Phytophthora infestans Assembly and Gene Annotation
About the Phytophtora infestans genome
Phytophthora infestans is the causal agent of the late potato blight disease and also infects tomatoes and other members of the Solanaceae. This oomycete caused several major crop losses including the Great Famine in Ireland. This pathogen can affect a large area reproducing asexually through spores. P. infestans sporangia are carried by the wind until they land in plant tissue. If the conditions are wet and cool they release their zoospores that can swim until encysting in the host. If conditions are warmer a germ tube from the sporangium can penetrate the plant.
Assembly
The assembly is available from the EMBL/Genbank/DDBJ databases under the accession GCA_000142945.1.
Annotation
The protein coding genes in this site are a direct import from Broad
Institute and MIT under the
"Phytophthora infestans Sequencing Project
". The data was imported
in December 2010. Non coding RNA genes have been annotated using
tRNAScan-SE (Lowe, T.M. and Eddy, S.R. 1997), RFAM (Griffiths-Jones et
al 2005), and RNAmmer (Lagesen K.,et al 2007); additional analysis tools
have also been applied.
Variation
Variation database contains data from the resequecing for 3 different strains PIC99189 (ERP000341) , 90128 (ERP000343) and T30-4 (ERP000344).
References
- Genome sequence and analysis of the Irish potato famine pathogen
Phytophthora
infestans.
Haas BJ, Kamoun S, Zody MC, Jiang RH, Handsaker RE, Cano LM, Grabherr M, Kodira CD, Raffaele S, Torto-Alalibo T et al. 2009. Nature. 461:393-398. - Identification and cloning of differentially expressed genes
involved in the interaction between potato and Phytophthora
infestans using a subtractive hybridization and cDNA-AFLP
combinational
approach.
Henriquez MA, Daayf F. 2010. J Integr Plant Biol. 52:453-467.
Picture credit: Thomas J. Volk, University of Wisconsin-La Crosse.
Other Data
The ESTs sequenced from different stages of pathogen infection were also downloaded from dbEST and aligned to the genome using exonerate.
More information
General information about this species can be found in Wikipedia.
Statistics
Summary
Assembly | ASM14294v1, INSDC Assembly GCA_000142945.1, Aug 2008 |
Database version | 112.1 |
Golden Path Length | 228,543,505 |
Genebuild by | BROAD |
Genebuild method | Import |
Data source | Broad Institute |
Gene counts
Coding genes | 17,785 |
Non coding genes | 1,668 |
Small non coding genes | 1,668 |
Pseudogenes | 6,183 |
Gene transcripts | 25,638 |
Other
Short Variants | 433,546 |