Draft genome sequences of the oomycete Pythium insidiosum strain CBS 573.85 from a horse with pythiosis and strain CR02 from the environment

Patumcharoenpol, Preecha; Rujirawat, Thidarat; Lohnoo, Tassanee; Yingyong, Wanta; Vanittanakom, Nongnuch; Kittichotirat, Weerayuth; Krajaejun, Theerapong

doi:10.1016/j.dib.2017.11.002

Cited by 20 publications

(17 citation statements)

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“…The genomic data of P. destruens represent a pathogen strain from the continent of Australia. Bioinformatics and comparative genomics analyses of the pathogen genome data reported by this and other studies [5][6][7][8][9][10] could provide insights into basic biology, genetic variation, host specificity, and underlying pathogenesis mechanism and lead to identifying potential target genes for the development of a novel control measure (i.e., drug and vaccine) against pythiosis.…”

Section: Objectivementioning

confidence: 82%

“…Detection and management of patients with pythiosis are complicated and problematic in the clinics due to the lack of efficient diagnostic and therapeutic tools, as well as basic knowledge of the disease. Genomes of 6 P. insidiosum strains isolated from different sources (i.e., human, horse, and water) and geographic locations in the continents of Asia and Americas (i.e., the United States, Costa Rica, Brazil, and Thailand) were sequenced and deposited in the public data repositories [5][6][7][8][9][10], and become an invaluable resource for bioinformatics and functional genetic studies of this organism.…”

Section: Objectivementioning

confidence: 99%

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Draft genome sequence of the oomycete Pythium destruens strain ATCC 64221 from a horse with pythiosis in Australia

et al. 2020

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Objectives: Genome sequences are a vital resource for accelerating the biological exploration of an organism of interest. Pythium destruens (a synonym of Pythium insidiosum) causes a difficult-to-treat infectious disease called pythiosis worldwide. Detection and management of pythiosis are challenging. Basic knowledge of the disease is lacking. Genomes of this organism isolated from different continents (i.e., Asia and the Americas) have been sequenced and publicly available. Here, we sequenced the genome of an Australian isolate of P. destruens. Genome data will facilitate the comparative analysis of this and related species at the molecular level. Data description: Genomic DNA of the P. destruens strain ATCC 64221, isolated from a horse with pythiosis in Australia, was used to prepare one paired-end library (with 180-bp insert) for next-generation sequencing, using the Illumina HiSeq 2500 short-read platform. Raw reads were cleaned and assembled by several bioinformatics tools. A total of 20,860,454 processed reads, accounted for 2,614,890,553 total bases, can be assembled into a 37.8-Mb genome, consisting 13,060 contigs (average length: 2896 bases; range: 300-142,967), N 50 of 11,370 bases, and 2.9% 'N' composition. The genome was determined 85.9% completeness, contained 14,424 predicted genes, and can be retrieved online at the NCBI/DDBJ databases under the accession number BCFQ01000000.1.

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Section: Objectivementioning

confidence: 82%

Section: Objectivementioning

confidence: 99%

Draft genome sequence of the oomycete Pythium destruens strain ATCC 64221 from a horse with pythiosis in Australia

et al. 2020

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“…The urease and urease accessory protein sequences of the plant Arabidopsis thaliana (accession numbers: (urease structure protein, URE); (urease accessory protein D, URED); (urease accessory protein F, UREF); and (urease accessory protein G, UREG)) ( Witte, Rosso & Romeis, 2005 ) were retrieved from the NCBI database. To assess the presence of the orthologs in P. insidiosum , all of these Arabidopsis proteins were TBLASTN searched against the genome of the P. insidiosum strain Pi35 (also known as Pi-S), and two Illumina-derived genomes of the P. insidiosum strains Pi07 (also known as CBS 573.85) and Pi45 ( Rujirawat et al, 2015 ; Kittichotirat et al, 2017 ; Patumcharoenpol et al, 2018 ), using the locally installed blast 2.2.28+ program ( ) and the cut-off E -value ≤10 −6 .…”

Section: Methodsmentioning

confidence: 99%

Biochemical and genetic analyses of the oomycetePythium insidiosumprovide new insights into clinical identification and urease-based evolution of metabolism-related traits

Krajaejun

Rujirawat

Kanpanleuk

et al. 2018

PeerJ

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The oomycete microorganism, Pythium insidiosum, causes the life-threatening infectious condition, pythiosis, in humans and animals worldwide. Affected individuals typically endure surgical removal of the infected organ(s). Detection of P. insidiosum by the established microbiological, immunological, or molecular methods is not feasible in non-reference laboratories, resulting in delayed diagnosis. Biochemical assays have been used to characterize P. insidiosum, some of which could aid in the clinical identification of this organism. Although hydrolysis of maltose and sucrose has been proposed as the key biochemical feature useful in discriminating P. insidiosum from other oomycetes and fungi, this technique requires a more rigorous evaluation involving a wider selection of P. insidiosum strains. Here, we evaluated 10 routinely available biochemical assays for characterization of 26 P. insidiosum strains, isolated from different hosts and geographic origins. Initial assessment revealed diverse biochemical characteristics across the P. insidiosum strains tested. Failure to hydrolyze sugars is observed, especially in slow-growing strains. Because hydrolysis of maltose and sucrose varied among different strains, use of the biochemical assays for identification of P. insidiosum should be cautioned. The ability of P. insidiosum to hydrolyze urea is our focus, because this metabolic process relies on the enzyme urease, an important virulence factor of other pathogens. The ability to hydrolyze urea varied among P. insidiosum strains and was not associated with growth rates. Genome analyses demonstrated that urease- and urease accessory protein-encoding genes are present in both urea-hydrolyzing and non-urea-hydrolyzing strains of P. insidiosum. Urease genes are phylogenetically conserved in P. insidiosum and related oomycetes, while the presence of urease accessory protein-encoding genes is markedly diverse in these organisms. In summary, we dissected biochemical characteristics and drew new insights into clinical identification and urease-related evolution of P. insidiosum.

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“…In this sense, the available oomycete genomes are mainly related to plant pathogens, which is a limitation for evolutionary studies . Moreover, when it comes to mammalian pathogens, for example Pythium , there is also a bias towards the number and origin of genome sequences available, both regarding geographic provenance and host …”

Section: Introductionmentioning

confidence: 98%

“…Moreover, when it comes to mammalian pathogens, for example Pythium, there is also a bias towards the number and origin of genome sequences available, both regarding geographic provenance and host. 14,16,17 Genetic studies have subdivided the genus Pythium into 10 distinct clades, named A to J, which include Pythium sensu lato. 8,10 Nevertheless, further phylogenetic analyses suggested that Pythium is a nonmonophyletic group with some species closely related to Peronosporales species.…”

Section: Introductionmentioning

confidence: 99%

New insights on evolutionary aspects of Pythium insidiosum and other peronosporaleans

Weiblen

Robe

Azevedo

et al. 2020

Mycoses

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Summary Background The evolution of pathogenic mechanisms is a major challenge, which requires a thorough comprehension of the phylogenetic relationships of pathogens. Peronosporaleans encompasses a heterogeneous group of oomycetes that includes some animal/human pathogens, like Pythium insidiosum. Objective We analysed here the phylogenetic positioning and other evolutionary aspects related to this species and other peronosporaleans, using a multi‐locus approach with one mitochondrial and three nuclear genes. Methodology Phylogenetic patterns of 55 oomycetes were inferred by maximum likelihood and Bayesian analysis, and a relaxed molecular clock method was applied to infer the divergence time of some peronosporaleans branches. Results Pythium insidiosum was monophyletic with a major and polytomous clade of American isolates; however, Pythium spp. was found to be paraphyletic with Phytopythium sp. and Phytophthora spp. In general, peronosporaleans subdivided into four lineages, one of which evidenced a close relationship of P insidiosum, P aphanidermatum and P arrhenomanes. This lineage diverged about 63 million years ago (Mya), whereas P insidiosum diversified at approximately 24 Mya. The divergence of American and Thai isolates seems to have occurred at approximately 17 Mya, with further American diversification at 2.4 Mya. Conclusion Overall, this study clarifies the phylogenetic relationships of P insidiosum regarding other peronosporaleans in a multi‐locus perspective, despite previous claims that phylogenomic analyses are needed to accurately infer the patterns and processes related to the evolution of different lineages in this group. Additionally, this is the first time that a molecular clock was applied to study the evolution of P insidiosum.

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Draft genome sequences of the oomycete Pythium insidiosum strain CBS 573.85 from a horse with pythiosis and strain CR02 from the environment

Cited by 20 publications

References 15 publications

Draft genome sequence of the oomycete Pythium destruens strain ATCC 64221 from a horse with pythiosis in Australia

Draft genome sequence of the oomycete Pythium destruens strain ATCC 64221 from a horse with pythiosis in Australia

Biochemical and genetic analyses of the oomycetePythium insidiosumprovide new insights into clinical identification and urease-based evolution of metabolism-related traits

New insights on evolutionary aspects of Pythium insidiosum and other peronosporaleans

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