Whole Genome Sequence of a North American Strain of the Emerging Oomycete Pathogen of Mammals, Pythium insidiosum

The oomycete genus Pythium comprises more than 250 described species, most of which are saprobes or facultative plant pathogens that cause seed rot and damping-off, root, stem and fruit rot, foliar blight, and postharvest decay. Pythium insidiosum is the only Pythiumspecies that regularly infects mammals. It is the causal agent of pythiosis, a deadly disease of horses, dogs, cattle and other mammals in tropical and subtropical regions. Pythiosis also affects humans, and it was first reported in Thailand in 1985.

Whole genome sequencing was applied to P. insidiosum ATCC 200269 strain CDC-B5653, which is a strain isolated from an infected human in the United States. A combination of Illumina MiSeq (300 bp paired-end; 14 millions reads) and PacBio (10 kb fragment library; 356,001 reads) sequencing data was used to assemble the genome with SPAdes version 3.1.0, yielding a total size of 45.6 Mb contained in 8,992 contigs, N₅₀ of 13 Kb, maximum contig length of 148 Kb, and 57% G+C content. We used Augustus version 3.0.1 to predict genes ab initio, using a gene model previously described for Pythium. The genome contained 225 tRNA and 18,045 putative protein-coding genes. Reciprocal BLAST analysis with other seven Pythium genomes and nine other oomycetes indicated that P. insidiosum shares gene content most closely with P. aphanidermatum and P. arrhenomanes. Oomycete core orthologs (285 genes) provide insights into the phylogenetic relationships within the genus Pythium sensu lato.