Predicting Lifestyle from Positive Selection Data and Genome Properties in Oomycetes

Abstract

As evidenced in parasitism, host and niche shifts are a source of genomic and phenotypic diversification. Exemplary is a reduction in the core metabolism as parasites adapt to a particular host, while the accessory genome often maintains a high degree of diversification. However, selective pressures acting on the genome of organisms that have undergone recent lifestyle or host changes have not been fully investigated. Here, we developed a comparative genomics approach to study underlying adaptive trends in oomycetes, a eukaryotic phylum with a wide and diverse range of economically important plant and animal parasitic lifestyles. Our analysis reveals converging evolution on biological processes for oomycetes that have similar lifestyles. Moreover, we find that certain functions, in particular carbohydrate metabolism, transport, and signaling, are important for host and environmental adaptation in oomycetes. Given the high correlation between lifestyle and genome properties in our oomycete dataset, together with the known convergent evolution of fungal and oomycete genomes, we developed a model that predicts plant pathogenic lifestyles with high accuracy based on functional annotations. These insights into how selective pressures correlate with lifestyle may be crucial to better understand host/lifestyle shifts and their impact on the genome.

Ten decadal advances in fungal biology leading towards human well-being

“…The use of whole-genomes in phylogenomic studies provides sufficient data to elucidate relationships deeper in geological time, as well as to resolve relationships that evolved in short divergence times, which may lead to resolve problems in taxonomy (James et al 2020 ). Further studies on these whole-genome sequences allow to perform functional genomic studies on the genes predicted from the whole genome sequences, thus providing new knowledge to predict their lifestyles (Gómez-Pérez and Kemen 2021 ). The availability of genomic data also enables to assess micro- and macro variations within a species in a population to determine their genomic evolution.…”

Proteins released into the plant apoplast by the obligate parasitic protist Albugo selectively repress phyllosphere-associated bacteria

“…Thus, selection may have resulted in adaptation of proteins for this purpose. In this vein, C06 was unique in showing hints of positive selection as analyzed in a previous study, which may indicate recent selective adaptation (Gómez-Pérez and Kemen, 2021). We therefore hypothesized antimicrobial proteins or peptides as a mechanism to defend such a fragile niche within the leaf as these might be able to evade plant recognition but nevertheless restrict the growth of other microbes.…”

Proteins released into the plant apoplast by the obligate parasitic protist Albugo selectively repress phyllosphere‐associated bacteria

“…Thus, selection may have resulted in adaptation of proteins for this purpose. In this vein, C06 was unique in showing hints of positive selection as analyzed in a previous study, which may indicate recent selective adaptation (G omez-P erez & Kemen, 2021). We therefore hypothesized antimicrobial proteins and peptides as a mechanism to defend such a fragile niche within the leaf as these might be able to evade plant recognition but nevertheless restrict the growth of other microbes.…”