To look at the genetic information of specific, individual cells, researchers from the Molecular Physiology Group led by Prof. Julian Hibberd are using single-cell transcriptomics optimised for plant cells: “This method is standardised for mammalian cells, which don’t have walls like plant cells. It’s a whole different world to use it in plants,” says Tianshu Sun, the postdoctoral research associate responsible for this task.
This approach makes it possible to identify genes expressed in specific cells. In this study, Tianshu focuses on mesophyll and bundle sheath cells, which are found only in the leaf of C4 plants and are responsible for the increase in CO2 concentration that leads to higher photosynthetic efficiency.
Time and development in genomic data
Plant genomes are incredibly complex, which is why researchers need diverse analyses and perspectives to fully understand the data gathered in this field.
To enrich the collected data, the team adds a temporal perspective by measuring the pseudo-time, allowing them to see which genes might be expressed earlier or later as cells differentiate into specific types in younger leaves. The researchers are particularly interested in genes expressed earlier in this developmental gradient because they tend to regulate many other, more functional, later genes: they are higher up in the gene regulation hierarchy.
Pseudo-time simply gives us another angle to look at our data and see what else we can get from it. Ideally, it will influence how we eventually engineer more efficient sunflowers.
The value of collaborations: useful data and new ideas
Despite the advantages of Flaveria, the model plant used in GAIN4CROPS is not a popular species like Arabidopsis or rice: there is less genomic data available.
“The group of Prof. Benjamin Stich at the Heinrich-Heine-Universität Düsseldorf is currently working on the genome assembly of Flaveria, which is crucial to interpret our data,” she explains.
We need the genome as a map to place our data and understand its significance. At the same time, our work complements Benjamin’s team’s efforts as our common goal is to understand the key steps in the evolution of C4 photosynthesis.
Tianshu further adds that working with teams from the diverse GAIN4CROPS consortium helps her gain a fresh perspective on her work and generate new ideas. “When you’re working on genomics, sometimes you dive too deep into your data and often don’t see a validation of your ideas,” she admits. “Discussing my work with others is very rewarding and allows me to witness ideas in action – which is exciting!”