Sequence-ID
Choose a tab to identify species either by the ITS or cox spacer region using BLAST against our curated database:
ITS updates
April 5, 2011 (version ITS 1.3)
Added species:
- P. chrysanthemi
- P. elongata
- P. capensis
December 9, 2011 (version ITS 1.4)
Added species:
- P. litoralis
- P. gregata
- P. gibbosa
- P. thermophila
- P. elongata
- P. himalsilva
- P. pini
- P. glovera
- P. pinifolia
- P. arenaria
- P. constricta
- P. gemini
- P. obscura
April 12, 2012 (version ITS 1.5)
Added species:
- P. cinnamomi var. parvispora
- P. cinnamomi var. robiniae
- P. fluvialis
June 19, 2012 (version ITS 1.6)
Added species:
- P. bilorbang
August 8, 2012 (version ITS 1.7)
Added species:
- P. litchii
cox spacer updates
To be updated.
Sequence format
Sequences need to follow the FASTA format:
>Name of the sequence CCACACCTAAAAAACTTTCCACGTGAACCGTATCAACCCTTTTAGTTGGG GGTCTTGTACCCTATCATGGCGAATGTTTGGACTTCGGTCCGGGCGAGTA GCTTTTTGTTTTAAACCCATTTCACAATTCTGATTATACTGTGGGGACGA AAGTCTCTGCTTTTAACTAGATAGCAACTTTCAGCAGTGGATGTCTAGGC TCGCACATCGATGAAGAACGCTGCGAACTGCGATACGTAATGCGAATTGC AGGATTCAGTGAGTCATCGAAATTTTGAACGCATATTGCACTTCCGGGTT AGTCCTGGGAGTATGCCTGTATCAGTGTCCGTACATCAAACTTGGCTTTC TTCCTTCCGTGTAGTCGGTGGAGGATGTGCCAGATGTGAAGTGTCTTGCG TGTTGTCCTTCGGGTCGACTGCGAGTCCTTTTAAATGTACTGAACTGTAC TTCTCTTTGCTCGAAAAGCGTGGTGTTGCTGGTTGTGGAGGCTGCCTGCG TGGCCAGTCGGCGACCGGTTTGTCTGCTGCGGCGTTTAAAGGAGGAGTGT TCGATTCGCGGTATGGTTGGCTTCGGCTGAACAGGCGCTTATTGAATGCT TTTCCTGCTGTGGCGTGATGGGCTGGTGAACCGTAGCTGTGTTTGGCTTG GCTTTTGAATCGGTTTTGCTGTTGCGAAGTAGAGTGGCGGCTTCGGCTGT CGAGGGTCGATCCATTTTGGGAATTTTGTGTGCACTTCGGTGCGCATCTC AA
Databases
- ITS. The database contains internal transcribed spacer (ITS) region in FASTA format. The database is highly selective and generally only includes sequences that are associated with an original Phytophthora species desciption paper or the classic Phytophthora phylogenetics references by Cooke et al. (2000) and Martin & Tooley (2003) as well as Blair et al. (2008). Other sources may be cited if they present unique, peer-reviewed sequences of authenticated isolates. Novel taxa tentatively named are selectively included and labeled as P. taxon "X". The ITS database contains all clades recognized by Blair et al. (2008) and Cooke et al. (2000) as well as a few Pythium species for reference.
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cox spacer. The database contains cox spacer sequences in FASTA format. Sequence data was obtained courtesy of Phytophthora-DB and have been validated using sequences from Blair et al. (2008).
Citation
If you use this Phytophthora-ID for publishable research please cite the following reference:
Grünwald, N. J., Martin, F. N., Larsen, M. M., Sullivan, Press, C. M., Coffey, M. D., Hansen, E. M., and Parke, J. L. 2011. Phytophthora-ID.org: A sequence-based Phytophthora identification tool. Plant Disease 95: 337-342.