Phytophthora infestans (ASM14294v1)

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).

Other Data

The ESTs sequenced from different stages of pathogen infection were also downloaded from dbEST and aligned to the genome using exonerate.

References

  1. 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.
  2. 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.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyASM14294v1, INSDC Assembly GCA_000142945.1, Aug 2008
Database version94.1
Base Pairs228,543,505
Golden Path Length228,543,505
Genebuild byBROAD
Genebuild methodImported from BROAD
Data sourceBroad Institute

Gene counts

Coding genes17,785
Non coding genes1,668
Small non coding genes1,668
Pseudogenes6,183
Gene transcripts25,638

Other

Short Variants433,546

About this species