An Effective Pipeline Based on Relative Coverage for the Genome Assembly of Phytoplasmas and Other Fastidious Prokaryotes.

ABSTRACT:

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 kn

SUBMITTER: Polano C 

PROVIDER: S-EPMC6128390 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature