Genome Sequencing of Paecilomyces Penicillatus Provides Insights into Its Phylogenetic Placement and Mycoparasitism Mechanisms on Morel Mushrooms

Abstract

Morels (Morchella spp.) are popular edible fungi with significant economic and scientific value. However, white mold disease, caused by Paecilomyces penicillatus, can reduce morel yield by up to 80% in the main cultivation area in China. Paecilomyces is a polyphyletic genus and the exact phylogenetic placement of P. penicillatus is currently still unclear. Here, we obtained the first high-quality genome sequence of P. penicillatus generated through the single-molecule real-time (SMRT) sequencing platform. The assembled draft genome of P. penicillatus was 40.2 Mb, had an N50 value of 2.6 Mb and encoded 9454 genes. Phylogenetic analysis of single-copy orthologous genes revealed that P. penicillatus is in Hypocreales and closely related to Hypocreaceae, which includes several genera exhibiting a mycoparasitic lifestyle. CAZymes analysis demonstrated that P. penicillatus encodes a large number of fungal cell wall degradation enzymes. We identified many gene clusters involved in the production of secondary metabolites known to exhibit antifungal, antibacterial, or insecticidal activities. We further demonstrated through dual culture assays that P. penicillatus secretes certain soluble compounds that are inhibitory to the mycelial growth of Morchella sextelata. This study provides insights into the correct phylogenetic placement of P. penicillatus and the molecular mechanisms that underlie P. penicillatus pathogenesis.

Keywords: PacBio; carbohydrate-active enzymes (CAZymes); paecilomyces penicillatus; phylogeny; whole genome sequencing.

Figure 1

Phylogenetic analysis of single-copy orthologous genes of P. penicillatus and 13 representative species of Hypocreales, one Sordariales species, and four Eurotiales species. S. pombe was used as an outgroup for this analysis. P. variotii is indicated in bold font, and P. pencililatus is highlighted in red font. Families of Hypocreales are labeled in blue font. The phylogenetic tree was generated using the maximum-likelihood method with 1000 bootstrap replicates. The tree scale indicates residue substitutions per site. Only bootstrap values greater than 0.6 are displayed.

Figure 2

Annotation of carbohydrate-related genes in the P. penicillatus genome.

Figure 3

Phylogenetic relationships of P. penicillatus, T. atroviride, and T. virens sgC chitinases. The presence of GH18 modules (IPR001223) is indicated with green stars, LysMs (IPR018392) are indicated in yellow triangles, and CBM18s (IPR001002) are represented by pink circles.

Figure 4

Confrontation cultures between P. penicillatus and M. sextelata on CMA medium. (A). Normal petri dish (B). Two-compartment petri dish.