraries. To compare the gene expression of S. mansoni eggs, females, and males, we performed RNA-Seq on these three parasite forms using 454/Roche technology and reconstructed the transcriptome using Trinity de novo assembly. The resulting contigs were mapped to the genome and were cross-referenced with predicted Smp genes and H3K4me3 ChIP-Seq public data. For the first time, we obtained separate, unbiased gene expression profiles for S. mansoni eggs and female and male adult worms, identifying enriched biological processes and specific enriched functions for each of the three parasite forms. Transcripts with no match to predicted genes were analyzed for their protein-coding potential and the presence of an encoded conserved protein domain. A set of 232 novel protein-coding genes with putative functions related to reproduction, metabolism, and cell biogenesis was detected, which contributes to the understanding of parasite biology. Large-scale RNA-Seq analysis using de novo assembly associated with genome-wide information for histone marks in the vicinity of gene models constitutes a new approach to transcriptome analysis that has not yet been explored in schistosomes. Importantly, all data have been consolidated into a UCSC Genome Browser search- and download-tool (http://schistosoma.usp.br/). This database provides new ways to explore the schistosome genome and transcriptome and will facilitate molecular research on this important parasite. Schistosomiasis is a public health problem caused by parasites of the genus Schistosoma, of which S. mansoni is the primary causative agent. The parasite has a complex life cycle; their sexual reproductive stage is dependent on female and male adult worms mating inside the mesenteric circulation of the human host, with the female releasing hundreds of eggs daily. This phase of the life cycle is responsible for the development of pathology, which is proportional to the number of eggs accumulating in the liver and intestine of the human host. Genome and transcriptome sequencing of this parasite represent important advances in schistosome research, but there is still a need for integrated analyses to better understand the biology of this parasite. In this study, we describe the first large-scale transcriptomes of eggs, and female and male adult worms, the parasite forms that are mainly responsible for the pathology of schistosomiasis. We were able to cross-reference the gene transcription regions with promoter regions, thus improving the gene annotations. Moreover, we identified the expression of novel protein-coding genes not yet described in the current genome annotation, advancing the biological knowledge regarding this parasite.