Expansion of the circadian transcriptome in Brassica rapa and genome-wide diversification of paralog expression patterns

Greenham, Kathleen; Sartor, Ryan C; Zorich, Stevan; Lou, Ping; Mockler, Todd C; McClung, C Robertson

doi:10.7554/eLife.58993

Like animals, plants have internal biological clocks that allow them to adapt to daily and yearly changes, such as day-night cycles or seasons turning. Unlike animals, however, plants cannot move when their environment becomes different, so they need to be able to weather these changes by adjusting which genes they switch on and off. To do this, plants keep track of how long days are using external cues such as light or temperature. One of the effects of climate change is that these cues become less reliable, making it harder for plants to adapt to their environment and survive. This is a potential problem for crop species, like Brassica rapa . This plant has many edible forms, including Chinese cabbage, oilseed, pak choi, and turnip. It is also a close relative of the well-studied model plant, Arabidopsis . Since evolving away from Arabidopsis , the genome of B. rapa tripled, meaning it has one, two, or three copies of each gene. This has allowed the extra gene copies to mutate and adapt to different purposes. The question is, what impact has this genome expansion had on the plant's biological clock? One way to find out is to perform RNA-sequencing experiments, which record the genes a plant is using at any one time. Here, Greenham, Sartor et al. report the results of a series of RNA-sequencing experiments performed every two hours across two days. Plants were first exposed to light-dark or temperature cycles and then samples were taken when the plants were in constant light and temperature. This revealed which genes B. rapa turned on and off in response to signals from the internal biological clock. It turns out that the biological clock of B. rapa controls close to three quarters of its genes. These genes showed distinct phases, increasing or decreasing in regular patterns. But the different copies of duplicated and triplicated genes did not necessarily all behave in the same way. Many of the copies had different rhythms, and some increased and decreased in patterns totally opposite to their counterparts. Not only did the daily patterns differ, but responses to stressors like drought were also altered. Comparing these patterns to the patterns seen in Arabidopsis revealed that often, one B. rapa gene behaved just like its Arabidopsis equivalent, while its copies had evolved new behaviors. The different behaviors of the copies of each gene in B. rapa relative to its biological clock allow this plant to grow in different environments with varying temperatures and day lengths. Understanding how these adaptations work opens new avenues of research into how plants detect and respond to environmental signals. This could help to guide future work into targeting genes to improve crop growth and stress resilience.

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