Whole genome analysis of Stenotrophomonas geniculata MK2 and antagonism against Botrytis cinerea in strawberry.

Abstract

A novel strain isolated from soil identified as Stenotrophomonas geniculata MK2 could control strawberries' postharvest disease gray mold. An in vitro investigation showed that MK2 had significant bioactivity against Botrytis cinerea, with an observed zone of inhibition of 85%. The strain MK2 was 88% effective in controlling gray mold on detached fruits. De novo whole genome sequencing analysis showed that strain MK2 has a single circular chromosome with a genome size of 736,465 bp, a G + C content of 66.34%, a coding ratio of 89.80%, and a protein-coding gene of 442. The NR database identified about 4284 genes among Stenotrophomonas spp. and S. geniculata, sharing the maximum number of 1277 genes with the MK2 strain. In COG annotation, most gene percentage was linked to general functions. In KEGG annotations, the majority of genes are associated with metabolism. According to the GO analysis, the maximum number of genes involved in the molecular process was linked to catalytic and transporter activity. CAZymes (carbohydrate-active enzymes) showed that enzymes related to glycosyl transferases (48), carbohydrate esterases (54), and glycoside hydrolases (51) are involved in the non-ribosomal synthesis of secondary metabolites. The PHI database showed that in strain MK2, the reduced virulence was 68 protein counts, and similarly unaffected pathogenicity protein counts were 52. AntiSMASH analysis for biosynthesis-related gene clusters involved in the production of secondary metabolites showed ten gene clusters coded for 2,3-dihydroxybenzoylserine, griseobactin, fuscachelin, benarthin, mirubactin, myxochelin, and bacillibactin. The MK2 strain could be a potent biocontrol agent for postharvest diseases.