Phytophthora database: A forensic database supporting the identification and monitoring of phytophthora

Jongsun Park, Bongsoo Park, Narayanan Veeraraghavan, Kyongyong Jung, Yong Hwan Lee, Jaime E. Blair, David Michael Geiser, Scott Alan Isard, Michele A. Mansfield, Ekaterina Nikolaeva, Sook Young Park, Joseph Russo, Seong H. Kim, Matthew Greene, Kelly L. Ivors, Yilmaz Balci, Masoomeh Peiman, Donald C. Erwin, Michael D. Coffey, Amy RossmanDavid Farr, Erica Cline, Niklaus J. Grünwald, Douglas G. Luster, Julia Schrandt, Frank Martin, Olaf K. Ribeiro, Izabela Makalowska, Seogchan Kang

Research output: Contribution to journalArticle

41 Citations (Scopus)

Abstract

Phytophthora spp. represent a serious threat to agricultural and ecological systems. Many novel Phytophthora spp. have been reported in recent years, which is indicative of our limited understanding of the ecology and diversity of Phytophthora spp. in nature. Systematic cataloging of genotypic and phenotypic information on isolates of previously described species serves as a baseline for identification, classification, and risk assessment of new Phytophthora isolates. The Phytophthora Database (PD) was established to catalog such data in a web-accessible and searchable format. To support the identification of new Phytophthora isolates via comparison of their sequences at one or more loci with the corresponding sequences derived from the isolates archived in the PD, we generated and deposited sequence data from more than 1,500 isolates representing the known diversity in the genus. Data search and analysis tools in the PD include BLAST, Phyloviewer (a program for building phylogenetic trees using sequences of selected isolates), and Virtual Gel (a program for generating expected restriction patterns for given sequences). The PD also provides a customized means of storing and sharing data via the web. The PD serves as a model that easily can be adopted to develop databases for other important pathogen groups.

Original languageEnglish (US)
Pages (from-to)966-972
Number of pages7
JournalPlant disease
Volume92
Issue number6
DOIs
StatePublished - Jun 1 2008

Fingerprint

Phytophthora
monitoring
forensic sciences
risk assessment
gels
ecology
loci
pathogens
phylogeny

All Science Journal Classification (ASJC) codes

  • Agronomy and Crop Science
  • Plant Science

Cite this

Park, Jongsun ; Park, Bongsoo ; Veeraraghavan, Narayanan ; Jung, Kyongyong ; Lee, Yong Hwan ; Blair, Jaime E. ; Geiser, David Michael ; Isard, Scott Alan ; Mansfield, Michele A. ; Nikolaeva, Ekaterina ; Park, Sook Young ; Russo, Joseph ; Kim, Seong H. ; Greene, Matthew ; Ivors, Kelly L. ; Balci, Yilmaz ; Peiman, Masoomeh ; Erwin, Donald C. ; Coffey, Michael D. ; Rossman, Amy ; Farr, David ; Cline, Erica ; Grünwald, Niklaus J. ; Luster, Douglas G. ; Schrandt, Julia ; Martin, Frank ; Ribeiro, Olaf K. ; Makalowska, Izabela ; Kang, Seogchan. / Phytophthora database : A forensic database supporting the identification and monitoring of phytophthora. In: Plant disease. 2008 ; Vol. 92, No. 6. pp. 966-972.
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abstract = "Phytophthora spp. represent a serious threat to agricultural and ecological systems. Many novel Phytophthora spp. have been reported in recent years, which is indicative of our limited understanding of the ecology and diversity of Phytophthora spp. in nature. Systematic cataloging of genotypic and phenotypic information on isolates of previously described species serves as a baseline for identification, classification, and risk assessment of new Phytophthora isolates. The Phytophthora Database (PD) was established to catalog such data in a web-accessible and searchable format. To support the identification of new Phytophthora isolates via comparison of their sequences at one or more loci with the corresponding sequences derived from the isolates archived in the PD, we generated and deposited sequence data from more than 1,500 isolates representing the known diversity in the genus. Data search and analysis tools in the PD include BLAST, Phyloviewer (a program for building phylogenetic trees using sequences of selected isolates), and Virtual Gel (a program for generating expected restriction patterns for given sequences). The PD also provides a customized means of storing and sharing data via the web. The PD serves as a model that easily can be adopted to develop databases for other important pathogen groups.",
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Park, J, Park, B, Veeraraghavan, N, Jung, K, Lee, YH, Blair, JE, Geiser, DM, Isard, SA, Mansfield, MA, Nikolaeva, E, Park, SY, Russo, J, Kim, SH, Greene, M, Ivors, KL, Balci, Y, Peiman, M, Erwin, DC, Coffey, MD, Rossman, A, Farr, D, Cline, E, Grünwald, NJ, Luster, DG, Schrandt, J, Martin, F, Ribeiro, OK, Makalowska, I & Kang, S 2008, 'Phytophthora database: A forensic database supporting the identification and monitoring of phytophthora', Plant disease, vol. 92, no. 6, pp. 966-972. https://doi.org/10.1094/PDIS-92-6-0966

Phytophthora database : A forensic database supporting the identification and monitoring of phytophthora. / Park, Jongsun; Park, Bongsoo; Veeraraghavan, Narayanan; Jung, Kyongyong; Lee, Yong Hwan; Blair, Jaime E.; Geiser, David Michael; Isard, Scott Alan; Mansfield, Michele A.; Nikolaeva, Ekaterina; Park, Sook Young; Russo, Joseph; Kim, Seong H.; Greene, Matthew; Ivors, Kelly L.; Balci, Yilmaz; Peiman, Masoomeh; Erwin, Donald C.; Coffey, Michael D.; Rossman, Amy; Farr, David; Cline, Erica; Grünwald, Niklaus J.; Luster, Douglas G.; Schrandt, Julia; Martin, Frank; Ribeiro, Olaf K.; Makalowska, Izabela; Kang, Seogchan.

In: Plant disease, Vol. 92, No. 6, 01.06.2008, p. 966-972.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Phytophthora database

T2 - A forensic database supporting the identification and monitoring of phytophthora

AU - Park, Jongsun

AU - Park, Bongsoo

AU - Veeraraghavan, Narayanan

AU - Jung, Kyongyong

AU - Lee, Yong Hwan

AU - Blair, Jaime E.

AU - Geiser, David Michael

AU - Isard, Scott Alan

AU - Mansfield, Michele A.

AU - Nikolaeva, Ekaterina

AU - Park, Sook Young

AU - Russo, Joseph

AU - Kim, Seong H.

AU - Greene, Matthew

AU - Ivors, Kelly L.

AU - Balci, Yilmaz

AU - Peiman, Masoomeh

AU - Erwin, Donald C.

AU - Coffey, Michael D.

AU - Rossman, Amy

AU - Farr, David

AU - Cline, Erica

AU - Grünwald, Niklaus J.

AU - Luster, Douglas G.

AU - Schrandt, Julia

AU - Martin, Frank

AU - Ribeiro, Olaf K.

AU - Makalowska, Izabela

AU - Kang, Seogchan

PY - 2008/6/1

Y1 - 2008/6/1

N2 - Phytophthora spp. represent a serious threat to agricultural and ecological systems. Many novel Phytophthora spp. have been reported in recent years, which is indicative of our limited understanding of the ecology and diversity of Phytophthora spp. in nature. Systematic cataloging of genotypic and phenotypic information on isolates of previously described species serves as a baseline for identification, classification, and risk assessment of new Phytophthora isolates. The Phytophthora Database (PD) was established to catalog such data in a web-accessible and searchable format. To support the identification of new Phytophthora isolates via comparison of their sequences at one or more loci with the corresponding sequences derived from the isolates archived in the PD, we generated and deposited sequence data from more than 1,500 isolates representing the known diversity in the genus. Data search and analysis tools in the PD include BLAST, Phyloviewer (a program for building phylogenetic trees using sequences of selected isolates), and Virtual Gel (a program for generating expected restriction patterns for given sequences). The PD also provides a customized means of storing and sharing data via the web. The PD serves as a model that easily can be adopted to develop databases for other important pathogen groups.

AB - Phytophthora spp. represent a serious threat to agricultural and ecological systems. Many novel Phytophthora spp. have been reported in recent years, which is indicative of our limited understanding of the ecology and diversity of Phytophthora spp. in nature. Systematic cataloging of genotypic and phenotypic information on isolates of previously described species serves as a baseline for identification, classification, and risk assessment of new Phytophthora isolates. The Phytophthora Database (PD) was established to catalog such data in a web-accessible and searchable format. To support the identification of new Phytophthora isolates via comparison of their sequences at one or more loci with the corresponding sequences derived from the isolates archived in the PD, we generated and deposited sequence data from more than 1,500 isolates representing the known diversity in the genus. Data search and analysis tools in the PD include BLAST, Phyloviewer (a program for building phylogenetic trees using sequences of selected isolates), and Virtual Gel (a program for generating expected restriction patterns for given sequences). The PD also provides a customized means of storing and sharing data via the web. The PD serves as a model that easily can be adopted to develop databases for other important pathogen groups.

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JO - Plant Disease

JF - Plant Disease

SN - 0191-2917

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