Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control

• Published in: Genome research Vol. 31; no. 2; pp. 225 - 238
• Main Authors: Michael, Todd P, Ernst, Evan, Hartwick, Nolan, Chu, Philomena, Bryant, Douglas, Gilbert, Sarah, Ortleb, Stefan, Baggs, Erin L, Sree, K Sowjanya, Appenroth, Klaus J, Fuchs, Joerg, Jupe, Florian, Sandoval, Justin P, Krasileva, Ksenia V, Borisjuk, Ljudmylla, Mockler, Todd C, Ecker, Joseph R, Martienssen, Robert A, Lam, Eric
• Format: Journal Article
• Language: English
• Published: United States Cold Spring Harbor Laboratory Press 01.02.2021
• Subjects: Asexual reproduction; BASIC BIOLOGICAL SCIENCES; Budding; Chloroplasts; Flowering; Gene expression; Genomes; Innate immunity; Leucine; Transcriptomes; Wolffia
• ISSN: 1088-9051; 1549-5469
• DOI: 10.1101/gr.266429.120

Rootless plants in the genus are some of the fastest growing known plants on Earth. have a reduced body plan, primarily multiplying through a budding type of asexual reproduction. Here, we generated draft reference genomes for (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 clones confirmed loss of several hundred genes that are highly conserved among flowering plants, including genes involved in root developmental and light signaling pathways. 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 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 and rice, many of the pathways associated with multicellular and developmental processes are not under TOD control in , where genes that cycle the conditions tested predominantly have carbon processing and chloroplast-related functions. The genome and TOD expression data set thus provide insight into the interplay between a streamlined plant body plan and optimized growth.