Wishing you a 'b-lighted' Halloween

The night before Halloween, I found myself desperately searching for a costume. After three years of donning humorous and cuddly attire, I gradually lost my self-perpetuated reputation for being hardcore This year I decided to go as the most badass entity imaginable: Phytophthora infestans, which literally translates to “growth-destroying attacker.” Although you may not know this fungus, you have probably heard of the havoc it wreaked on Ireland in during the Great Potato Famine. During the 1800s, millions of Irish people died or emigrated to avoid starvation caused by the potato devastation.

Today, Phytophthora is no less of a grim reaper. The disease it causes in potatoes accounts for $6.7 billion dollars in lost harvests annually. Like HIV, the fungus’ genome can change exceptionally quickly and can constantly adapt to overcome potatoes’ developed resistance to attacks.

Just when I thought I could not conjure a better costume, scientists working at UW thwarted my plans. I thought I was safe because sequencing, or finding the code of life for the Phytophthora infestans genome, has eluded scientists for many years.
A genome consists of the entire DNA of a species and stores the information needed to express proteins vital to each cellular process. To know thy enemy is to know its DNA sequence, and we did not know jack. Phytophthora’s genome is so riddled with repeating DNA that normal sequencing techniques did not make its genome any less enigmatic.
Repetition in Phytophthora’s DNA also contributes to its virulence. David Schwartz, a UW-Madison professor of genetics and chemistry, led a recent UW study to solve the fungal genome dilemma.

“The repeat-rich regions change rapidly over time, acting as a kind of incubator to enable the rapid birth and death of genes that are key to plant infection,” Schwartz said.
Schwartz said critical genes may be gained and lost so rapidly that the hosts simply cannot keep up.

While the positions of the smaller fragments of the Phytopthroa genome could be easily detmined by sequencing its DNA, the team had no idea where the pieces fit the larger genome at the start of the study.

To get around these constraints, Schwartz developed a technique called optical mapping in the 1990s. Optical mapping uses fluorescence microscopy to widen the scope of the sequencing analysis. Although this technique does not capture detail, it reveals large-scale DNA fragments and the relative size of DNA, making it easier to piece the puzzle together.

Combining optical mapping data with sequencing data, Schwartz’s team finally completed the genomic picture of the Late Blight culprit.

The result was a genome up to four times the size of Phytophthora’s relatives, mostly because of the repetitive regions. The repeats contain few genes, but these genes are specialized for infection. Comprehensive understanding of the genome could elicit further research that may curb the terror Phytophthora unleashes on potatoes.

With this newfound knowledge, my costume would not have been the scariest thing at the Third Eye Blind concert, but I can sleep better at night knowing the genomic discovery of Phytophthora infestans may open the door to eradicating Late Blight once and for all.