Anyone who reads even a little about science and technology will already be familiar with the idea of genome sequencing. This process involves breaking down the body’s DNA into fragments to study their compositions or sequences. The fragments are then aligned and combined to reconstruct the original sequence.
But why sequence the body’s genome? What is the value for ordinary people and the world at large? The answers are obvious as soon as it comes to the medical field. Understanding what makes the disease a “tick” offers scientists a way to treat or prevent it. Sequencing the genome of a crop or animal can improve agricultural yields or make species more resilient in a changing climate.
It is a little more difficult to explain the value of genome sequencing of plant pathogens, the organisms that cause plant diseases. But this has become a critical part of the work of microbiologists and plant pathologists. And importantly, far beyond the laboratory: by carefully studying the genomes of plant pathogens, researchers have been able to design specific double-stranded RNA fungicides to short-circuit the ability of some pathogens to damage plants.
These fungicides are not yet commercially available, but they have huge potential – only the target species will be affected and so the process is likely to be more environmentally friendly than any involving chemical fungicides. This study has the potential to protect crops by benefiting agriculture and contributing to food security.
For the past 13 years, I have focused on sequencing the genome of a plant pathogen. This is where this scientific journey has led.
Pine trees are at risk
I sequenced the genome of a fungus called fusarium in 2009; this was the first sequence of the fungus genome to take place on the African continent.
I started studying this pathogen more than 20 years ago because it was killing seedlings in South African pine nurseries. fusarium causes resin cancer on pine trees, which causes the trees to emit resin or resin. In severe cases, the fungus causes the death of the tree. This fungus is considered the most important pathogenic threat to the global pine industry. It is also potentially devastating in some areas of the southern United States, Central America, Europe and Asia, where pines occur naturally.
Trees are extremely important for carbon capture. They also produce oxygen – it is believed that one tree can produce enough oxygen for four people a day. Trees also have tremendous economic value, providing timber for our homes and paper and packaging for many applications in our daily lives. It is difficult to estimate the total value of pine plantations worldwide, but it is estimated that South African industry contributes more than $ 2 billion to the country’s gross domestic product annually.
Genome sequencing was just the beginning. Subsequent studies published in 2021 include the killing of genes from the genome and the study of what happened. This process is a bit like first identifying and arranging all the parts, then removing those parts one by one to see how different they are for the functioning of the fungus. Sometimes we need to understand how gene products (proteins) interact with each other, and then more than one gene can be removed from the genome.
In this way, my colleagues and I can learn which genes are important for the processes that fusarium used to cause cancer of digestion and which are not. We are now working to target important genes in pathogen management studies.
This is a time-consuming job: this fungus has about 14,000 genes. This is more than the yeast used to ferment beer, which has 6,000 genes, but less than the estimated 25,000 genes in the human genome. Fortunately, technology is evolving rapidly to allow routine gene knockouts. This includes a protein that acts somewhat like DNA-specific scissors, allowing the deletion of a specific DNA sequence. The position at which the protein is cleaved is guided by the use of small pieces of RNA sequence that are identical to the target DNA sequence.
Read more: What is CRISPR, the gene editing technology that won the Nobel Prize in Chemistry?
Another of our key findings is this fusarium has acquired, through horizontal gene transfer from other organisms, a group of five genes that apparently enhance its growth.
This finding is very useful in developing a specific diagnostic tool using LAMP PCR (Loop-mediated isothermal amplification) to identify this pathogen. This is a special type of highly sensitive test that has been developed to allow the detection of pathogens on site. In addition, it does not require special training. This is useful because the trees have only recently been infected with fusarium may be asymptomatic. It is crucial to determine the presence of the pathogen as early as possible so that its spread can be better managed.
New skills, new opportunities
The increase in research sequencing the genomes of plant pathogens has also opened up opportunities for scientists to develop new skills. The data generated by genome sequencing is sometimes ahead of the number of available researchers to analyze it. During a pandemic blockade in South Africa, some students in my research program learned how to encode and develop skills in bioinformatics using computers to capture and analyze biological data instead of working in a laboratory.
With these new skills, as well as rapidly evolving technology, we can break Fusarium circinatum code once and for all. And this will help protect pine trees from a dangerous, expensive pathogen.