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Title: The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization

Author
item CUOMO, CHRISTINA - MIT/HARVARD, MA
item GULDENER, ULRICH - INST BIOINFORMATICS GRMNY
item XU, JIN-RONG - PURDUE UNIV, IN
item TRAIL, FRANCES - MI STATE UNIV, LANSING MI
item TURGEON, B. GILLIAN - CORNELL UNIV, ITHACA NY
item DI PIETRO, ANTONIO - UNIV DE CORDOBA, SPAIN
item WALTON, JONATHAN - MI STATE UNIV, LANSING MI
item MA, LI-JUN - MIT/HARVARD, MA
item BAKER, SCOTT - PAC NW NATL LAB, WA
item REP, MARTIJN - UNIV OF AMERSTERDAM
item ADAM, GERHARD - BOKU, VIENNA AUSTRIA
item ANTONIW, JOHN - ROTHAMSTED RES, UK
item BALDWIN, THOMAS - ROTHAMSTED RES, UK
item CALVO, SARAH - MIT/HARVARD, MA
item CHANG, YUEH-LONG - UNIV OF MN, ST. PAUL MN
item DECAPRIO, DAVID - MIT/HARVARD, MA
item GALE, LIANE - UNIV OF MN, ST. PAUL MN
item GNERRE, SANTE - MIT/HARVARD, MA
item GOSWAMI, RUBELLA - UNIV OF MN, ST. PAUL MN
item HAMMOND-KOSACK, KIM - ROTHAMSTED RES, UK
item HARRIS, LINDA - AG & AGRI-FOOD CANADA
item Broz, Karen
item KENNELL, JACK - ST LOUIS UNIV, MO
item KROKEN, SCOTT - UNIV OF ARIZONA TUCSON
item MAGNUSON, JON - PAC NW NATL LAB, WA
item MANNHAUPT, GERTRUD - INST BIOINFORMATICS GRMNY
item MAUCELI, EVAN - MIT/HARVARD, MA
item MEWES, HANS-WERNER - INST BIOINFORMATICS GRMNY
item MITTERBAUER, RUDOLF - BOKU, VIENNA AUSTRIA
item MUEHLBAUER, GARY - UNIV OF MN, ST. PAUL MN
item MUNSTERKOTTER, MARTIN - INST BIOINFORMATICS GRMNY
item NELSON, DAVID - UNIV OF TN, MEMPHIS TN
item O Donnell, Kerry
item OUELLET, THERESE - AG & AGRI-FOOD CANADA
item QI, WEIHONG - MI STATE UNIV, LANSING MI
item QUESNEVILLE, HADI - INST JACQUES MONOD FRANCE
item RONCERO, M. ISABEL - UNIV DE CORDOBA, SPAIN
item SEONG, KYE-YONG - UNIV OF MN, ST. PAUL MN
item TETKO, IGOR - INST BIOINFORMATICS GRMNY
item URBAN, MARTIN - ROTHAMSTED RES, UK
item WAALWIJK, CEES - PLNT RES INTL NETHERLANDS
item Ward, Todd
item YAO, JIQIANG - PURDUE UNIV, IN
item BIRREN, BRUCE - MIT/HARVARD, MA
item Kistler, Harold

Submitted to: Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/4/2007
Publication Date: 9/7/2007
Citation: Cuomo, C.A., Guldener, U., Xu, J., Trail, F., Turgeon, B., Di Pietro, A., Walton, J.D., Ma, L., Baker, S.E., Rep, M., Adam, G., Antoniw, J., Baldwin, T., Calvo, S., Chang, Y., Decaprio, D., Gale, L., Gnerre, S., Goswami, R.S., Hammond-Kosack, K., Harris, L.J., Hilburn, K.L., Kennell, J., Kroken, S., Magnuson, J.K., Mannhaupt, G., Mauceli, E., Mewes, H., Mitterbauer, R., Muehlbauer, G., Munsterkotter, M., Nelson, D., O Donnell, K., Ouellet, T., Qi, W., Quesneville, H., Roncero, M.G., Seong, K., Tetko, I.V., Urban, M., Waalwijk, C., Ward, T.J., Yao, J., Birren, B.W., Kistler, H.C. 2007. The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization. Science. 317(5843):1400-1402.

Interpretive Summary: Fusarium graminearum is among the most economically important plant pathogens world wide and representative of the most destructive and widely studied genus of plant pathogenic fungi. In order to provide a comprehensive new resource for studying this group of toxigenic plant pathogens we sequenced and annotated the genome of F. graminearum. In addition, we compared this sequence to that of a second strain of F. graminearum, providing for the first analysis of genome wide diversity in this organism. A key finding of this study is that the genome contains regions of concentrated genetic diversity enriched for genes involved in plant interactions, indicating that the generation of diversity in plant-associated genes in adaptive. Another key finding is that the F. graminearum genome is nearly completely devoid of repetitive sequences, and that repeats are mutated by the process of repeat-induced point mutation (RIP), indicating that the evolution of diversity by gene duplication is highly constrained in this genome. This work will significantly impact nearly all research on F. graminearum by making available for the first time a comprehensive catalogue of genes and genomic variation within this important plant pathogen.

Technical Abstract: The filamentous fungus Fusarium graminearum is a major destructive pathogen of cultivated cereals. We have sequenced and annotated the F. graminearum genome, and found it includes very few repetitive sequences. We experimentally demonstrate that repeats are mutated by the process of repeat-induced point mutation (RIP), previously shown only in a few other fungi. RIP may impact gene duplication and evolution in F. graminearum, as very few highly identical paralogous genes are observed. With sequence from a second strain, we identified ~10,000 single nucleotide polymorphisms (SNPs) and found that discrete genomic regions, including all telomeres, are enriched for SNPs. Regions of high SNP frequency also display high divergence with other Fusarium species as well as high rates of recombination. Multiple sets of genes implicated in plant-fungus interactions are enriched in these high diversity regions, including predicted secreted proteins and genes specifically expressed in planta. The identification of these discrete regions of genome innovation provides a framework for understanding the evolution of F. graminearum related to interactions with its plant host.