Return of the Lemnaceae: duckweed as a model plant system in the genomics and postgenomics era

Abstract

The aquatic Lemnaceae family, commonly called duckweed, comprises some of the smallest and fastest growing angiosperms known on Earth. Their tiny size, rapid growth by clonal propagation, and facile uptake of labeled compounds from the media were attractive features that made them a well-known model for plant biology from 1950 to 1990. Interest in duckweed has steadily regained momentum over the past decade, driven in part by the growing need to identify alternative plants from traditional agricultural crops that can help tackle urgent societal challenges, such as climate change and rapid population expansion. Propelled by rapid advances in genomic technologies, recent studies with duckweed again highlight the potential of these small plants to enable discoveries in diverse fields from ecology to chronobiology. Building on established community resources, duckweed is reemerging as a platform to study plant processes at the systems level and to translate knowledge gained for field deployment to address some of society's pressing needs. This review details the anatomy, development, physiology, and molecular characteristics of the Lemnaceae to introduce them to the broader plant research community. We highlight recent research enabled by Lemnaceae to demonstrate how these plants can be used for quantitative studies of complex processes and for revealing potentially novel strategies in plant defense and genome maintenance.

Figure 1

The Lemnaceae family is a sister lineage to other extant monocot families that has readapted to an aquatic lifestyle. (A) Phylogenetic relationship between the greater duckweed (Spirodela, Lemnaceae, Alismatales) and other branches of the angiosperms. The genus names are shown immediately to the right of the tree diagram, followed by the family names. WGD events are shown in black circles at the approximate time during their evolutionary history. “A field in a flask”: a culture of Wo. globosa (B) or Sp. polyrhiza (C) plants in a flask of growth medium. (D) Turions are a dormant form of many Lemnaceae species that enable these simple plants to overwinter at the bottom of their resident water bodies. Pictured is a clone of Sp. polyrhiza under low phosphate conditions in the growth medium. A typical growing frond cluster is shown in the middle, surrounded by turions. DF, daughter frond; MF, mother frond; T, turion.

Figure 2

Morphological variations among diverse genera and species of duckweed. Six different species from four genera of duckweeds are shown to illustrate the various sizes and shapes of these aquatic plants. The genome sequences of three of these clones (Sp. polyrhiza 9509, Le. minor 5500, and Wo. australiana 8730) are currently available.

Figure 3

Phylogeny and variations in genome size of different Lemnaceae species. Left: Evolutionary relationships between Lemnaceae species based on maximum likelihood analysis of concatenated alignment of 139 atpF-atpH and psbK-psbI intergenic spacer sequences from all 36 Lemnaceae species with taro (Colocasia esculenta) as an outgroup. Numbers in parentheses represent the number of clones analyzed. Species that could not be confidently resolved into a single clade were collapsed into a multispecies clade. One interesting observation is that the plastidic barcode sequences of Wo. brasiliensis consistently showed higher similarity to those of We. hyalina and We. rotunda, while morphologically it is distinctly a Wolffia species. This apparent discrepancy could be due to potential hybridization events in the past that resulted in the transfer of plastid genome sequences from a Wolffiella ancestor to a Wolffia lineage. Future genome sequencing of relevant species that may be involved will help clarify this issue. For a detailed methods description, see https://github.com/kenscripts/tpc_dw_review/. Right: The genome sizes for 28 selected species from six groups representing all five genera were estimated using several methods, and in some cases the genome sizes for a significant number of clones from the same species were measured (Sp. polyrhiza, Sp. Intermedia, La. punctata, and Le. minor). Genome size estimates were carried out by flow cytometry (FC, black outline), which requires the inclusion of accurate controls, or by K-mer frequency analysis (kmer, red outline), which relies on high quality short-read sequencing data. Numbers in red depict the number of clones used for each species in genome size estimations. The genome size of We. neotropica was estimated based on K-mer frequency.

Figure 4

Integration of metabolomics and genomics analysis in the Lemnaceae. (A) Comprehensive mass spectrometry-based metabolomics as a tool for pathway elucidation and characterization of biosynthetic enzymes and genes. Plant extracts are analyzed using high-resolution LC–MS (HR-LC–MS). Raw chromatograms typically consist of several thousand mass signals, and data can be deconvoluted using computation tools. (B) One method for compound identification from complex mixtures involves matching the mass spectra from an extract corresponding to a peak onto an entry in spectral libraries. An example for metabolite NP006950 (Weizmass library) is shown, illustrating that chromatographic retention, accurate mass, and mass fragmentation of a peak fraction in a Lemna gibba extract (upper black peak) matched a library entry (lower red peak) that can be assigned with high confidence (Shahaf et al., 2016). (C) These techniques, in combination with chemical classification, allow the metabolic landscape of Lemnaceae to be defined. (D) This knowledge can help identify metabolic genes/enzymes using either structure-based reaction prediction or genome mining approaches (such as metabolic gene cluster prediction that hints at possible biosynthetic pathways) as well as possible secondary metabolites (such as by correlation with the metabolomics dataset).