A study conducted at the State University of Campinas (UNICAMP) in Brazil has identified orphan genes in wild sugarcane (Saccharum spontaneum), a species with exceptional resistance to biotic stresses such as nematodes, fungi, bacteria and other pests and diseases, and abiotic stresses such as cold, drought, salinity and nutrient-poor soil.
According to an article about the study published in the journal Frontiers in plant sciences the scientists in charge set out to see if the orphan genes in S. spontaneum played an important role in its stress-resistant properties.
All living things have genes that are very similar to the genome of other organisms. For example, plants share the genes involved in photosynthesis. On the other hand, most organisms also have orphan or lineage specific genes.
Orphan genes are found in a particular taxonomic group with no significant sequence similarity to genes from other lineages. They are sometimes referred to as taxonomically restricted genes for this reason.
For example, birds have some genes that are very different from those of mammals. Recent research has shown that even organisms from closely related species that belong to the same genus may have genes not shared by other species.
The researchers were interested in S. spontaneum because of features such as previous whole genome duplication events that resulted in multiple copies of the same gene. Scientific evidence suggests that orphan genes may originate in copies of pre-existing genes whose sequences change over time due to mutations and ultimately differ completely from the original sequences.
Another possible explanation for the origin of orphan genes could be the reorganization of genomic regions that do not code for genes, often seen in organisms with complex genomes, such as sugar cane.
“In the study, we identified parts of the genome of S. spontaneum that have no similarities with genes in any other organism. We think they may be responsible for physiological or species-specific traits,” said Cláudio Benício Cardoso -Silva, first author of the article. He conducted the project as a postdoctoral researcher at UNICAMP’s Center for Molecular Biology and Genetic Engineering (CBMEG).
“As these plants evolved, some genes were expressed to a greater or lesser extent in response to different types of abiotic stress, especially cold. This may mean that they are regulated as a result of this stress,” said Cardoso-Silva, whose postdoctoral fellow is the author of the study. research was supervised by Anete Pereira de Souza, professor of plant genetics at UNICAMP’s Institute of Biology and final author of the paper.
The researchers don’t believe they can categorically conclude that the orphan genes they identified make the plant more stress tolerant based on the results of the study. “But the fact that they are regulated under stress conditions serves as a warning to the possibility that they may play an important role in these processes,” he said.
The next step will be to experiment with plants subject to different types of stress to investigate how orphan genes behave in terms of expression compared to unstressed plants. Once the best candidate genes have been confirmed, biotechnology applications related to their insertion into commercially valuable plants can be studied, leading in the future to the possibility of developing sugar cane varieties that are more resistant to environmental pressures.
“We’ve spotlighted this opportunity for anyone who wants to use the data in the paper to advance the research, or for scientists working in gene transformation and editing, which is a different area of research, to explore one or two genes.” as candidates and do the validation,” said Cardoso-Silva, who continues to work with genomics at the State University of North Rio de Janeiro (UENF). “My current research focuses on the evolutionary aspect of gene family expansion,” he explained.
“Today we have CRISPR [the gene editing technique]which gives biotech professionals the chance to select genes for tolerance to drought, salinity, cold or heat at a time when crop resilience with less input is paramount,” Souza said.
More information:
Cláudio Benício Cardoso-Silva et al, Taxonomically restricted genes are associated with responses to biotic and abiotic stress in sugarcane (Saccharum spp.), Frontiers in plant sciences (2022). DOI: 10.3389/fpls.2022.923069