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

Abstract

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