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
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
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.