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RNASEQ VS ENRICHMENT SEQUENCING TECHNIQUES: LIFTING THE LID ON THE POTATO-P. INFESTANS INTERACTIONS
Kaur, Amanpreet Singh, Vikrant Armstrong , Miles Hein, Ingo Mullins, Ewen
Kaur, Amanpreet
Singh, Vikrant
Armstrong , Miles
Hein, Ingo
Mullins, Ewen
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Abstract
Late blight, caused by an oomycete; Phytophthora infestans continues to be the primary
disease of concern for potato farmers. The pathogen virulence is attributed to the presence
of effectors (pathogenicity factors), which if recognised by plant resistance (R) genes,
triggers the immune response. Not surprisingly P. infestans has evolved accordingly, which
has driven effector diversity in P. infestans populations. Yet, our understanding of this
adaptive evolution remains poor. Therefore, tracking effector diversity in light of disease
resistance gene deployment is critically important if robust IPM strategies are to be
developed in support of Farm to Fork (F2F) goals.
Enrichment sequencing techniques enable cost effective, high-confidence identification of
functional R genes and effectors. Although merits of enrichment sequencing over WGS has
been previously demonstrated, but its comparison with gene expression remains elusive. In
this regard, P. infestans infected potato plants were subjected to RNAseq, PenSeq and
RenSeq at different time points. The analysis reveals the presence of some unknown
effectors (PITG_08949, PITG_14932, PITG_02900, etc.) with 100% gene coverage at very
early stages of infection which was otherwise not possible with RNAseq.
This information combined with R gene expression during infection have potential to widen
our current knowledge of potato-P. infestans interactions, and can be used as a platform for
introducing informed phase of potato breeding.