Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control
- Todd P. Michael1,9,
- Evan Ernst2,
- Nolan Hartwick1,
- Philomena Chu3,
- Douglas Bryant4,
- Sarah Gilbert3,
- Stefan Ortleb5,
- Erin L Baggs6,
- K. Sowjanya Sree7,
- Klaus J Appenroth8,
- Joerg Fuchs5,
- Florian Jupe1,
- Justin P Sandoval1,
- Ksenia V Krasileva6,
- Ljudmylla Borisjuk5,
- Todd C Mockler4,
- Joseph Ecker1,
- Robert A Martienssen2 and
- Eric Lam3
- 1 The Salk Institute for Biological Studies;
- 2 Cold Spring Harbor Laboratory;
- 3 Rutgers, The State University of New Jersey;
- 4 Donald Danforth Plant Science Center;
- 5 Leibniz Institute of Plant Genetics and Crop Plant Research;
- 6 University of California, Berkeley;
- 7 Central University of Kerala;
- 8 Friedrich Schiller University of Jena
Abstract
Rootless plants in the genus Wolffia are some of the fastest growing known plant 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 amongst flowering plants, including genes involved in root developmental and light signaling pathways. Wolffia has also lost most of the conserved 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 multi-cellular and developmental processes are not under TOD control in W. australiana, where genes that cycle the condition tested predominantly have carbon processing and chloroplast-related functions. The Wolffia genome and TOD expression dataset thus provide insight into the interplay between a streamlined plant body plan and optimized growth.
- Received May 25, 2020.
- Accepted December 16, 2020.
- Published by Cold Spring Harbor Laboratory Press
This manuscript is Open Access.
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International license), as described at http://creativecommons.org/licenses/by-nc/4.0/.
