Comparative transcriptomics of Steinernema and Caenorhabditis single embryos reveals gene expression divergence during early embryogenesis. Comparative transcriptomics of Steinernema and Caenorhabditis single embryos reveals gene expression divergence during early embryogenesis

Abstract: Cells express distinct sets of genes in a precise spatio-temporal manner during embryonic development. There is a wealth of information about embryonic development in C. elegans, but much less is known about embryonic development at the molecular level in nematodes from other taxa. We are interested in insect pathogenic nematodes from the genus Steinernema as models of parasitism and symbiosis as well as a satellite model for evolution in comparison to C. elegans. We sequenced the transcriptomes of single embryos of two Steinernema species and two Caenorhabditis species at eleven specific stages during embryonic development for comparative analysis. We found that zygotic transcription initiates at different developmental stages in each species, with the Steinernema species initiating transcription at earlier developmental stages than Caenorhabditis. We found that ortholog expression conservation during development is highest at the later embryonic stages than at the earlier ones. Moreover, we found that the components of the neddylation pathway are highly upregulated during Steinernema early embryonic development contributing further to these early differences seen between the genera at the post-translational level. The surprisingly higher conservation of orthologous gene expression in later embryonic stages strongly suggests a funnel-shaped model of developmental gene expression divergence in nematodes. This work provides novel insight into embryonic development across distantly related nematode species and demonstrates that the mechanisms controlling early development are more diverse than previously thought at both the transcriptional and post-translational level. Overall design: We sequenced the transcriptomes of single embryos of two Steinernema species and two Caenorhabditis species during embryonic development at eleven specific stages (zygote, 2-cell, 4-cell, 8-cell, 24-44-cell, 64-78-cell, comma, 1.5-fold, 2-fold, moving, and L1) for comparative analysis.

摘要：在胚胎发育过程中，细胞会以精确的时空模式表达特定的基因组合。关于秀丽隐杆线虫（Caenorhabditis elegans）的胚胎发育已有大量研究数据，但其他分类类群中线虫胚胎发育的分子机制目前相关认知仍较为匮乏。本研究关注斯氏线虫属（Steinernema）的昆虫病原线虫，将其作为寄生与共生关系的研究模型，同时作为相较于秀丽隐杆线虫的演化辅助研究模型。为开展跨物种比较分析，我们对两个斯氏线虫属物种与两个隐杆线虫属（Caenorhabditis）物种的单个胚胎，在胚胎发育的11个特定阶段进行了转录组测序。研究发现，不同物种的合子转录起始于不同的发育阶段：斯氏线虫属物种的转录起始阶段早于隐杆线虫属物种。我们还发现，发育过程中直系同源基因（ortholog）的表达保守性在胚胎发育后期高于早期。此外，斯氏线虫早期胚胎发育过程中，类泛素化修饰（Neddylation）通路的组分呈现显著上调，这进一步从翻译后修饰层面加剧了两属线虫之间的早期发育差异。胚胎发育后期直系同源基因表达保守性意外升高的现象，强烈支持线虫发育过程中基因表达分化的漏斗形模型假说。本研究为远缘线虫物种间的胚胎发育比较研究提供了全新视角，并证实调控早期发育的机制在转录与翻译后修饰层面均比此前认知更为多样。
整体实验设计：为开展跨物种比较分析，我们对两个斯氏线虫属物种与两个隐杆线虫属物种的单个胚胎，在胚胎发育的11个特定阶段（合子期、2细胞期、4细胞期、8细胞期、24-44细胞期、64-78细胞期、逗号期、1.5倍期、2倍期、活动期以及L1期）进行了转录组测序。