Phytophthora database 2.0: Update and future direction

Bongsoo Park, Frank Martin, David Michael Geiser, Hye Seon Kim, Michele A. Mansfield, Ekaterina Nikolaeva, Sook Young Park, Michael D. Coffey, Joseph Russo, Seong H. Kim, Yilmaz Balci, Zoila Gloria Abad, Treena Burgess, Niklaus J. Grünwald, Kyeongchae Cheong, Jaeyoung Choi, Yong Hwan Lee, Seogchan Kang

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

The online community resource Phytophthora database (PD) was developed to support accurate and rapid identification of Phytophthora and to help characterize and catalog the diversity and evolutionary relationships within the genus. Since its release in 2008, the sequence database has grown to cover 1 to 12 loci for .2,600 isolates (representing 138 described and provisional species). Sequences of multiple mitochondrial loci were added to complement nuclear loci-based phylogenetic analyses and diagnostic tool development. Key characteristics of most newly described and provisional species have been summarized. Other additions to improve the PD functionality include: (i) geographic information system tools that enable users to visualize the geographic origins of chosen isolates on a global-scale map, (ii) a tool for comparing genetic similarity between isolates via microsatellite markers to support population genetic studies, (iii) a comprehensive review of molecular diagnostics tools and relevant references, (iv) sequence alignments used to develop polymerase chain reaction-based diagnostics tools to support their utilization and new diagnostic tool development, and (v) an online community forum for sharing and preserving experience and knowledge accumulated in the global Phytophthora community. Here we present how these improvements can support users and discuss the PDfs future direction.

Original languageEnglish (US)
Pages (from-to)1204-1208
Number of pages5
JournalPHYTOPATHOLOGY
Volume103
Issue number12
DOIs
StatePublished - Dec 1 2013

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Phytophthora
loci
sequence alignment
geographic information systems
provenance
population genetics
complement
polymerase chain reaction
microsatellite repeats
phylogeny

All Science Journal Classification (ASJC) codes

  • Agronomy and Crop Science
  • Plant Science

Cite this

Park, B., Martin, F., Geiser, D. M., Kim, H. S., Mansfield, M. A., Nikolaeva, E., ... Kang, S. (2013). Phytophthora database 2.0: Update and future direction. PHYTOPATHOLOGY, 103(12), 1204-1208. https://doi.org/10.1094/PHYTO-01-13-0023-R
Park, Bongsoo ; Martin, Frank ; Geiser, David Michael ; Kim, Hye Seon ; Mansfield, Michele A. ; Nikolaeva, Ekaterina ; Park, Sook Young ; Coffey, Michael D. ; Russo, Joseph ; Kim, Seong H. ; Balci, Yilmaz ; Abad, Zoila Gloria ; Burgess, Treena ; Grünwald, Niklaus J. ; Cheong, Kyeongchae ; Choi, Jaeyoung ; Lee, Yong Hwan ; Kang, Seogchan. / Phytophthora database 2.0 : Update and future direction. In: PHYTOPATHOLOGY. 2013 ; Vol. 103, No. 12. pp. 1204-1208.
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Park, B, Martin, F, Geiser, DM, Kim, HS, Mansfield, MA, Nikolaeva, E, Park, SY, Coffey, MD, Russo, J, Kim, SH, Balci, Y, Abad, ZG, Burgess, T, Grünwald, NJ, Cheong, K, Choi, J, Lee, YH & Kang, S 2013, 'Phytophthora database 2.0: Update and future direction', PHYTOPATHOLOGY, vol. 103, no. 12, pp. 1204-1208. https://doi.org/10.1094/PHYTO-01-13-0023-R

Phytophthora database 2.0 : Update and future direction. / Park, Bongsoo; Martin, Frank; Geiser, David Michael; Kim, Hye Seon; Mansfield, Michele A.; Nikolaeva, Ekaterina; Park, Sook Young; Coffey, Michael D.; Russo, Joseph; Kim, Seong H.; Balci, Yilmaz; Abad, Zoila Gloria; Burgess, Treena; Grünwald, Niklaus J.; Cheong, Kyeongchae; Choi, Jaeyoung; Lee, Yong Hwan; Kang, Seogchan.

In: PHYTOPATHOLOGY, Vol. 103, No. 12, 01.12.2013, p. 1204-1208.

Research output: Contribution to journalArticle

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T2 - Update and future direction

AU - Park, Bongsoo

AU - Martin, Frank

AU - Geiser, David Michael

AU - Kim, Hye Seon

AU - Mansfield, Michele A.

AU - Nikolaeva, Ekaterina

AU - Park, Sook Young

AU - Coffey, Michael D.

AU - Russo, Joseph

AU - Kim, Seong H.

AU - Balci, Yilmaz

AU - Abad, Zoila Gloria

AU - Burgess, Treena

AU - Grünwald, Niklaus J.

AU - Cheong, Kyeongchae

AU - Choi, Jaeyoung

AU - Lee, Yong Hwan

AU - Kang, Seogchan

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N2 - The online community resource Phytophthora database (PD) was developed to support accurate and rapid identification of Phytophthora and to help characterize and catalog the diversity and evolutionary relationships within the genus. Since its release in 2008, the sequence database has grown to cover 1 to 12 loci for .2,600 isolates (representing 138 described and provisional species). Sequences of multiple mitochondrial loci were added to complement nuclear loci-based phylogenetic analyses and diagnostic tool development. Key characteristics of most newly described and provisional species have been summarized. Other additions to improve the PD functionality include: (i) geographic information system tools that enable users to visualize the geographic origins of chosen isolates on a global-scale map, (ii) a tool for comparing genetic similarity between isolates via microsatellite markers to support population genetic studies, (iii) a comprehensive review of molecular diagnostics tools and relevant references, (iv) sequence alignments used to develop polymerase chain reaction-based diagnostics tools to support their utilization and new diagnostic tool development, and (v) an online community forum for sharing and preserving experience and knowledge accumulated in the global Phytophthora community. Here we present how these improvements can support users and discuss the PDfs future direction.

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Park B, Martin F, Geiser DM, Kim HS, Mansfield MA, Nikolaeva E et al. Phytophthora database 2.0: Update and future direction. PHYTOPATHOLOGY. 2013 Dec 1;103(12):1204-1208. https://doi.org/10.1094/PHYTO-01-13-0023-R