Researchers glimpse pathogen's bag of tricks

Healthy wheat (left) and Fusarium-infected wheat (right)Photo courtesy of Corby Kistler

The biological world is replete with pathogens that can shrewdly adapt their genes to outwit their hosts. Scientifically speaking, the challenge to overcoming these infectious agents is to identify — and neutralize — the genetic tricks they rely on most. Now, by decoding and analyzing the genome of Fusarium graminearum, a major plant pathogen, an international team of scientists has uncovered a surprising distribution of genetic variation with ties to pathogenesis.

F. graminearum preys primarily on wheat and barley. A member of a group of fungi known collectively as Fusarium, it represents one of the most significant plant pathogens worldwide. In the US this year, wheat harvests in Kansas and Nebraska were hit especially hard. F. graminearum not only damages crops, it also leaves behind toxins that can sicken humans and livestock who consume infected plants. Efforts to limit infection through newly developed anti-fungal compounds are costly and unfortunately, not entirely effective.

In the September 7 issue of the journal Science, researchers describe the results of an effort to decode the F. graminearum genome. The work is part of an ongoing collaboration between the Broad Institute of MIT and Harvard and the fungal research community to select and sequence the genomes of fungal organisms relevant to medicine, agriculture and industry. The F. graminearum genome project, funded by the National Research Initiative of the US Department of Agriculture Cooperative State Research, Education and Extension Service, was led by senior author H. Corby Kistler of the University of Minnesota together with first author Christina Cuomo of the Broad Institute of MIT and Harvard.

Perhaps the most significant discovery to emerge involves the genetic variability among different strains of F. graminearum. By comparing the newly sequenced fungal genome to a second one, derived from a separate strain analyzed by researchers at Syngenta, the scientists pinpointed more than 10,000 single letter DNA differences — called single nucleotide polymorphisms or SNPs — between the two strains.

What is remarkable about these SNPs is their distribution. Rather than being sprinkled evenly across the genome, they appear clustered in discrete locations. Such clustering may have functional consequences for the fungus. Many genes that are critical to the fungal interaction with host plants are found in the regions that are changing the most rapidly. These genes include potential virulence factors, including enzymes and secreted proteins that help puncture plant cells to enable the fungus to penetrate its host. “This high diversity in plant-associated genes may allow the fungus to rapidly adapt to a changing host environment” said first author Christina Cuomo, a research scientist at the Broad Institute.

Thanks to their genomic analyses, the researchers now hold a list of high-priority F. graminearum genes, helping to steer the course of future research. But, given the number of genes that made the cut — more than four hundred in total — that course will likely be a very busy one.

The F. graminearum genome project represents the first phase of a larger effort to decode and compare the genomes of three important Fusarium species, including F. graminearum, F. verticillioides, and F. oxysporum. The researchers at the Broad Institute who contributed to the study include Bruce Birren, head of the Broad’s Fungal Genome Initiative; members of the Genome Sequencing Platform; and Genome Biology Program scientists Sarah Calvo, Christina Cuomo, David DeCaprio, Sante Gnerre, Li-Jun Ma, and Evan Mauceli. Other primary contributors include co-authors Ulrich Guldener of MIPS, Jin-Rong Xu of Purdue University, and Frances Trail of Michigan State University.