Tom Denyer1, Pin-Jou Wu1, Kelly Colt2, Bradley W. Abramson2,3, Zhili Pang4, Pavel Solansky1, Allen Mamerto2, Tatsuya Nobori2,5,6, Joseph R. Ecker2,5,6, Eric Lam4, Todd P. Michael2 and Marja C.P. Timmermans1 1Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany; 2Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA; 3Applied Sciences and Life Sciences Laboratory, Noblis, Reston, Virginia 20191, USA; 4Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA; 5Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, California 92037, USA; 6Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA Corresponding authors: eric.lamrutgers.edu, tmichaelsalk.edu, marja.timmermansuni-tuebingen.de Abstract

Single-cell genomics permits a new resolution in the examination of molecular and cellular dynamics, allowing global, parallel assessments of cell types and cellular behaviors through development and in response to environmental circumstances, such as interaction with water and the light–dark cycle of the Earth. Here, we leverage the smallest, and possibly most structurally reduced, plant, the semiaquatic Wolffia australiana, to understand dynamics of cell expression in these contexts at the whole-plant level. We examined single-cell-resolution RNA-sequencing data and found Wolffia cells divide into four principal clusters representing the above- and below-water-situated parenchyma and epidermis. Although these tissues share transcriptomic similarity with model plants, they display distinct adaptations that Wolffia has made for the aquatic environment. Within this broad classification, discrete subspecializations are evident, with select cells showing unique transcriptomic signatures associated with developmental maturation and specialized physiologies. Assessing this simplified biological system temporally at two key time-of-day (TOD) transitions, we identify additional TOD-responsive genes previously overlooked in whole-plant transcriptomic approaches and demonstrate that the core circadian clock machinery and its downstream responses can vary in cell-specific manners, even in this simplified system. Distinctions between cell types and their responses to submergence and/or TOD are driven by expression changes of unexpectedly few genes, characterizing Wolffia as a highly streamlined organism with the majority of genes dedicated to fundamental cellular processes. Wolffia provides a unique opportunity to apply reductionist biology to elucidate signaling functions at the organismal level, for which this work provides a powerful resource.

Footnotes

[Supplemental material is available for this article.]

Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.279091.124.

Freely available online through the Genome Research Open Access option.

Received February 9, 2024. Accepted June 20, 2024.