Genome-wide transcriptome profiling and spatial expression analyses identify signals and switches of development in tapeworms.
Genome-wide transcriptome profiling and spatial expression analyses identify signals and switches of development in tapeworms.
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DOI：
10.1186/s13227-018-0110-5
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发表时间：
2018
期刊：
影响因子：
4.1
通讯作者：
Berriman M
中科院分区：
文献类型：
--
作者：
Olson PD;Zarowiecki M;James K;Baillie A;Bartl G;Burchell P;Chellappoo A;Jarero F;Tan LY;Holroyd N;Berriman M
绦虫是被忽视的热带病的病原体，造成严重的健康问题和经济损失。它们还表现出对寄生生活方式的适应，这种生活方式混淆了它们与其他动物的发育比较。确定调节其复杂个体发育的遗传因素对于了解其生物学的独特方面和推进新的治疗方法至关重要。在这里，我们使用RNA测序来识别绦虫微孔膜虫幼虫和节段虫不同区域转录中上调的信号成分、转录因子和转录后/翻译后调节因子(gene of interest，GOI)，并将其与一系列基因的空间基因表达分析相结合。Rna-seq读数共同映射到H.microstoma v.2基因组组件中>； 12,000个基因模型的90%，表明转录组图谱捕获了高比例的预测基因。对幼虫和整个成虫的转录本以及头节颈、成熟球果和妊娠球果的转录本进行了对比，结果发现有4.5-30%的基因被确定为差异表达。其中，我们发现了190个独特的GOI在一个或多个对比中上调，包括大量的锌指、同源框和其他转录因子，Wnt、Notch、Hedgehog和转化生长因子-β/骨形态发生蛋白信号转导的组成部分，以及转录后调节因子(如Boule、Pumilio)。基于整体表达和代表“信号”和“开关”的特定基因组的热图聚类表明，在头节颈部区域的表达更类似于幼虫的表达，而不是成虫的成熟或妊娠区域，这进一步反映在上调的GOI的大量重叠中。对幼虫和成虫的空间表达分析证实了从定量RNA-SEQ数据得出的推断，并且在大多数情况下表明与包括自由生活的扁虫在内的其他动物的基因的典型作用一致。对幼虫变态过程中上调的发育因子的总结表明，尽管发育结果存在显着差异，但球茎的生长涉及许多相同的潜在基因调控网络。大多数已鉴定的基因是首次在绦虫中进行研究，这为我们进一步了解扁虫这一重要群体的发育遗传学奠定了基础。本文的在线版本(10.1186/s13227-0180110-5)包含补充材料，可供授权用户使用。
Tapeworms are agents of neglected tropical diseases responsible for significant health problems and economic loss. They also exhibit adaptations to a parasitic lifestyle that confound comparisons of their development with other animals. Identifying the genetic factors regulating their complex ontogeny is essential to understanding unique aspects of their biology and for advancing novel therapeutics. Here we use RNA sequencing to identify up-regulated signalling components, transcription factors and post-transcriptional/translational regulators (genes of interest, GOI) in the transcriptomes of Larvae and different regions of segmented worms in the tapeworm Hymenolepis microstoma and combine this with spatial gene expression analyses of a selection of genes. RNA-seq reads collectively mapped to 90% of the > 12,000 gene models in the H. microstoma v.2 genome assembly, demonstrating that the transcriptome profiles captured a high percentage of predicted genes. Contrasts made between the transcriptomes of Larvae and whole, adult worms, and between the Scolex-Neck, mature strobila and gravid strobila, resulted in 4.5–30% of the genes determined to be differentially expressed. Among these, we identified 190 unique GOI up-regulated in one or more contrasts, including a large range of zinc finger, homeobox and other transcription factors, components of Wnt, Notch, Hedgehog and TGF-β/BMP signalling, and post-transcriptional regulators (e.g. Boule, Pumilio). Heatmap clusterings based on overall expression and on select groups of genes representing ‘signals’ and ‘switches’ showed that expression in the Scolex-Neck region is more similar to that of Larvae than to the mature or gravid regions of the adult worm, which was further reflected in large overlap of up-regulated GOI. Spatial expression analyses in Larvae and adult worms corroborated inferences made from quantitative RNA-seq data and in most cases indicated consistency with canonical roles of the genes in other animals, including free-living flatworms. Recapitulation of developmental factors up-regulated during larval metamorphosis suggests that strobilar growth involves many of the same underlying gene regulatory networks despite the significant disparity in developmental outcomes. The majority of genes identified were investigated in tapeworms for the first time, setting the stage for advancing our understanding of developmental genetics in an important group of flatworm parasites. The online version of this article (10.1186/s13227-018-0110-5) contains supplementary material, which is available to authorized users.
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DOI：
10.1093/bioinformatics/btp347
发表时间：
2009-08-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Assefa S;Keane TM;Otto TD;Newbold C;Berriman M
通讯作者：
Berriman M
DOI：
10.1051/parasite/2014070
发表时间：
2014
期刊：
Parasite (Paris, France)
影响因子：
--
作者：
Brehm K;Koziol U
通讯作者：
Koziol U
影响因子：
10.7
作者：
Amoutzias, G. D.;Veron, A. S.;Robertson, D. L.
通讯作者：
Robertson, D. L.
影响因子：
2.4
作者：
Cebrià, F;Bueno, D;Romero, R
通讯作者：
Romero, R
影响因子：
4.7
作者：
Bozzi Y;Casarosa S;Caleo M
通讯作者：
Caleo M