Background For the plant pathogenic phytoplasmas, as well as for several fastidious prokaryotes, axenic cultivation is extremely difficult or not possible yet; therefore, even with second generation sequencing methods, obtaining the sequence of their genomes is challenging due to host sequence contamination. Objective With the Phytoassembly pipeline here presented, we aim to provide a method to obtain high quality genome drafts for the phytoplasmas and other uncultivable plant pathogens, by exploiting the coverage differential in the ILLUMINA sequences from the pathogen and the host, and using the sequencing of a healthy, isogenic plant as a filter. Validation The pipeline has been benchmarked using simulated and real ILLUMINA runs from phytoplasmas whose genome is known, and it was then used to obtain high quality drafts for three new phytoplasma genomes. Conclusion For phytoplasma infected samples containing >2-4% of pathogen DNA and an isogenic reference healthy sample, the resulting assemblies can be next to complete. The Phytoassembly source code is available on GitHub at https://github.com/cpolano/phytoassembly.

中文翻译：

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基于相对覆盖度的植原体和其他挑剔原核生物基因组组装的有效流程


背景对于植物病原植原体以及几种要求严格的原核生物来说，无菌培养极其困难或尚不可能；因此，即使使用第二代测序方法，由于宿主序列污染，获得其基因组序列也具有挑战性。目的 通过本文提出的 Phytoassemble 流程，我们的目标是提供一种方法，通过利用病原体和宿主的 ILLUMINA 序列的覆盖差异，并使用健康的同基因植物作为过滤器。验证 该流程已使用来自基因组已知的植原体的模拟和真实 ILLUMINA 运行进行了基准测试，然后用于获得三个新植原体基因组的高质量草图。结论 对于含有 >2-4% 病原体 DNA 的植原体感染样品和同基因参考健康样品，所得组装可以接近完成。 Phytoassemble 源代码可在 GitHub 上获取：https://github.com/cpolano/phytoassemble。