Whole genome sequence of the emerging oomycete pathogen Pythium insidiosum strain CDC-B5653 isolated from an infected human in the USA.

Pythium insidiosum ATCC 200269 strain CDC-B5653, an isolate from necrotizing lesions on the mouth and eye of a 2-year-old boy in Memphis, Tennessee, USA, was sequenced using a combination of Illumina MiSeq (300 bp paired-end, 14 millions reads) and PacBio (10  Kb fragment library, 356,001 reads). The sequencing data were assembled using SPAdes version 3.1.0, yielding a total genome size of 45.6 Mb contained in 8992 contigs, N50 of 13 Kb, 57% G + C content, and 17,867 putative protein-coding genes. This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession JRHR00000000.

Direct link to deposited data

http://www.ncbi.nlm.nih.gov/nuccore/JRHR00000000.1.

Experimental design, materials and methods

The oomycete genus Pythium comprises more than 250 described species [1], 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 [2]. P. insidiosum is the only Pythium species that causes disease in mammals. It is the causal agent of pythiosis, a deadly disease of horses, dogs, and other mammals in tropical and subtropical regions [3], [4]. Pythiosis also affects humans, and was first reported in Thailand in 1985 [5], [6].

Whole genome sequencing was applied to P. insidiosum ATCC 200269 strain CDC-B5653, which was originally isolated from necrotizing lesions on the mouth and eye of a 2-year-old boy in Memphis, Tennessee, USA. A combination of Illumina MiSeq (300 bp paired-end, 14 millions reads) and PacBio (10 Kb fragment library, 356,001 reads) sequencing data were used to assemble the genome using SPAdes version 3.1.0 [7], yielding a total size of 45.6 Mb contained in 8992 contigs, N50 of 13 Kb, maximum contig length of 148 Kb, and 57% G + C content. We used Augustus version 3.0.1 [8] to predict genes ab initio, using a gene model previously described for Pythium [9]. This genome contains 225 tRNA and 17,867 putative protein-coding genes. To create a representative set of orthologous groups for P. insidiosum and its closest relatives, genomes from the following seven Pythium species were included: P. ultimum var. ultimum, P. arrhenomanes, P. irregulare, P. aphanidermatum, P. iwayamai, P. ultimum var. sporangiiferum, and P. vexans (now Phytopythium vexans [10]). These genomes were downloaded from the Pythium Genome Database (http://pythium.plantbiology.msu.edu/download.shtml) [9], [11]. Reciprocal BLAST analysis on all genomes indicated that P. insidiosum shares 5922 unique orthologous genes with the other Pythium genomes and has 649 taxon specific genes. P. insidiosum shares more orthologs (233) with P. aphanidermatum and P. arrhenomanes than with the remaining Pythium species. These findings indicate that the three species are evolutionarily close to each other, which is consistent with estimates of Pythium phylogeny based on ITS sequences [1]. Further analysis will examine genes and gene families that distinguish the P. insidiosum genome from those of plant other pathogenic oomycetes.

Specifications
Organism/cell line/tissue	Pythium insidiosum strain CDC-B5653
Sex	Not applicable
Sequencer or array type	Illumina MiSeq and PacBio
Data format	Assembled
Experimental factors	CDC sample originally isolated from necrotizing lesions on the mouth and eye of a 2-year-old boy
Experimental features	Whole genome shotgun sequencing followed by genome assembly and gene description
Consent	Not applicable
Sample source location	ATCC 200269