Genome Analysis of a Zygomycete Fungus Choanephora cucurbitarum Elucidates Necrotrophic Features Including Bacterial Genes Related to Plant Colonization

Abstract

A zygomycete fungus, Choanephora cucurbitarum is a plant pathogen that causes blossom rot in cucurbits and other plants. Here we report the genome sequence of Choanephora cucurbitarum KUS-F28377 isolated from squash. The assembled genome has a size of 29.1 Mbp and 11,977 protein-coding genes. The genome analysis indicated that C. cucurbitarum may employ a plant pathogenic mechanism similar to that of bacterial plant pathogens. The genome contained 11 genes with a Streptomyces subtilisin inhibitor-like domain, which plays an important role in the defense against plant immunity. This domain has been found only in bacterial genomes. Carbohydrate active enzyme analysis detected 312 CAZymes in this genome where carbohydrate esterase family 6, rarely found in dikaryotic fungal genomes, was comparatively enriched. The comparative genome analysis showed that the genes related to sexual communication such as the biosynthesis of β-carotene and trisporic acid were conserved and diverged during the evolution of zygomycete genomes. Overall, these findings will help us to understand how zygomycetes are associated with plants.

Genome-reconstruction for eukaryotes from complex natural microbial communities

“…To ensure that our proposed methodology can result in improved eukaryotic gene predictions in the context of a complex metagenomic sample, we spiked the genome of Choanephora cucurbitarum (Min et al 2017) into a complex, 15-Gbp, soil shotgun metagenomic sample (Fig. 3B).…”

CAZymes-based ranking of fungi (CBRF): an interactive web database for identifying fungi with extrinsic plant biomass degrading abilities

“…As mentioned above in data retrieval section CAZy database is widely distributed, each CAZy family further includes several enzymes that are grouped based on their structural features (Busk and Lange 2013; Davies and Henrissat 1995;Henrissat 1991;Henrissat andBairoch 1993, 1996;Henrissat and Davies 1997). Previous studies have extensively reported that microorganisms with wide variety of CAZymes can exhibit higher plant biomass degrading abilities (Daly et al 2017;López et al 2018;Min et al 2017;Miyauchi et al 2017;O'Connell et al 2012) (Fig. 1).…”

Genome mining of Streptomyces scabrisporus NF3 reveals symbiotic features including genes related to plant interactions

“…CAZymes are enzyme families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds, like glycoside hydrolases, glycosyl transferases, polysaccharide lyases, carbohydrate esterases and some auxiliary redox enzymes such as polysaccharide mono-oxygenases[ 60 ]. In the context of plant interactions, various novel CAZymes with a role in degradation of plant polysaccharides could be identified by mining newly sequenced genomes or metagenomes[ 14 , 61 – 63 ]. Some studies go as far as using the presence of plant cell-wall degrading enzymes as a basis for bacterial classification as endophytes or as pathogens[ 14 ], under the hypothesis that endophytes are positively selected by the plant and only need to produce cellulases and pectinases, while pathogens requiring the degradation of the entire cell wall implement lignocellulose-degrading enzymes.…”