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Home / Equine Research Bank / BMC Res Notes / Draft genome sequence of the oomycete Pythium destruens stra...
BMC research notes2020; 13(1); 329; doi: 10.1186/s13104-020-05168-1

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

Abstract: 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. Methods: 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 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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Publication Date: 2020-07-09 PubMed ID: 32646477PubMed Central: PMC7346664DOI: 10.1186/s13104-020-05168-1Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research sequenced the genome of the Pythium destruens species, which causes a disease called pythiosis, from an Australian horse. The scientists hope this will enhance understanding and management of the disease.

Methodology

  • The research began by extracting genomic DNA from the P. destruens strain ATCC 64221, which had been isolated from a horse suffering from pythiosis in Australia.
  • A paired-end library was prepared with a 180-bp insert using this DNA. This process effectively involved creating a collection of DNA fragments that can be sequenced using the next-generation technique.
  • The Illumina HiSeq 2500 short-read platform was used to sequence the genome. This is a high-throughput sequencing system capable of generating billions of DNA sequences in a single run.
  • The raw reads produced were cleaned and assembled using several bioinformatics tools. This step involved removing extraneous or corrupt data, and assembling the strings of DNA letters into a coherent sequence.

Findings

  • A total of 20,860,454 processed reads were created, accounting for 2,614,890,553 total bases. These were assembled into a 37.8-Mb genome.
  • The genome was made up of 13,060 contigs (continuous sequences of DNA), with an average length of 2896 bases and a range from 300 to 142,967 bases.
  • The genome had a ‘N’ composition of 2.9% and N of 11,370 bases. ‘N’ in DNA sequences usually represents any nucleotide, where the exact letter couldn’t be determined.
  • The completeness of the genome was determined to be 85.9%, meaning that almost all of the organism’s DNA was successfully sequenced.
  • 14,424 genes were predicted from the genome. Genes hold the information necessary to build and maintain an organism’s cells and pass genetic traits to offspring.
  • The genome sequence has been made publicly available online at the NCBI/DDBJ databases under the accession number BCFQ01000000.1.

Implications

  • Having the genome sequence of the P. destruens from Australia will help in the comparative analysis of this and related species at the molecular level.
  • This would eventually contribute to a better understanding of pythiosis – a disease currently difficult to treat, and knowledge about it is still lacking.

Cite This Article

APA
Krajaejun T, Kittichotirat W, Patumcharoenpol P, Rujirawat T, Lohnoo T, Yingyong W. (2020). Draft genome sequence of the oomycete Pythium destruens strain ATCC 64221 from a horse with pythiosis in Australia. BMC Res Notes, 13(1), 329. https://doi.org/10.1186/s13104-020-05168-1

Publication

BMC research notes
ISSN: 1756-0500
NlmUniqueID: 101462768
Country: England
Language: English
Volume: 13
Issue: 1
Pages: 329
PII: 329

Researcher Affiliations

Krajaejun, Theerapong
  • Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand. mr_en@hotmail.com.
Kittichotirat, Weerayuth
  • Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkhuntien, Bangkok, Thailand. weerayuth.kit@kmutt.ac.th.
Patumcharoenpol, Preecha
  • Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkhuntien, Bangkok, Thailand.
Rujirawat, Thidarat
  • Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
Lohnoo, Tassanee
  • Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
Yingyong, Wanta
  • Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.

MeSH Terms

  • Animals
  • Australia
  • Genome
  • High-Throughput Nucleotide Sequencing
  • Horse Diseases
  • Horses
  • Pythiosis
  • Pythium / genetics
  • Pythium / isolation & purification
  • Sequence Analysis, DNA

Grant Funding

  • CF_61007 / Mahidol University
  • RSA6280092 / Thailand Research Fund

Conflict of Interest Statement

The authors declare that they have no competing interests.

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Citations

This article has been cited 7 times.
  1. Kittichotirat W, Rujirawat T, Patumcharoenpol P, Krajaejun T. Comparative Genomic Analysis Reveals Gene Content Diversity, Phylogenomic Contour, Putative Virulence Determinants, and Potential Diagnostic Markers within Pythium insidiosum Traits. J Fungi (Basel) 2023 Jan 27;9(2).
    doi: 10.3390/jof9020169pubmed: 36836284google scholar: lookup
  2. Krajaejun T, Rujirawat T, Lohnoo T, Yingyong W, Sae-Chew P, Reamtong O, Kittichotirat W, Patumcharoenpol P. Secretome Profiling by Proteogenomic Analysis Shows Species-Specific, Temperature-Dependent, and Putative Virulence Proteins of Pythium insidiosum. J Fungi (Basel) 2022 May 20;8(5).
    doi: 10.3390/jof8050527pubmed: 35628782google scholar: lookup
  3. Yuan XL, Zhang CS, Kong FY, Zhang ZF, Wang FL. Genome Analysis of Phytophthora nicotianae JM01 Provides Insights into Its Pathogenicity Mechanisms. Plants (Basel) 2021 Aug 6;10(8).
    doi: 10.3390/plants10081620pubmed: 34451665google scholar: lookup
  4. Krajaejun T, Kittichotirat W, Patumcharoenpol P, Rujirawat T, Lohnoo T, Yingyong W. Genome data of four Pythium insidiosum strains from the phylogenetically-distinct clades I, II, and III. BMC Res Notes 2021 May 21;14(1):197.
    doi: 10.1186/s13104-021-05610-ypubmed: 34020710google scholar: lookup
  5. Mar Htun Z, Laikul A, Pathomsakulwong W, Yurayart C, Lohnoo T, Yingyong W, Kumsang Y, Payattikul P, Sae-Chew P, Rujirawat T, Jittorntam P, Jaturapaktrarak C, Chongtrakool P, Krajaejun T. Identification and Biotyping of Pythium insidiosum Isolated from Urban and Rural Areas of Thailand by Multiplex PCR, DNA Barcode, and Proteomic Analyses. J Fungi (Basel) 2021 Mar 24;7(4).
    doi: 10.3390/jof7040242pubmed: 33804838google scholar: lookup
  6. Krajaejun T, Patumcharoenpol P, Rujirawat T, Kittichotirat W, Tangphatsornruang S. MGI short-read genome assemblies of Pythium insidiosum (reclassified as Pythium periculosum) strains Pi057C3 and Pi050C3. BMC Res Notes 2023 Nov 6;16(1):316.
    doi: 10.1186/s13104-023-06587-6pubmed: 37932861google scholar: lookup
  7. Krajaejun T, Patumcharoenpol P, Rujirawat T, Kittichotirat W, Tangphatsornruang S, Lohnoo T, Yingyong W. PacBio long read-assembled draft genome of Pythium insidiosum strain Pi-S isolated from a Thai patient with pythiosis. BMC Res Notes 2023 Oct 13;16(1):271.
    doi: 10.1186/s13104-023-06532-7pubmed: 37833791google scholar: lookup
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