The P. insidiosum strains Pi057C3 and Pi050C3 (also known as ATCC90586), classified in the phylogenetic clade-III, were isolated from human pythiosis patients in Thailand and the United States, respectively. Species and genotype identification of these organisms was achieved by rDNA sequence homology analysis [5, 6]. The organisms were incubated in Sabouraud dextrose broth and shaken at 37 °C for 7 days. The organism was harvested for genomic DNA (gDNA) extraction using the optimized method developed for P. insidiosum [15]. The obtained gDNA (300 ng) from each P. insidiosum strain was subjected to the library construction using an MGI Eazy FS Library Prep Kit (MGI Tech, Shenzhen, China) following the company’s instruction. Employing the manufacturer’s protocol, the 150-bp paired-end sequencing was conducted on an MGISEQ-2000RS sequencer to generate the shotgun genome sequences.
In total, 46,422,128 reads comprising 6,963,319,140 bases from strain Pi057C3 and 66,245,520 reads comprising 9,936,827,970 bases from strain Pi050C3 were obtained. All cleaned reads were de novo sequence assembled using SPAdes v3.14.0 [16] and its default settings, except the size of k-mers which was adjusted to k21, k33, k55, k77, and k99. As a result, a draft assembled genome of strain Pi057C3 contained 14,134 contigs with an average length of 3,010 bases (range: 200 – 937,540), N50 of 241, L50 of 45,748, total bases of 42,546,169, CG content of 57.6%, and genome coverage of 164x, whereas that of strain Pi050C3 contained 14,511 contigs with an average length of 2,984 bases (range: 200 – 964,331), N50 of 245, L50 of 45,208, total bases of 43,294,389, CG content of 57.7%, and genome coverage of 230x. The gene prediction software Augustus v3.3.3 [17] assigned 12147 and 12249 open reading frames (ORFs) in the genomes of strains Pi057C3 and Pi050C3, respectively. The assembled genome sequences have been stored in the National Center for Biotechnology Information (NCBI), and DNA Data Bank of Japan (DDBJ) databases and are publicly accessible via the accession numbers JAKCXL000000000.1 (strain Pi057C3) and JAKCXM000000000.1 (strain Pi050C3) (Table 1).
In summary, the genomes of P. insidiosum strains Pi057C3 (genome size: 42.5 Mb) and PI050C3 (genome size: 43.3 Mb) isolated from Thai and American patients with pythiosis have been sequenced and become publicly available. These genome data will be analyzed as a part of our population genomic study to elucidate the genome-scale biodiversity of this pathogen.
Table 1: Overview of data files/data sets.
Label
|
Name of data file/data set
|
File types
(file extension)
|
Data repository and identifier (DOI or accession number)
|
Accession number
|
Data file 1
|
Pythium insidiosum strain Pi057C3, whole genome shotgun sequencing project
|
FASTA
|
GenBank (https://www.ncbi.nlm.nih.gov/nuccore/JAKCXM000000000.1) [18]
|
JAKCXM000000000.1
|
Data file 2
|
Pythium insidiosum strain Pi050C3 (ATCC90586), whole genome shotgun sequencing project
|
FASTA
|
GenBank (https://www.ncbi.nlm.nih.gov/nuccore/JAKCXL000000000.1) [19]
|
JAKCXL000000000.1
|