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

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 times makes this a challenge even in the diminutive model plant Arabidopsis thaliana. Here we develop the Lesser Duckweed Lemna minuta as a model with a reduced body plan, small genome size and clonal growth pattern that enables simultaneous tracing of cells from the entire plant over the complete developmental cycle. We generated a chromosome-resolved genome for the 360 megabase genome and defined the growth trajectory of the entire plant with single nuclei RNA sequencing. The L. minuta gene complement represents a primarily non-redundant 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. Thirteen distinct cell types representing meristem, the leaf-stem fusion called a frond, and root-like tissues were defined using gene orthology with single cell expression from model plants, gene ontology categories, and cell trajectory analysis. Dividing meristem cells give rise to two main branches of root-transition and mesophyll cells, which then give rise to terminally differentiated parenchyma, epidermal and root cells. Mesophyll tissues express high levels of elemental transport genes consistent with this tissue playing a role in L. minuta wastewater detoxification. The L. minuta genome and cell map provide a paradigm to decipher developmental genes and pathways for an entire plant. Sentence summaryGenome and single nuclei transcriptome of the Lesser Duckweed Lemna minuta enables tracing of all developmental, transitional and terminal cells of an entire plant.