Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control
- Todd P. Michael1,
- Evan Ernst2,3,11,
- Nolan Hartwick1,11,
- Philomena Chu4,12,
- Douglas Bryant5,13,
- Sarah Gilbert4,14,
- Stefan Ortleb6,
- Erin L. Baggs7,
- K. Sowjanya Sree8,
- Klaus J. Appenroth9,
- Joerg Fuchs6,
- Florian Jupe1,15,
- Justin P. Sandoval1,
- Ksenia V. Krasileva7,
- Ljudmylla Borisjuk6,
- Todd C. Mockler5,
- Joseph R. Ecker1,10,
- Robert A. Martienssen2,3 and
- Eric Lam4
- 1Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA;
- 2Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;
- 3Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;
- 4Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA;
- 5Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA;
- 6Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben 06466, Germany;
- 7Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94720, USA;
- 8Department of Environmental Science, Central University of Kerala, Periye, Kerala 671316, India;
- 9Friedrich Schiller University of Jena, Jena 07737, Germany;
- 10Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
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↵11 These authors contributed equally to this work.
Abstract
Rootless plants in the genus Wolffia are some of the fastest growing known plants on Earth. Wolffia have a reduced body plan, primarily multiplying through a budding type of asexual reproduction. Here, we generated draft reference genomes for Wolffia australiana (Benth.) Hartog & Plas, which has the smallest genome size in the genus at 357 Mb and has a reduced set of predicted protein-coding genes at about 15,000. Comparison between multiple high-quality draft genome sequences from W. australiana clones confirmed loss of several hundred genes that are highly conserved among flowering plants, including genes involved in root developmental and light signaling pathways. Wolffia has also lost most of the conserved nucleotide-binding leucine-rich repeat (NLR) genes that are known to be involved in innate immunity, as well as those involved in terpene biosynthesis, while having a significant overrepresentation of genes in the sphingolipid pathways that may signify an alternative defense system. Diurnal expression analysis revealed that only 13% of Wolffia genes are expressed in a time-of-day (TOD) fashion, which is less than the typical ∼40% found in several model plants under the same condition. In contrast to the model plants Arabidopsis and rice, many of the pathways associated with multicellular and developmental processes are not under TOD control in W. australiana, where genes that cycle the conditions tested predominantly have carbon processing and chloroplast-related functions. The Wolffia genome and TOD expression data set thus provide insight into the interplay between a streamlined plant body plan and optimized growth.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.266429.120.
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Freely available online through the Genome Research Open Access option.
- Received May 25, 2020.
- Accepted December 16, 2020.
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
