Phytophthora sojae Assembly and Gene Annotation

About the Phytophtora sojae genome

Phytophthora sojae is an oomycete and a soil-borne plant pathogen that causes 'damping off' seedlings and root rot of adult soybean plants. This is a prevalent disease in most soybean growing regions, and a major cause of crop loss. Central to the infection process are the zoopores that are produced in wet conditions and move in water attracted to soybean roots. Zoospores can attach to roots, germinate and infect the plant tissues. Diseased roots develop lesions that may spread up the stem and eventually kill the entire plant. Phytophthora sojae also produces oospores that can remain dormant in the soil over the winter, or longer, and germinate when conditions are favourable. Oospores may also be spread by animals or machinery.

Assembly

The genome was assembled by JGI and is also available from the EMBL/Genbank/DDBJ databases under the accession GCA_000149755.1.

Annotation

The protein coding genes in this site were imported from JGI. 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.

References

1. Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis.
   Tyler BM, Tripathy S, Zhang X, Dehal P, Jiang RH, Aerts A, Arredondo FD, Baxter L, Bensasson D, Beynon JL et al. 2006. Science. 313:1261-1266.
2. Expressed sequence tags from phytophthora sojae reveal genes specific to development and infection.
   Torto-Alalibo TA, Tripathy S, Smith BM, Arredondo FD, Zhou L, Li H, Chibucos MC, Qutob D, Gijzen M, Mao C et al. 2007. Mol. Plant Microbe Interact.. 20:781-793.

Picture credit: Nicholls H: Stopping the Rot. PLoS Biol 2/7/2004: e213M Reproduced courtesy of Matteo Garbelotto, UC Berkeley.

Other Data

Transcriptomics data from ten different developmental and infection stages of P.sojae (SRP006969) were also added as BAM tracks.

More information

General information about this species can be found in Wikipedia.