NEW YORK (GenomeWeb News) – An international research team reported today in the advanced, online edition of Nature that they have sequenced the genome of a pathogenic water mold behind Ireland's 19th century potato famine.
The team, led by researchers at the Broad Institute and the UK's Sainsbury Laboratory, used whole-genome shotgun sequencing to sequence the 240 million base genome of Phytophthora infestans. In the process, they identified clues about how the pathogen infiltrates and infects host plants. Based on their findings, the team suspects the pest can evolve by quickly shuffling infection-related genes in repeat-rich, gene-poor parts of the genome.
Once classified as a fungus, more recent evidence suggests P. infestans actually belongs to a group of water molds, or oomycetes, that resemble fungi but are more closely related to the malaria parasite, brown algae, and diatoms. The pest infects potatoes, tomatoes, and similar plants, especially common in cool, wet conditions, causing a blight that can quickly destroy crops.
While best known for its role in the Irish potato famine, the pathogen contributes to large crop losses to this day — contributing to billions of dollars in potato crop losses each year. The pathogen is also notorious for its adaptability, rapidly gaining the ability to infect plants that were once P. infestans-resistant.
"This pathogen has an exquisite ability to adapt and change, and that's what makes it so dangerous," senior author Chad Nusbaum, co-director of the Broad Institute's Genome Sequencing and Analysis Program, said in a statement.
Nusbaum and his colleagues used whole-genome shotgun sequencing to sequence 229 million bases of the roughly 240 million base P. infestans genome to about eight times coverage.
The team also compared the P. infestans genome with those of the soybean pathogen P. sojae, which causes soybean root rot, and the tree pathogen P. ramorum, which causes sudden oak death. They found that the P. infestans genome was two-and-a-half to four times larger than the genomes of the other Phytophthora species.
Even so, the researchers noted, the potato blight pathogen did not show a significant increase in protein-coding genes over related species. They identified 17,797 protein-coding genes in the P. infestans genome — comparable to the 16,988 and 14,451 protein-coding genes detected in the P. sojae and P. ramorum genomes, respectively.
Rather, the team reported, the P. infestans genome expansion coincides with large increases in non-coding, repetitive DNA, which makes up nearly three-quarters of the genome.
Their subsequent experiments suggest the genome contains two types of DNA: gene-rich regions containing genes similar to those in other Phytophthera species, and gene-poor regions that change quickly and apparently contribute to plant infection. These regions apparently alternate with one another in the genome.
"Our findings suggest a 'two-speed' genome, meaning that different parts of the genome are evolving at different rates," co-lead author Sophien Kamoun, head of the Sainsbury Laboratory, said in a statement.
Based on these findings, the team speculated that so-called effector genes, which code for proteins excreted during plant infection, reside in repetitive parts of the P. infestans genome, where they can change quickly, contributing to the pathogen's adaptability and ability to infect plants.
"In contrast to the well-conserved regions where most genes are found, 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," co-lead author Brian Haas, the Broad's genome annotation, outreach, bioinformatics, and analysis manager, said in a statement. "As a result, these critical genes may be gained and lost so rapidly that the hosts simply can't keep up."
By sequencing more strains, Kamoun noted, it should be possible to not only determine whether that is the case, but also to gain additional insights into how the pathogen's genome responds to plants' immune responses. The researchers also hope that applying some of the knowledge gained by sequencing the P. infestans genome could point to ways of combating the pathogen.
"We now have a comprehensive view of its genome, revealing the unusual properties that drive its remarkable adaptability," Nusbaum said. "Hopefully, this knowledge can foster novel approaches to diagnose and respond to outbreaks."
The P. infestans genome sequence and annotation has been deposited to GenBank and are also available through the Broad's Phytophthora infestans database.