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ToolsDenyer, Tom, Wu, Pin-Jou, Colt, Kelly, Abramson, Bradley W., Pang, Zhili, Solansky, Pavel, Mamerto, Allen, Nobori, Tatsuya, Ecker, Joseph R., Lam, Eric, Michael, Todd P. and Timmermans, Marja C. P. (2024) Streamlined spatial and environmental expression signatures characterize the minimalist duckweed Wolffia australiana. Genome Research, 34 (7). pp. 1106-1120. ISSN 1088-9051
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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.
| Item Type: | Article |
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| Additional Information: | Data access statement: All raw and processed sequencing data generated in this study have been submitted to the NCBI BioProject (https://www.ncbi .nlm.nih.gov/bioproject/) database under accession number PRJNA1124135. For individual SRA accession numbers, please see Supplemental Table S5. The scRNA-seq atlas can be easily explored via the interactive browser at ttps://www.zmbp-resources .uni-tuebingen.de/timmermans/plant-single-cell-browser/. The scRNA-seq Seurat objects and associated matrices are accessible via the same Browser. Funding Information: This work was supported by a grant from the Alexander von Humboldt Foundation to M.C.P.T. from the Tang Fund to T.P.M. and by the Max Planck Society (P.-J.W., through funding to Detlef Weigel). Research on duckweed in the Lam laboratory was supported by the U.S. Department of Energy, Office of Biological and Environmental Research program under award number DE-SC0018244. In addition, this work was supported by a Hatch project (12116) and a multistate capacity project (NJ12710) from the New Jersey Agricultural Experiment Station at Rutgers University (E.L., Z.P.). This work was also supported by the Waitt Advanced Biophotonics Core Facility of the Salk Institute with funding from the National Institutes of Health (National Cancer Institute, Cancer Center Support Grants: P30 CA01495, National Institute on Aging, San Diego Nathan Shock Center P30 AG068635) and the Waitt Foundation. |
| Uncontrolled Keywords: | genetics,genetics(clinical) ,/dk/atira/pure/subjectarea/asjc/1300/1311 |
| Faculty \ School: | Faculty of Science > The Sainsbury Laboratory |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 14 Jan 2025 01:00 |
| Last Modified: | 18 Jan 2025 01:08 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/98198 |
| DOI: | 10.1101/gr.279091.124 |
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