The high-tech fight against vegetable fungi

A team of researchers has used bioinformatics technology to identify the genes of fungi that affect crops such as cucumber, watermelon, squash and rockmelon, in order to define the ideal treatment to attack the pathogens.

The fungi Pseudoperonospora humuli and Pseudoperonospora cubensis affect the plant family Cucurbitaceae and produce the downy mildew disease.

The purpose of the research is to understand at a genomic level the differences between these fungi. If expressed genes are identified in a fungus but not in another, they serve as markers that will allow the application of the appropriate treatment in these crops, said Dr Elsa Gongora Castillo, a plant biotechnologist who works at North Carolina State University.

“It’s a bit like human disease but in plants, to understand the pathogen and its interaction with the plant allows to develop a functional cure to treat the affected plants,” she explained.

The research seeks to define alternative systems beyond conventional fungicides to be applied to cucumber, pumpkin, cantaloupe and watermelon.

Samples of leaves from these plants are collected for in vitro cultures to isolate the fungi; then the DNA and RNA of fungi are extracted to sequence them and, through bioinformatic analysis, the researcher can determine the expression, the presence or absence of genes in the genomes of a species against each other.

“With the sequences of pathogens, I identify the genes and their expression level; in other words, to study genes, I compare two of them, in this case genes from Pseudoperonospora cubensis against Pseudoperonospora humuli, I see how many sequences there are for a given gene of P. cubensis and how many are there for the same gene P. humuli; if there is a difference in the number of sequences, we say that this gene is expressed or repressed; or if the gene is present or not in the genome,” explained Dr Gongora.

The analysis is expected to provide help in creating study models with which to understand other large-scale phenomena.