Clermont Université, Université d'Auvergne, Centre de Recherche en Nutrition Humaine Auvergne, EA 4678, Conception, Ingénierie et Développement de l'Aliment et du Médicament, BP 10448, F63000 Clermont-Ferrand, France.
Nat Commun. 2012;3:1137. doi: 10.1038/ncomms2156.
High-quality annotation of microsporidian genomes is essential for understanding the biological processes that govern the development of these parasites. Here we present an improved structural annotation method using transcriptional DNA signals. We apply this method to re-annotate four previously annotated genomes, which allow us to detect annotation errors and identify a significant number of unpredicted genes. We then annotate the newly sequenced genome of Anncaliia algerae. A comparative genomic analysis of A. algerae permits the identification of not only microsporidian core genes, but also potentially highly expressed genes encoding membrane-associated proteins, which represent good candidates involved in the spore architecture, the invasion process and the microsporidian-host relationships. Furthermore, we find that the ten-fold variation in microsporidian genome sizes is not due to gene number, size or complexity, but instead stems from the presence of transposable elements. Such elements, along with kinase regulatory pathways and specific transporters, appear to be key factors in microsporidian adaptive processes.
高质量的微孢子虫基因组注释对于理解这些寄生虫发育的生物学过程至关重要。在这里，我们提出了一种使用转录 DNA 信号改进的结构注释方法。我们将此方法应用于重新注释四个先前注释的基因组，从而可以检测到注释错误并识别出大量未预测的基因。然后，我们对新测序的 Anncaliia algerae 基因组进行注释。对 A. algerae 的比较基因组分析不仅可以识别微孢子虫核心基因，还可以识别可能高度表达的编码膜相关蛋白的基因，这些基因是参与孢子结构、入侵过程和微孢子虫-宿主关系的良好候选基因。此外，我们发现微孢子虫基因组大小的十倍差异不是由于基因数量、大小或复杂性引起的，而是由于转座元件的存在。这些元素以及激酶调节途径和特定的转运蛋白似乎是微孢子虫适应过程中的关键因素。
