Improved Spirodela polyrhiza genome and proteomic analyses reveal a conserved chromosomal structure with high abundance of chloroplastic proteins favoring energy production

Abstract

Duckweeds are a monophyletic group of rapidly reproducing aquatic monocots in the Lemnaceae family. Given their clonal, exponentially fast reproduction, a key question is whether genome structure is conserved across the species in the absence of meiotic recombination. Here, we studied the genome and proteome of Spirodela polyrhiza, or Greater Duckweed, which has the largest body plan yet the smallest genome size in the family (1C = 150 Mb). Using Oxford Nanopore sequencing combined with Hi-C scaffolding, we generated a highly contiguous, chromosome-scale assembly of S. polyrhiza line Sp7498 (Sp7498_HiC). Both the Sp7498_HiC and Sp9509 genome assemblies reveal large chromosomal misorientations relative to a recent PacBio assembly of Sp7498, highlighting the need for orthogonal long-range scaffolding techniques such as Hi-C and BioNano optical mapping. Shotgun proteomics of Sp7498 verified the expression of ~2,250 proteins and revealed a high abundance of proteins involved in photosynthesis and carbohydrate metabolism among other functions. In addition, a strong increase in chloroplast proteins was observed that correlated to chloroplast density. This Sp7498_HiC genome was generated cheaply and quickly with a single Oxford Nanopore MinION flow cell and one Hi-C library in a classroom setting. Combining these data with a mass spectrometry-generated proteome illustrates the utility of duckweed as a model for genomics- and proteomics-based education.

The Dynamics of NO3− and NH4+ Uptake in Duckweed Are Coordinated with the Expression of Major Nitrogen Assimilation Genes

“…We evaluated the key N assimilation genes encoding NR, NiR, GS, NADH-GOGAT, and Fd-GOGAT, which have been identified as the major players in the assimilation of inorganic N in many plant species ( Figure S1 ), using S. polyrhiza as the representative species due to the availability of a well-characterized whole-genome sequence [ 37 , 40 , 41 , 42 ]. To validate the sequences available in the GenBank, we re-sequenced the cDNA clones prepared for the four GS genes, NR , NiR , NADH-GOGAT and SpFd-GOGAT for the S. polyrhiza ecotype NB5548 used in this study (the corresponding sequence accession IDs are: SpGS1;1 -MZ605906, SpGS1;2 -MZ605907, SpGS1;3 -MZ605908, SpGS2 -MZ605909, SpNR- OL421561, SpNiR- OL421562, SpNADH-GOGAT- OL421563, SpFd-GOGAT -MZ605910).…”

“…We evaluated the key N assimilation genes encoding NR, NiR, GS, NADH-GOGAT, and Fd-GOGAT, which have been identified as the major players in the assimilation of inorganic N in many plant species (Figure S1), using S. polyrhiza as the representative species due to the availability of a well-characterized whole-genome sequence [37,[40][41][42].…”

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

“…In addition, their rapid lifecycle of just 34 hrs (Michael et al 2020), small size and susceptibility to model pathogens make them the perfect system for high-throughput experimentation. The genomic and genetic resources are also developing at a rapid pace, with multiple genomes available (Michael et al 2017; An et al 2019; Harkess et al 2021; Ho et al 2019; P. N. T. Hoang et al 2018; W.…”

Automated imaging of duckweed growth and development

“…Interestingly, each genus has unique features in their growth characteristics and morphology, ranging from the number of roots to their mechanisms of vegetative propagation 2 (Landolt and Kandeler, 1987). Previous microscopy studies have revealed distinct characteristics in duckweed species, such as the high number of stomata, presence/absence of the "pseudoroot", organization and distribution of chloroplasts, and the location from which new daughter fronds initiate (Sree et al, 2015b;Landolt and Kandeler, 1987;Hoang et al, 2019;Harkess et al, 2021).…”