PAMDB, a multilocus sequence typing and analysis database and website for plant-associated microbes

Nalvo F. Almeida, Yan Shuangchun, Cai Rongman, Christopher R. Clarke, Cindy E. Morris, Norman W. Schaads, Erin L. Schuenzel, George H. Lacy, S. Xiaoan, Jeffrey B. Jones, Jose A. Castillo, Carolee Theresa Bull, Scotland Leman, David S. Guttman, Joao C. Setubal, Boris A. Vinatzer

Research output: Contribution to journalArticle

103 Citations (Scopus)

Abstract

Although there are adequate DNA sequence differences among plantassociated and plant-pathogenic bacteria to facilitate molecular approaches for their identification, identification at a taxonomic level that is predictive of their phenotype is a challenge. The problem is the absence of a taxonomy that describes genetic variation at a biologically relevant resolution and of a database containing reference strains for comparison. Moreover, molecular evolution, population genetics, ecology, and epidemiology of many plant-pathogenic and plant-associated bacteria are still poorly understood. To address these challenges, a database with web interface was specif cally designed for plant-associated and plant-pathogenic microorganisms. The Plant-Associated Microbes Database (PAMDB) comprises, thus far, data from multilocus sequence typing and analysis (MLST/MLSA) studies of Acidovorax citrulli, Pseudomonas syringae, Ralstonia solanacearum, and Xanthomonas spp. Using data deposited in PAMDB, a robust phylogeny of Xanthomonas axonopodis and related bacteria has been inferred, and the diversity existing in the Xanthomonas genus and in described Xanthomonas spp. has been compared with the diversity in P. syringae and R. solanacearum. Moreover, we show how PAMDB makes it easy to distinguish between different pathogens that cause almost identical diseases. The scalable design of PAMDB will make it easy to add more plant pathogens in the future.

Original languageEnglish (US)
Pages (from-to)208-215
Number of pages8
JournalPHYTOPATHOLOGY
Volume100
Issue number3
DOIs
StatePublished - Mar 1 2010

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microorganisms
Xanthomonas
Ralstonia solanacearum
Pseudomonas syringae
Acidovorax avenae subsp. citrulli
Xanthomonas axonopodis
plant pathogenic bacteria
multilocus sequence typing
bacteria
plant pathogens
epidemiology
population genetics
taxonomy
ecology
phenotype
nucleotide sequences
genetic variation
pathogens
phylogeny

All Science Journal Classification (ASJC) codes

  • Agronomy and Crop Science
  • Plant Science

Cite this

Almeida, N. F., Shuangchun, Y., Rongman, C., Clarke, C. R., Morris, C. E., Schaads, N. W., ... Vinatzer, B. A. (2010). PAMDB, a multilocus sequence typing and analysis database and website for plant-associated microbes. PHYTOPATHOLOGY, 100(3), 208-215. https://doi.org/10.1094/PHYTO-100-3-0208
Almeida, Nalvo F. ; Shuangchun, Yan ; Rongman, Cai ; Clarke, Christopher R. ; Morris, Cindy E. ; Schaads, Norman W. ; Schuenzel, Erin L. ; Lacy, George H. ; Xiaoan, S. ; Jones, Jeffrey B. ; Castillo, Jose A. ; Bull, Carolee Theresa ; Leman, Scotland ; Guttman, David S. ; Setubal, Joao C. ; Vinatzer, Boris A. / PAMDB, a multilocus sequence typing and analysis database and website for plant-associated microbes. In: PHYTOPATHOLOGY. 2010 ; Vol. 100, No. 3. pp. 208-215.
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Almeida, NF, Shuangchun, Y, Rongman, C, Clarke, CR, Morris, CE, Schaads, NW, Schuenzel, EL, Lacy, GH, Xiaoan, S, Jones, JB, Castillo, JA, Bull, CT, Leman, S, Guttman, DS, Setubal, JC & Vinatzer, BA 2010, 'PAMDB, a multilocus sequence typing and analysis database and website for plant-associated microbes', PHYTOPATHOLOGY, vol. 100, no. 3, pp. 208-215. https://doi.org/10.1094/PHYTO-100-3-0208

PAMDB, a multilocus sequence typing and analysis database and website for plant-associated microbes. / Almeida, Nalvo F.; Shuangchun, Yan; Rongman, Cai; Clarke, Christopher R.; Morris, Cindy E.; Schaads, Norman W.; Schuenzel, Erin L.; Lacy, George H.; Xiaoan, S.; Jones, Jeffrey B.; Castillo, Jose A.; Bull, Carolee Theresa; Leman, Scotland; Guttman, David S.; Setubal, Joao C.; Vinatzer, Boris A.

In: PHYTOPATHOLOGY, Vol. 100, No. 3, 01.03.2010, p. 208-215.

Research output: Contribution to journalArticle

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AU - Almeida, Nalvo F.

AU - Shuangchun, Yan

AU - Rongman, Cai

AU - Clarke, Christopher R.

AU - Morris, Cindy E.

AU - Schaads, Norman W.

AU - Schuenzel, Erin L.

AU - Lacy, George H.

AU - Xiaoan, S.

AU - Jones, Jeffrey B.

AU - Castillo, Jose A.

AU - Bull, Carolee Theresa

AU - Leman, Scotland

AU - Guttman, David S.

AU - Setubal, Joao C.

AU - Vinatzer, Boris A.

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Y1 - 2010/3/1

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Almeida NF, Shuangchun Y, Rongman C, Clarke CR, Morris CE, Schaads NW et al. PAMDB, a multilocus sequence typing and analysis database and website for plant-associated microbes. PHYTOPATHOLOGY. 2010 Mar 1;100(3):208-215. https://doi.org/10.1094/PHYTO-100-3-0208