Expansion and Divergence of Argonaute Genes in the Oomycete Genus Phytophthora

Abstract

Modulation of gene expression through RNA interference is well conserved in eukaryotes and is involved in many cellular processes. In the oomycete Phytophthora, research on the small RNA machinery and function has started to reveal potential roles in the pathogen, but much is still unknown. We examined Argonaute (AGO) homologs within oomycete genome sequences, especially among Phytophthora species, to gain a clearer understanding of the evolution of this well-conserved protein family. We identified AGO homologs across many representative oomycete and stramenopile species, and annotated representative homologs in P. sojae. Furthermore, we demonstrate variable transcript levels of all identified AGO homologs in comparison to previously identified Dicer-like (DCL) and RNA-dependent RNA polymerase (RDR) homologs. Our phylogenetic analysis further refines the relationship of the AGO homologs in oomycetes and identifies a conserved tandem duplication of AGO homologs in a subset of Phytophthora species.

Polymorphism analyses and protein modelling inform on functional specialization of Piwi clade genes in the arboviral vector Aedes albopictus

“…Recent studies provided evidence of evolutionary expansion and functional divergence of Argonautes in Dipterans, including examples in both the Ago and Piwi subclades [3]. Differences in function and copy number have also been found in other taxa such as nematodes [4], oomycetes [5] and higher plants [6], showing that this protein family is subject to a dynamic evolutionary history. In eukaryotes, Argonautes are key components of RNA interference (RNAi) mechanisms, which can be distinguished in three main pathways: the small interfering RNA (siRNA), microRNA (miRNA) and the PIWI-interacting RNA (piRNA) pathways.…”

Small RNAs in Plant Immunity and Virulence of Filamentous Pathogens

“…The presence of active RNAi is supported by the well-established target gene knockdown approach, which has been employed as a tool to study gene functions in several Phytophthora species by using hairpin or antisense RNA constructs (1, 147). Canonical RNAi core enzymes in Phytophthora include a single RDR, two DCLs (14,44), and variable numbers of AGOs (15). The two DCLs in each Phytophthora species form two well-supported clusters, consistent with the accumulation of two major classes of sRNAs, predominantly 21 nt and 25/26 nt, respectively (14,44,119).…”

“…A similar pattern was also observed for PsDCLs and PsRDR. Other PsAGOs had low expression levels overall but some were induced in zoospores, indicating a role in reproduction (15). Co-immunoprecipitation assays in P. infestans revealed that PiAGO1 was predominantly associated with 20-22-nt sRNAs and PiAGO4 primarily bound to 24-26-nt sRNAs, whereas PiAGO5 did not appear to have a size preference for sRNA binding (5).…”

“…Compared to fungal pathogens, Phytophthora has an expanded number of AGOs (Figure 2), which are also variable in different species. For example, P. infestans, P. ramorum, and P. sojae encode five, six, and nine AGO genes, respectively (15). These AGOs form two well-supported clades, with AGO1 from each species clustered together and separated from the other homologs.…”

Characterization of Two Satellite DNA Families in the Genome of the Oomycete Plant Pathogen Phytophthora parasitica

“…The importance of small RNA-based silencing and epigenetics in the biology and pathogenicity of Phytophthora has emerged with the evidence of silencing events (van West et al, 2008), the identification of the silencing machinery, and the characterization of sRNAs in various species (Vetukuri et al, 2012;Fahlgren et al, 2013;Åsman et al, 2016;Bollmann et al, 2016Bollmann et al, , 2018Wang et al, 2016;Jia et al, 2017). These studies revealed that Phytophthora possess several small RNA populations diverging by their size (Vetukuri et al, 2012;Fahlgren et al, 2013).…”