SUMMARYSingle-cell transcriptome profiling of heterogeneous tissues can provide high-resolution windows into developmental dynamics and environmental responses, but its application to plants has been limited. Here, we used the high-throughput Drop-seq approach to profile >12,000 cells from Arabidopsis roots. This identified numerous distinct cell types, covering all major root tissues and developmental stages, and illuminated specific marker genes for these populations. In addition, we demonstrate the utility of this approach to study the impact of environmental conditions on developmental processes. Analysis of roots grown with or without sucrose supplementation uncovers changes in the relative frequencies of cell types in response to sucrose. Finally, we characterize the transcriptome changes that occur across endodermis development and identify nearly 800 genes with dynamic expression as this tissue differentiates. Collectively, we demonstrate that single-cell RNA-seq can be used to profile developmental processes in plants and show how they can be altered by external stimuli.

Innovation, conservation, and repurposing of gene function in root cell type development Graphical abstract Highlights d Tomato cell type-resolution translatome atlas reveals cell type function d Conservation and repurposing in gene regulation between Arabidopsis and tomato d The tomato exodermis is lignified, suberized, and enriched for nitrogen regulation d The root meristem is molecularly homologous across plant species

TitleViral diversity in autochthonous croatian grapevine cultivars Permalink https://escholarship.org/uc/item/86j0p6dv JournalPlant Disease, 101 (7)

SUMMARYPlant roots integrate environmental signals and developmental programs using exquisite spatiotemporal control. This is apparent in the deposition of suberin, an apoplastic diffusion barrier, which regulates the entry and exit of water, solutes and gases, and is environmentally plastic. Suberin is considered a hallmark of endodermal differentiation, but we find that it is absent in the tomato endodermis during normal development. Instead, suberin is present in the exodermis, a cell type that is absent in the model organismArabidopsis thaliana. Here, we uncover genes driving exodermal suberization and describe its effects on drought responses in tomato, unravelling the similarities and differences with the paradigmatic Arabidopsis endodermis. Cellular resolution imaging, gene expression, and mutant analyses reveal loss of this program from the endodermis, and its co-option in the exodermis. Functional genetic analyses of the tomato MYB92 transcription factor and ASFT enzyme demonstrate the importance of exodermal suberin for a plant water-deficit response. Controlling the degree of exodermal suberization could be a new strategy for breeding climate-resilient plants.

Multicellular organisms control interactions with their environment through the development of specialized barriers in specific cell types. A conserved barrier in plant roots is the endodermal Casparian strip (CS). The CS is made of polymerized lignin and forms a ring-like structure that seals the apoplastic space between the endodermal cells. Most angiosperms also have another root cell type, the exodermis, that is reported to form a barrier. Our understanding of exodermal developmental and molecular regulation, as well as function, is limited as this cell type is absent from the model species Arabidopsis thaliana. Using tomato (Solanum lycopersicum) as a model system we demonstrate that in this species, the exodermis does not form a CS. Instead, it forms a polar lignin cap with equivalent barrier function to the endodermal CS. We demonstrate that although endodermal regulators are conserved between Arabidopsis and tomato, exodermal differentiation occurs by a distinct regulatory pathway involving the SlSCZ and SlEXO1 transcription factors. Although the exodermis and endodermis both produce barriers that restrict mineral ion uptake, they have unique and overlapping roles in their selectivity. Whether conservation and similarities between the endodermis and exodermis exist in other species remains to be determined. Nonethless, in tomato, these distinct lignin structures have convergent function with different genetic regulation.

Plant species have evolved myriads of solutions to adapt to dynamic environments, 35 including complex cell type development and regulation. To understand this diversity, we profiled tomato root cell type translatomes and chromatin accessibility. Using xylem differentiation in tomato, relative to Arabidopsis, examples of functional innovation, repurposing and conservation of transcription factors are described. Repurposing and innovation of genes are further observed within an exodermis regulatory network and illustrate its function. Translatome 40 analyses of rice, tomato and Arabidopsis tissues suggest that root meristems are more conserved, and that the functions of constitutively expressed genes are more conserved than those of cell 45 Arabidopsis inflorescence stem vascular bundles and is not expressed in primary root xylem 4 (15), and two HD-ZIPIII TFs, SlPHB/PHV (Solyc02g069830) and SlCORONA (Solyc03g120910), whose Arabidopsis orthologs regulate root protoxylem vessel differentiation via positional signals derived from a miR165/166 gradient (2,11,16). Contrary to their function in Arabidopsis, over-expression of SlbZIP11 or SlKNAT1 was sufficient to specify additional protoxylem cell files ( Fig. 2C-D), although these files were often non-contiguous for the 5 SlbZIP11 lines (Fig. 2C) (statistical analyses in Fig. S5, Data S3). The bHLH and MYB overexpression lines had no vascular phenotype. Relative to Arabidopsis, In the case of SlKNAT1, this demonstrates "repurposed" regulation, while in the case of SlbZIP11 it represents innovation in function. miRNA-resistant versions of SlCORONA and SlPHB/PHV were sufficient to regulate protoxylem vessel identity and patterning within the vascular cylinder 10 similar to their Arabidopsis function and are thus conserved regulators (Fig. 2D, E).Cell type/tissue translatomes are likely dynamic over developmental time and in response to the environment. In Arabidopsis, cell type-enriched genes that maintain expression despite stress are also critical regulators of cell fate (3, 17). However, the majority of plant cell type profiles are 15

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