Horizontal Gene Transfer and Tandem Duplication Shape the Unique CAZyme Complement of the Mycoparasitic Oomycetes Pythium oligandrum and Pythium periplocum

Abstract

Crop protection strategies that are effective but that reduce our reliance on chemical pesticides are urgently needed to meet the UN sustainable development goals for global food security. Mycoparasitic oomycetes such as Pythium oligandrum and Pythium periplocum , have potential for the biological control of plant diseases that threaten crops and have attracted much attention due to their abilities to antagonize plant pathogens and modulate plant immunity. Studies of the molecular and genetic determinants of mycoparasitism in these species have been less well developed than those of their fungal counterparts. Carbohydrate-active enzymes (CAZymes) from P. oligandrum and P. periplocum are predicted to be important components of mycoparasitism, being involved in the degradation of the cell wall of their oomycete and fungal prey species. To explore the evolution of CAZymes of these species we performed an in silico identification and comparison of the full CAZyme complement (CAZyome) of the two mycoparasitic Pythium species ( P. oligandrum and P. periplocum ), with seven other Pythium species, and four Phytophthora species. Twenty CAZy gene families involved in the degradation of cellulose, hemicellulose, glucan, and chitin were expanded in, or unique to, mycoparasitic Pythium species and several of these genes were expressed during mycoparasitic interactions with either oomycete or fungal prey, as revealed by RNA sequencing and quantitative qRT-PCR. Genes from three of the cellulose and chitin degrading CAZy families (namely AA9, GH5_14, and GH19) were expanded via tandem duplication and predominantly located in gene sparse regions of the genome, suggesting these enzymes are putative pathogenicity factors able to undergo rapid evolution. In addition, five of the CAZy gene families were likely to have been obtained from other microbes by horizontal gene transfer events. The mycoparasitic species are able to utilize complex carbohydrates present in fungal cell walls, namely chitin and N-acetylglucosamine for growth, in contrast to their phytopathogenic counterparts. Nonetheless, a preference for the utilization of simple sugars for growth appears to be a common trait within the oomycete lineage.

Dual-Transcriptomic, Microscopic, and Biocontrol Analyses of the Interaction Between the Bioeffector Pythium oligandrum and the Pythium Soft-Rot of Ginger Pathogen Pythium myriotylum

“…The limited upregulation of the host/prey targeted cellulases in P. oligandrum in the confrontation with P. myriotylum contrasts somewhat with their expression in P. oligandrum in the interaction with P. infestans from the study of Liang et al (2020). Here the majority of the AA9 cellulases were upregulated (with a subset expressed at a high level) at 12 and 24 h after contact between P. oligandrum and P. infestans compared to control samples before contact was made (Liang et al, 2020). Differences in the timing of the sampling for expression analysis, using a different P. oligandrum strain (CBS530.74), or other hosts (e.g., differences in the cell wall composition between the hosts) could contribute to the differences in cellulase gene expression when P. oligandrum confronted P. myriotylum compared to when P. infestans was confronted.…”

“…Note that the ATCC 38472 strain of P. oligandrum is used in the commercial oospore-containing product Polyversum R . In a comparative genomics analysis of P. oligandrum with other oomycetes, there was an expansion of carbohydrate-active enzyme (CAZy) families (Lombard et al, 2014) involved in the degradation of cellulose (Liang et al, 2020), perhaps related to the ability of P. oligandrum to degrade the cellulose in the cell wall of an oomycete host or prey. P. oligandrum is often referred to as a mycoparasite as its antagonism includes the coiling of P. oligandrum hyphae around hyphae of its host (Berry et al, 1993).…”

“…P. oligandrum possesses an arsenal of hydrolytic enzymes such as cellulases and proteases that are important for antagonism toward particular hosts. The CAZyme content of P. oligandrum was described recently by Liang et al (2020) . The production of antimicrobial compounds by P. oligandrum also contributes to the antagonism ( Benhamou et al, 1999 ).…”

Transcriptome Analysis of Potato Infected with the Necrotrophic Pathogen Alternaria solani

“…RNA preparation and sequencing was performed as described previously [ 42 ]. Briefly, approximately 100 mg of plant material (5 leaf discs) was used for RNA extraction using the Qiagen RNeasy Plant Mini kit (Qiagen, Hilden, Germany), according to the manufacturer’s protocol, with an added DNase treatment interruption step.…”

Plant Beneficial Microbes Controlling Late Blight Pathogen, Phytophthora infestans

“…This protection strategy has been recognized as an important mechanism of biological control. Mycoparasitics such as the oomycete Pythium oligandrum [105], Pythium periplocum [106] and different species from Trichoderma including T. asperellum, T. atroviride, T. virens, and T. harzianum are successfully used against P. infetans. These mycoparasitic grow faster than their pathogenic plant counterparts, which means that they can occupy rhizosphere space and nutrition, thus promoting both plant growth [107] resistance in host plants [108,109].…”