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 M. Geiser; Scott 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 Rossman; David Farr; Erica Cline; Niklaus J. Grünwald; Douglas G. Luster; Julia Schrandt; Frank Martin; Olaf K. Ribeiro; Izabela Makalowska; Seogchan Kang

doi:10.1094/PDIS-92-6-0966

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 M. Geiser, Scott 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 journal › Article › peer-review

46 Scopus citations

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 language	English (US)
Pages (from-to)	966-972
Number of pages	7
Journal	Plant Disease
Volume	92
Issue number	6
DOIs	https://doi.org/10.1094/PDIS-92-6-0966
State	Published - Jun 2008
Externally published	Yes

Keywords

Culture collection
Disease management
Invasive pathogens
Molecular diagnosis

ASJC Scopus subject areas

Agronomy and Crop Science
Plant Science

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10.1094/PDIS-92-6-0966

Cite this

Park, J., Park, B., Veeraraghavan, N., Jung, K., Lee, Y. H., Blair, J. E., Geiser, D. M., Isard, S., Mansfield, M. A., Nikolaeva, E., Park, S. Y., Russo, J., Kim, S. H., Greene, M., Ivors, K. L., Balci, Y., Peiman, M., Erwin, D. C., Coffey, M. D., ... Kang, S. (2008). Phytophthora database: A forensic database supporting the identification and monitoring of phytophthora. Plant Disease, 92(6), 966-972. https://doi.org/10.1094/PDIS-92-6-0966

Park, J, Park, B, Veeraraghavan, N, Jung, K, Lee, YH, Blair, JE, Geiser, DM, Isard, S, 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

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

year = "2008",

month = jun,

doi = "10.1094/PDIS-92-6-0966",

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AU - Park, Jongsun

AU - Park, Bongsoo

AU - Veeraraghavan, Narayanan

AU - Jung, Kyongyong

AU - Lee, Yong Hwan

AU - Blair, Jaime E.

AU - Geiser, David M.

AU - Isard, Scott

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

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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.

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KW - Invasive pathogens

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IS - 6

ER -

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

Abstract

Keywords

ASJC Scopus subject areas

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