FREE SHIPPING over $40
OVER 9000 FIVE-STAR REVIEWS
5% OFF ALL SUBSCRIPTIONS
100% HAPPINESS GUARANTEE
Analyze Diet
0
Home / Equine Research Bank / BMC Res Notes / Data on whole genome sequencing of the oomycete Pythium insi...
BMC research notes2018; 11(1); 880; doi: 10.1186/s13104-018-3968-3

Data on whole genome sequencing of the oomycete Pythium insidiosum strain CBS 101555 from a horse with pythiosis in Brazil.

Abstract: The oomycete Pythium insidiosum infects humans and animals worldwide, and causes the life-threatening condition, called pythosis. Most patients lose infected organs or die from the disease. Comparative genomic analyses of different P. insidiosum strains could provide new insights into its pathobiology, and can lead to discovery of an effective treatment method. Several draft genomes of P. insidiosum are publicly available: three from Asia (Thailand), and one each from North (the United States) and Central (Costa Rica) Americas. We report another draft genome of P. insidiosum isolated from South America (Brazil), to serve as a resource for comprehensive genomic studies. Methods: In this study, we report genome sequence of the P. insidiosum strain CBS 101555, isolated from a horse with pythiosis in Brazil. One paired-end (180-bp insert) library of processed genomic DNA was prepared for Illumina HiSeq 2500-based sequencing. Assembly of raw reads provided genome size of 48.9 Mb, comprising 60,602 contigs. A total of 23,254 genes were predicted and classified into 18,305 homologous gene clusters. Compared with the reference genome (the P. insidiosum strain Pi-S), 1,475,337 sequence variants (SNPs and INDELs) were identified in the organism. The genome sequence data has been deposited in DDBJ under the accession numbers BCFP01000001-BCFP01060602.
Get Full Text
Publication Date: 2018-12-11 PubMed ID: 30537981PubMed Central: PMC6290497DOI: 10.1186/s13104-018-3968-3Google Scholar: Lookup
The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
LinkedInCopy
  • Journal Article

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.

The research is about sequencing the entire genome of the Pythium insidiosum strain CBS 101555, a microorganism that causes a deadly disease, pythiosis, in humans and animals. This particular strain is isolated from a horse in Brazil. Comparative genomic studies with existing genomes can potentially help understand the disease better and find an effective treatment.

Understanding Pythium insidiosum

  • Pythium insidiosum is an oomycete or water mold that is responsible for causing pythiosis in humans and animals.
  • The condition is serious, often leading to the loss of infected organs or even death in many cases.
  • Studying and comparing different P. insidiosum strains can provide insights into the pathobiology of the disease and possibly guide the discovery of effective treatment methods.

Current P. insidiosum genome data and the need for more

  • Presently, there are a few publicly available draft genomes of P. insidiosum. They are from North America (the United States), Central America (Costa Rica) and Asia (Thailand).
  • The researchers in this study have reported another draft genome, this time of a strain isolated from South America (Brazil). Having such diverse geographical information can lead to comprehensive genomic studies.

The genome sequencing process

  • The researchers prepared one paired-end library with a 180-bp insert from the genomic DNA of the P. insidiosum strain CBS 101555, which was isolated from a horse suffering from pythiosis in Brazil.
  • The sequencing was done using Illumina HiSeq 2500.
  • The assembly of raw reads provided a genome size of 48.9 Mb, comprised of 60,602 contigs.
  • In total, 23,254 genes were predicted and were classified into 18,305 homologous gene clusters.
  • When compared with the reference genome (P. insidiosum strain Pi-S), there were 1,475,337 sequence variants identified, which were made up of SNPs and INDELs.

Deposition of the genome sequence data

  • The genome sequence data that was produced from this research has been deposited in the DDBJ, with the accession numbers BCFP01000001-BCFP01060602.
  • This data will be beneficial for future research and comparative genomic studies aimed at better understanding the oomycete P. insidiosum and how it causes the disease pythiosis.

Cite This Article

APA
Krajaejun T, Kittichotirat W, Patumcharoenpol P, Rujirawat T, Lohnoo T, Yingyong W. (2018). Data on whole genome sequencing of the oomycete Pythium insidiosum strain CBS 101555 from a horse with pythiosis in Brazil. BMC Res Notes, 11(1), 880. https://doi.org/10.1186/s13104-018-3968-3

Publication

BMC research notes
ISSN: 1756-0500
NlmUniqueID: 101462768
Country: England
Language: English
Volume: 11
Issue: 1
Pages: 880
PII: 880

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
  • Brazil
  • Horses / parasitology
  • Pythiosis / parasitology
  • Pythium / genetics
  • Whole Genome Sequencing

Grant Funding

  • BRG5980009 / Thailand Research Fund
  • KMUTT 55th Anniversary Commemorative Fund / King Mongkut's University of Technology Thonburi
  • CF_60001 / Faculty of Medicine, Ramathibodi Hospital, Mahidol University
  • CF_61007 / Faculty of Medicine, Ramathibodi Hospital, Mahidol University

References

This article includes 23 references
  1. Gaastra W, Lipman LJ, De Cock AW, Exel TK, Pegge RB, Scheurwater J, Vilela R, Mendoza L. Pythium insidiosum: an overview.. Vet Microbiol 2010 Nov 20;146(1-2):1-16.
    doi: 10.1016/j.vetmic.2010.07.019pubmed: 20800978google scholar: lookup
  2. Mendoza L, Hernandez F, Ajello L. Life cycle of the human and animal oomycete pathogen Pythium insidiosum.. J Clin Microbiol 1993 Nov;31(11):2967-73.
    pmc: PMC266174pubmed: 8263182doi: 10.1128/jcm.31.11.2967-2973.1993google scholar: lookup
  3. Supabandhu J, Fisher MC, Mendoza L, Vanittanakom N. Isolation and identification of the human pathogen Pythium insidiosum from environmental samples collected in Thai agricultural areas.. Med Mycol 2008 Feb;46(1):41-52.
    doi: 10.1080/13693780701513840pubmed: 17885956google scholar: lookup
  4. Presser JW, Goss EM. Environmental sampling reveals that Pythium insidiosum is ubiquitous and genetically diverse in North Central Florida.. Med Mycol 2015 Sep;53(7):674-83.
    doi: 10.1093/mmy/myv054pubmed: 26229152google scholar: lookup
  5. Miller RI. Investigations into the biology of three 'phycomycotic' agents pathogenic for horses in Australia.. Mycopathologia 1983 Jan 17;81(1):23-8.
    doi: 10.1007/BF00443905pubmed: 6682179google scholar: lookup
  6. Zambrano CG, Fonseca AOS, Valente JSS, Braga CQ, Sallis ESV, Azevedo MI. Isolation and characterization of Pythium species from swampy areas in the Rio Grande do Sul, Brazil, and evaluation of pathogenicity in an experimental model.. Pesquisa Veterinária Brasileira 2017;37:459–464.
    doi: 10.1590/s0100-736x2017000500006google scholar: lookup
  7. Krajaejun T, Sathapatayavongs B, Pracharktam R, Nitiyanant P, Leelachaikul P, Wanachiwanawin W, Chaiprasert A, Assanasen P, Saipetch M, Mootsikapun P, Chetchotisakd P, Lekhakula A, Mitarnun W, Kalnauwakul S, Supparatpinyo K, Chaiwarith R, Chiewchanvit S, Tananuvat N, Srisiri S, Suankratay C, Kulwichit W, Wongsaisuwan M, Somkaew S. Clinical and epidemiological analyses of human pythiosis in Thailand.. Clin Infect Dis 2006 Sep 1;43(5):569-76.
    doi: 10.1086/506353pubmed: 16886148google scholar: lookup
  8. Kittichotirat W, Patumcharoenpol P, Rujirawat T, Lohnoo T, Yingyong W, Krajaejun T. Draft genome and sequence variant data of the oomycete Pythium insidiosum strain Pi45 from the phylogenetically-distinct Clade-III.. Data Brief 2017 Dec;15:896-900.
    doi: 10.1016/j.dib.2017.10.047pmc: PMC5681328pubmed: 29159227google scholar: lookup
  9. Patumcharoenpol P, Rujirawat T, Lohnoo T, Yingyong W, Vanittanakom N, Kittichotirat W, Krajaejun T. Draft genome sequences of the oomycete Pythium insidiosum strain CBS 573.85 from a horse with pythiosis and strain CR02 from the environment.. Data Brief 2018 Feb;16:47-50.
    doi: 10.1016/j.dib.2017.11.002pmc: PMC5847485pubmed: 29541657google scholar: lookup
  10. Rujirawat T, Patumcharoenpol P, Lohnoo T, Yingyong W, Lerksuthirat T, Tangphatsornruang S, Suriyaphol P, Grenville-Briggs LJ, Garg G, Kittichotirat W, Krajaejun T. Draft Genome Sequence of the Pathogenic Oomycete Pythium insidiosum Strain Pi-S, Isolated from a Patient with Pythiosis.. Genome Announc 2015 Jun 18;3(3).
    doi: 10.1128/genomeA.00574-15pmc: PMC4472884pubmed: 26089407google scholar: lookup
  11. Ascunce MS, Huguet-Tapia JC, Braun EL, Ortiz-Urquiza A, Keyhani NO, Goss EM. Whole genome sequence of the emerging oomycete pathogen Pythium insidiosum strain CDC-B5653 isolated from an infected human in the USA.. Genom Data 2016 Mar;7:60-1.
    doi: 10.1016/j.gdata.2015.11.019pmc: PMC4778604pubmed: 26981361google scholar: lookup
  12. Lohnoo T, Jongruja N, Rujirawat T, Yingyon W, Lerksuthirat T, Nampoon U, Kumsang Y, Onpaew P, Chongtrakool P, Keeratijarut A, Brandhorst TT, Krajaejun T. Efficiency comparison of three methods for extracting genomic DNA of the pathogenic oomycete Pythium insidiosum.. J Med Assoc Thai 2014 Mar;97(3):342-8.
    pubmed: 25123015
  13. Rujirawat T, Sridapan T, Lohnoo T, Yingyong W, Kumsang Y, Sae-Chew P, Tonpitak W, Krajaejun T. Single nucleotide polymorphism-based multiplex PCR for identification and genotyping of the oomycete Pythium insidiosum from humans, animals and the environment.. Infect Genet Evol 2017 Oct;54:429-436.
    doi: 10.1016/j.meegid.2017.08.004pubmed: 28826756google scholar: lookup
  14. Chaiprasert A, Krajaejun T, Pannanusorn S, Prariyachatigul C, Wanachiwanawin W, Sathapatayavongs B. Pythium insidiosum Thai isolates: molecular phylogenetic analysis.. Asian Biomed 2009;3:623–633.
  15. Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads.. EMBnet J 2011;17:10.
    doi: 10.14806/ej.17.1.200google scholar: lookup
  16. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs.. Genome Res 2008 May;18(5):821-9.
    doi: 10.1101/gr.074492.107pmc: PMC2336801pubmed: 18349386google scholar: lookup
  17. Holt C, Yandell M. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects.. BMC Bioinformatics 2011 Dec 22;12:491.
    doi: 10.1186/1471-2105-12-491pmc: PMC3280279pubmed: 22192575google scholar: lookup
  18. Kittichotirat W, Bumgarner RE, Asikainen S, Chen C. Identification of the pangenome and its components in 14 distinct Aggregatibacter actinomycetemcomitans strains by comparative genomic analysis.. PLoS One 2011;6(7):e22420.
    doi: 10.1371/journal.pone.0022420pmc: PMC3139650pubmed: 21811606google scholar: lookup
  19. Rujirawat T, Patumcharoenpol P, Lohnoo T, Yingyong W, Kumsang Y, Payattikul P, Tangphatsornruang S, Suriyaphol P, Reamtong O, Garg G, Kittichotirat W, Krajaejun T. Probing the Phylogenomics and Putative Pathogenicity Genes of Pythium insidiosum by Oomycete Genome Analyses.. Sci Rep 2018 Mar 7;8(1):4135.
    doi: 10.1038/s41598-018-22540-1pmc: PMC5841299pubmed: 29515152google scholar: lookup
  20. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA. The COG database: an updated version includes eukaryotes.. BMC Bioinformatics 2003 Sep 11;4:41.
    doi: 10.1186/1471-2105-4-41pmc: PMC222959pubmed: 12969510google scholar: lookup
  21. Galperin MY, Makarova KS, Wolf YI, Koonin EV. Expanded microbial genome coverage and improved protein family annotation in the COG database.. Nucleic Acids Res 2015 Jan;43(Database issue):D261-9.
    doi: 10.1093/nar/gkሣpmc: PMC4383993pubmed: 25428365google scholar: lookup
  22. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform.. Bioinformatics 2009 Jul 15;25(14):1754-60.
    doi: 10.1093/bioinformatics/btp324pmc: PMC2705234pubmed: 19451168google scholar: lookup
  23. Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing.. arXiv preprint 2012.

Citations

This article has been cited 10 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. Sridapan T, Krajaejun T. Nucleic Acid-Based Detection of Pythium insidiosum: A Systematic Review. J Fungi (Basel) 2022 Dec 23;9(1).
    doi: 10.3390/jof9010027pubmed: 36675848google scholar: lookup
  3. Yolanda H, Lohnoo T, Rujirawat T, Yingyong W, Kumsang Y, Sae-Chew P, Payattikul P, Krajaejun T. Selection of an Appropriate In Vitro Susceptibility Test for Assessing Anti-Pythium insidiosum Activity of Potassium Iodide, Triamcinolone Acetonide, Dimethyl Sulfoxide, and Ethanol. J Fungi (Basel) 2022 Oct 24;8(11).
    doi: 10.3390/jof8111116pubmed: 36354883google scholar: lookup
  4. 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
  5. Yolanda H, Krajaejun T. History and Perspective of Immunotherapy for Pythiosis. Vaccines (Basel) 2021 Sep 26;9(10).
    doi: 10.3390/vaccines9101080pubmed: 34696188google scholar: lookup
  6. 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
  7. 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
  8. Krajaejun T, Kittichotirat W, Patumcharoenpol P, Rujirawat T, Lohnoo T, Yingyong W. Draft genome sequence of the oomycete Pythium destruens strain ATCC 64221 from a horse with pythiosis in Australia. BMC Res Notes 2020 Jul 9;13(1):329.
    doi: 10.1186/s13104-020-05168-1pubmed: 32646477google scholar: lookup
  9. 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
  10. 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
Subscribe to our newsletter
Join 99,357 horse owners like you who receive our email updates on horse health and nutrition.