Comparative Genomic Analysis among Four Representative Isolates of Phytophthora sojae Reveals Genes under Evolutionary Selection.

Wenwu Ye,Yuanchao Wang,Brett M Tyler,Yang Wang

doi:10.3389/fmicb.2016.01547

Wenwu Ye, Yuanchao Wang + Show 2 more

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https://doi.org/10.3389/fmicb.2016.01547

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Abstract

Comparative genomic analysis is useful for identifying genes affected by evolutionary selection and for studying adaptive variation in gene functions. In Phytophthora sojae, a model oomycete plant pathogen, the related study is lacking. We compared sequence data among four isolates of P. sojae, which represent its four major genotypes. These isolates exhibited >99.688%, >99.864%, and >98.981% sequence identities at genome, gene, and non-gene regions, respectively. One hundred and fifty-three positive selection and 139 negative selection candidate genes were identified. Between the two categories of genes, the positive selection genes were flanked by larger intergenic regions, poorly annotated in function, and less conserved; they had relatively lower transcription levels but many genes had increased transcripts during infection. Genes coding for predicted secreted proteins, particularly effectors, were overrepresented in positive selection. Several RxLR effector genes were identified as positive selection genes, exhibiting much stronger positive selection levels. In addition, candidate genes with presence/absence polymorphism were analyzed. This study provides a landscape of genomic variation among four representative P. sojae isolates and characterized several evolutionary selection-affected gene candidates. The results suggest a relatively covert two-speed genome evolution pattern in P. sojae and will provide clues for identification of new virulence factors in the oomycete plant pathogens.

Highlights

Oomycetes form a distinct phylogenetic lineage of fungus-like eukaryotic microorganisms and belong to the kingdom Stramenopila, which includes brown algae and diatoms (Beakes et al, 2012)
The genome sequences among the four P. sojae isolates were nearly identical, but P7076 was closest to P6497, and P7074 was most distant from P6497 and quite close to P7064
Five PSS genes had stronger indication of PS, i.e., dN/dS > 2 and P < 0.05, and all of the five genes were RxLR effector genes (PsAvh158, −163, −181, −229, and −238). These results suggest that the RxLR effector genes might be dominant targets that are affected by strong PS stress in the P. sojae genome

Summary

Introduction

Oomycetes form a distinct phylogenetic lineage of fungus-like eukaryotic microorganisms and belong to the kingdom Stramenopila, which includes brown algae and diatoms (Beakes et al, 2012). The Phytophthora genus contains more than 100 described species (Kroon et al, 2012), of which many are plant pathogens of considerable economic importance. The soybean (Glycine max L.) root and stem rot agent, P. sojae, has caused considerable problems for the agricultural industry. Genome sequences of the hemibiotrophic P. sojae (Tyler et al, 2006), P. ramorum (Tyler et al, 2006), P. infestans (Haas et al, 2009), P. capsici (Lamour et al, 2012), and P. litchii (Ye et al, 2016) have been made available and analyzed. Accompanying the genomes of phytopathogenic species in other oomycete genera, such as the obligate biotrophic Hyaloperonospora arabidopsidis (Baxter et al, 2010) and Albugo spp. Accompanying the genomes of phytopathogenic species in other oomycete genera, such as the obligate biotrophic Hyaloperonospora arabidopsidis (Baxter et al, 2010) and Albugo spp. (Kemen et al, 2011; Links et al, 2011), and the necrotrophic Pythium spp. (Levesque et al, 2010; Adhikari et al, 2013), the data have revealed striking variation in genome size and content, a plastic set of pathogenesis-associated genes, and adaptation related to trophic modes, thereby contributing to a greatly accelerated study of host–pathogen interactions (Jiang and Tyler, 2012; Judelson, 2012)

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