Phenotypic diversification by gene silencing in Phytophthora plant pathogens

Abstract

Advances in genome sequencing technologies have enabled generation of unprecedented information on genome content and organization. Eukaryote genomes in particular may contain large populations of transposable elements (TEs) and other repeated sequences. Active TEs can result in insertional mutations, altered transcription levels and ectopic recombination of DNA. The genome of the oomycete plant pathogen, Phytophthora infestans, contains vast numbers of TE sequences. There are also hundreds of predicted disease-promoting effector proteins, predominantly located in TE-rich genomic regions. Expansion of effector gene families is also a genomic signature of related oomycetes such as P. sojae. Deep sequencing of small RNAs (sRNAs) from P. infestans has identified sRNAs derived from all families of transposons, highlighting the importance of RNA silencing for maintaining these genomic invaders in an inactive form. Small RNAs were also identified from specific effector encoding genes, possibly leading to RNA silencing of these genes and variation in pathogenicity and virulence toward plant resistance genes. Similar findings have also recently been made for the distantly related species, P. sojae. Small RNA "hotspots" originating from arrays of amplified gene sequences, or from genes displaying overlapping antisense transcription, were also identified in P. infestans. These findings suggest a major role for RNA silencing processes in the adaptability and diversification of these economically important plant pathogens. Here we review the latest progress and understanding of gene silencing in oomycetes with emphasis on transposable elements and sRNA-associated events.

Keywords: Phytophthora; effectors; oomycete; small RNAs; transposable element.

Figure 1. Initiation of pathways to endogenous RNA silencing of genes in P. infestans, using examples from sRNA sequencing. In transposon silencing islands (top), heterochromatin formation may spread from a nearby transposon (blue) to also silence the neighboring RxLR effector gene, PITG_04350 (green). This involves histone modifications, and production of sRNAs (red arrows) via DCL, AGO and histone deacetylase. Silencing of amplified copies of endogenous genes (middle; red) may involve excessive transcription or formation of aberrant transcripts that are targeted for destruction via the RNA silencing pathway; genomic hotspots of aligning sRNAs indicate the involvement of DCL and AGO proteins. It is possible that one or more copies in the gene family array are expressed, while others may be silenced. Concurrent overlapping antisense transcription (bottom; red) may lead to formation of double stranded RNA (dsRNA) which can be processed into sRNAs, leading to mRNA destruction via AGO, transcriptional regulation or silencing. In middle and bottom models, gene position on the P. infestans genome sequence is shown below the gene model; vertical black bars indicate the abundance of aligning sRNAs. More detailed proposed models for sRNA biogenesis and silencing in Phytophthora can be found elsewhere.^,