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Oomycete genomics

Oomycete genomics

Genome sequence drafts of a number of oomycete species have been completed and several others are in progress. The sequenced species include notorious plant pathogens of importance to world agriculture (see Lamour et al. 2007 for a recent review). Phytophthora capsici, Phytophthora infestans, and Phytophthora sojae infect diverse crops, such as pepper, potato, and soybean, respectively. Phytophthora ramorum affects native and ornamental woody plants resulting in environmental damage. The downy mildew, Hyaloperonospora arabidopsidis (previously H. parasitica), is a pathogen of Arabidopsis thaliana and figures prominently in research on this model plant.

Phytophthora infestans genome project


The 240 Mbp genome of Phytophthora infestans was sequenced, assembled and annotated by Chad Nusbaum's team at the MIT Broad Institute in collaboration with the P. infestans research community. An analysis of the genome sequence, authored by over 90 scientists from 34 institutions, was published in September 2009:

Haas, B.J., Kamoun, S., Zody, M.C., Jiang, R.H.Y., Handsaker, R.E., Cano, L.M., Grabherr, M., Kodira, C.D., Raffaele, S., Torto-Alalibo, T., Bozkurt, T.O., Ah-Fong, A.M.V., Alvarado, L., Anderson, V.L., Armstrong, M.R., Avrova, A., Baxter, L., Beynon, J., Boevink, P.C., Bollmann, S.R., Bos, J.I.B., Bulone, V., Cai, G., Cakir, C., Carrington, J.C., Chawner, M., Conti, L., Costanzo, S., Ewan, R., Fahlgren, N., Fischbach, M.A., Fugelstad, J., Gilroy, E.M., Gnerre, S., Green, P.J., Grenville-Briggs, L.J., Griffith, J., Grunwald, N.J., Horn, K., Horner, N.R., Hu, C.-H., Huitema, E., Jeong, D.-H., Jones, A.M.E., Jones, J.D.G., Jones, R.W., Karlsson, E.K., Kunjeti, S.G., Lamour, K., Liu, Z., Ma, L., MacLean, D., Chibucos, M.C., McDonald, H., McWalters, J., Meijer, H.J.G., Morgan, W., Morris, P.F., Munro, C.A., O'Neill, K., Ospina-Giraldo, M., Pinzon, A., Pritchard, L., Ramsahoye, B., Ren, Q., Restrepo, S., Roy, S., Sadanandom, A., Savidor, A., Schornack, S., Schwartz, D.C., Schumann, U.D., Schwessinger, B., Seyer, L., Sharpe, T., Silvar, C., Song, J., Studholme, D.J., Sykes, S., Thines, M., van de Vondervoort, P.J.I., Phuntumart, V., Wawra, S., Weide, R., Win, J., Young, C., Zhou, S., Fry, W., Meyers, B.C., van West, P., Ristaino, J., Govers, F., Birch, P.R.J., Whisson, S.C., Judelson, H.S., and Nusbaum, C. 2009. Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature 461:393-398. Supplementary Material

On September 18-19 2007, ~30 scientists attended the genome analysis meeting in Boston.

Listen to 'Broad's way', a musical celebration of the P. infestans genome sequence.

Press coverage of the P. infestans genome sequence paper

Nature Podcast interview, 10 September 2009

BBC world radio segment.

Chad Nusbaum talks about sequencing genome of Phytophthora infestans on NPR Science Friday.

Killer genes cause potato famine (BBC)

Save Our Spuds: Scientists answer call on potato blight (AFP)

Genome of potato blight organism decoded (Financial Times)

How blight becomes a killer (MSNBC)

Des scientifiques decodent le genome du mildiou de la pomme de terre.

Funded proposals

Nusbaum, H.C., Fry, W.E., Judelson, H.S., Ristaino, J., Kamoun, S. 2005. "Microbial Genome Sequencing: The genome sequence of Phytophthora infestans". NSF Emerging Frontiers and USDA National Research Initiative.

Nusbaum, H.C., Fry, W.E., Judelson, H.S., Kamoun, S. 2003. "Microbial Genome Sequencing: Phytophthora". NSF Emerging Frontiers.

Related links

Genome project portal at the Broad Institute.

Global Initiative on Late Blight

NSF Potato Functional Genomics

Molecular Plant Pathology - Pathogen Profile "Phytophthora infestans enters the genomics era"

Plant Disease article "Late blight of potato and tomato in the genomics era"

Ristaino Lab web page

Fry Lab web page

Judelson Lab web page

Kamoun Lab web page