Illustration of a Thlaspi arvense leaf (green DNA fragments) infected with powdery mildew (white DNA fragments) and the DNA contained in it. Image credit: Galanti et al. (CC BY 4.0)
The genetic code of organisms is made of DNA, a molecule consisting of long sequences of four different base pairs. To gain insights into the organisms’ genetic information, it is necessary to establish which base pairs are in its DNA and in what order. This is known as ‘sequencing’, and it allows scientists to ‘read out’ the genetic information of an organism.
Technically, sequencing often involves shearing the organisms’ DNA into smaller pieces, so that the enzymes that do the sequencing can fully ‘read’ each molecule of DNA. However, when DNA is isolated from an organism, for example a plant, not only the DNA from the plant will be obtained. A small portion of DNA from other organisms, including viruses, bacteria, fungi and even insects that visited the plant will also be isolated and sequenced. These ‘non-target’ DNA fragments are usually discarded because they do not match the reference genome of the sequenced plant.
However, the genetic information of these other organisms can provide additional insights into the plant. This is particularly true when scientists sequence a large collection of individual plants from the same species. In this case, the DNA of other organisms isolated along with each plant’s own DNA can tell researchers about differences between the plants, such as whether they are able to resist a particular disease or establish symbiosis with a specific fungus.
Galanti et al. wanted to find out more about the genetic background and characteristics of a European plant called the field pennycress, Thlaspi arvense. To do this, they used the fact that plants from different regions would acquire different pests depending on their genetic background, and the fact that the DNA from different creatures living with the plant would be gathered when the plant DNA was collected.
First, Galanti et al. collected pennycress seeds from across Europe and grew them in the same environment, and then they let these plants be colonized by pests. Next, the researchers tested whether the DNA of pests living on the plants reflected differences in resistance to these pests, and whether that could explain why some plants were more or less resistant based on their geographic origin and genetic background.
Galanti et al. found that, in general, plants collected in warmer and thermally stable climates, where pests usually thrive, had fewer pests in the controlled environment, suggesting that these plants had developed resistance to the pests. With this information, the researchers were also able to unravel the genetic bases of resistance, finding genetic variants in the plants with pests that were close to defense genes.
These results highlight the potential of acquiring important insights from non-target DNA fragments, especially to study plant-pathogen interactions. This could be useful in plant breeding programmes.
