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

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.

Single nuclei transcriptome of the Lesser Duckweed Lemna minuta reveals cell trajectories for an entire plant

“…Consistent with the high copy number repeat k-mer frequency estimate, we identified that 58.2% of the genome was repeat sequence, which is double that of sp9509 and similar to W. australiana clone 8730 (wa8730) (Table 1; Supplemental Table S2). The lm5633 genome has a gypsy/copia ratio of ~2, similar to that found in sp9509, but distinct to wa8730 where the ratio is closer to 1 (Supplemental Table S2) (Michael et al, 2017; Michael et al, 2020). The larger genome size of lm5633 compared to sp9509 was primarily due to the increase in retained TE fragments, which is seen in the number of repeats found intervening in the evolutionarily conserved linkage of core circadian clock genes (Fig.…”

“…The larger genome size of lm5633 compared to sp9509 was primarily due to the increase in retained TE fragments, which is seen in the number of repeats found intervening in the evolutionarily conserved linkage of core circadian clock genes (Fig. 3B) (Michael et al, 2020). Similar to S. polyrhiza , we did not detect high-copy number centromere repeats (Michael et al, 2017), but we did identify telomere (AAACCCT) arrays that are longer (average=10 kb; longest 25 kb) than sp9509 (average=3 kb; longest=6 kb), yet shorter than what we have found in wa8730 (average=18 kb; longest=70 kb) (Supplemental Table S3) (Michael et al, 2020).…”

“…Gene families and overrepresented groups were determined with Orthofinder (v2.4.0) and CAFE5 (https://github.com/hahnlab/CAFE5). Genomes were accessed from Phytozome13 (https://phytozome-next.jgi.doe.gov/) or from specific publications such as the Colocasia esculenta (Taro) (Yin et al, 2021), Spirodela intermedia (Hoang et al, 2020), Spirodela polyrhiza clone 9509 (Hoang et al, 2018) and Wolffia australiana clone 8730 (Michael et al, 2020). Orthofinder results were parsed and used for CAFE5 by modifying the species tree with “make_ultrametric.py” and filtering orthocounts.tsv with “clade_and_size_filter.py”.…”

“…1). These basal monocots are some of the smallest and fastest growing plants on Earth, ranging in size from under a millimeter to centimeter, with some species doubling in under a day (Michael et al, 2020). There are five genera in the Lemnaceae with three having a flat leaf-like structure called a frond and root-like structures that may act as rudders or anchors ( Spirodela, Lemna and Landoltia ); the other two lack roots and are spherical or flat ( Wolffia and Wolffiella ).…”

Underwater CAM photosynthesis elucidated by Isoetes genome

“…We predicted 3,241 cycling genes, which is 10% of the expressed genes. While 10% is low compared to land plants that have been tested under this condition (LDHH)usually at 30-50% genes 8,33,34 , a recent study found a reduced number of cycling genes in another aquatic plant Wolffia australiana (duckweed/watermeal) 35 . Accordingly, decreased cycling may be a feature of aquatic plants.…”