The genome and preliminary single-nuclei transcriptome ofLemna minutareveals mechanisms of invasiveness

Abstract

The ability to trace every cell in some model organisms has led to the fundamental understanding of development and cellular function. However, in plants the complexity of cell number, organ size and developmental time makes this a challenge even in the diminutive model plant Arabidopsis (Arabidopsis thaliana). Duckweed, basal non-grass aquatic monocots, provide an opportunity to follow every cell of an entire plant due to their small size, reduced body plan, and fast clonal growth habit. Here we present a chromosome-resolved genome for the highly invasive Lesser Duckweed (Lemna minuta) and generate a preliminary cell atlas leveraging low cell coverage single-nuclei sequencing. We resolved the 360 megabase genome into 21 chromosomes, revealing a core non-redundant gene set with only the ancient tau whole genome duplication shared with all monocots, and paralog expansion as a result of tandem duplications related to phytoremediation. Leveraging SMARTseq2 single-nuclei sequencing, which provided higher gene coverage yet lower cell count, we profiled 269 nuclei covering 36.9% (8,457) of the L. minuta transcriptome. Since molecular validation was not possible in this non-model plant, we leveraged gene orthology with model organism single cell expression datasets, gene ontology, and cell trajectory analysis to define putative cell types. We found that the tissue that we computationally defined as mesophyll expressed high levels of elemental transport genes consistent with this tissue playing a role in L. minuta wastewater detoxification. The L. minuta genome and preliminary cell map provide a paradigm to decipher developmental genes and pathways for an entire plant.

Core circadian clock and light signaling genes brought into genetic linkage across the green lineage

“…However, despite the orthology of these sMYB– PRR gene pairs, these regions are not in syntenic blocks in Arabidopsis ( Lou et al, 2012 ). Similar sMYB– PRR linkages have been noted in other eudicot species such as cranberry and blueberry, and monocot species such as duckweed ( Wolffia , Lemna , Spirodela ; Michael et al, 2020 ; Abramson et al, 2022 ; Kawash et al, 2021 ). These results suggest the sMYB– PRR linkage is evolutionarily conserved and that it may predate the land plants.…”

Characterization of EDS1-independent plant defense responses against bacterial pathogens using Duckweed/Pseudomonaspathosystems

“…Illumina paired end reads were assembled with Spades (v3.14.0) with the default settings (Bankevich et al 2012). Resulting contigs were annotated using a pipeline consisting of four major steps: repeat masking, transcript assembly, gene model prediction, and functional annotation as described (Abramson et al 2021). Repeats were identified using EDTA (v1.9.8) (Ou et al 2019) and these repeats were used for softmasking.…”

“…Given the absence of the EDS1 pathway in S. polyrhiza (E. L. Baggs et al 2020), we hypothesized that duckweeds could be used as a model for understanding EDS1-independent innate immunity. Lemnaceae are globally distributed and only absent from the Arctic and Antarctica (Landolt 1992;Crawford et al 2006); several Lemnaceae species are even noted in the invasive species compendium ("Invasive Species Compendium" n.d.) (Abramson et al 2021). The wide distribution of duckweeds means their range overlaps that of a number of model plant pathogens.…”

“…T. N. Hoang et al 2020; W. Wang et al 2014; Michael et al 2017; Wenguo Wang et al 2016; Abramson et al 2021). Spirodela polyrhiza has a relatively small genome of 158 Mb with less than 20,000 protein coding genes and has lost members of expansin and cellulose biosynthesis (W.…”

“…The small genome and body plan is conducive to the Lemnaceae's rapid lifecycle with a doubling time of as little as 34 hours (Michael et al 2020). Lemnaceae are very easy to grow in the laboratory which has stimulated research into their use as biofuels (Van Hoeck et al 2015;Y.-L. Xu et al 2018;Su et al 2014) and enabled the growth of genomic resources for the species, including multiple genomes and transcriptomic datasets (Michael et al 2020; P. T. N. Hoang et al 2020; W. Wang et al 2014;Michael et al 2017;Wenguo Wang et al 2016;Abramson et al 2021). Spirodela polyrhiza has a relatively small genome of 158 Mb with less than 20,000 protein coding genes and has lost members of expansin and cellulose biosynthesis (W. Wang et al 2014;Michael et al 2017).…”