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A pan-grass transcriptome reveals patterns of cellular divergence in crops

ABSTRACT: Different plant species within the grasses were parallel targets of domestication, giving rise to crops with distinct evolutionary histories and traits. Key traits that distinguish these species are mediated by specialized cell types. Here, we compare the transcriptomes of root cells in three grass species—Zea mays (maize), Sorghum bicolor (sorghum), and Setaria viridis (Setaria). We first show that single-cell and single-nucleus RNA-seq provide complementary readouts of cell identity in both dicots and monocots, warranting a combined analysis. Cell types were mapped across species to identify robust, orthologous marker genes. The comparative cellular analysis shows that the transcriptomes of some cell types diverged more rapidly than others—driven, in part, by recruitment of gene modules from other cell types. The data also show that a recent whole genome duplication provides a rich source of new, highly localized gene expression domains that favor fast- evolving cell types. Together, the cell-by-cell comparative analysis shows how fine-scale cellular profiling can extract conserved modules from a pan transcriptome and shed light on the evolution of cells that mediate key functions in crops.

ORGANISM(S): Arabidopsis thaliana Zea mays Setaria viridis Sorghum bicolor

PROVIDER: GSE225118 | GEO | 2023/02/27

REPOSITORIES: GEO

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Project description:Plant secondary cell walls constitute the majority of plant biomass and are an important source of biomaterials. Secondary cell walls are particularly prominent in xylem cells present in the vascular tissue. Although the process of vascularization has been extensively studied in the dicot Arabidopsis thaliana, remarkably little is known about these processes in grass species despite their emerging importance as biomass feedstocks. The targeted biofuel crop Sorghum bicolor has a sequenced and well-annotated genome, making it an ideal monocot model for addressing vascularization and biomass deposition. Here we generated tissue-specific transcriptome data using laser capture microdissection in the developing vascular and non-vascular tissues of the sorghum root. Many sorghum genes with enriched expression in developing vasculature were orthologous to genes previously associated with vascular development in other species. However, a number of transcription factor families, including NAC domain, MYB and ARF varied in their complement of vascular expressed genes to a considerable degree in sorghum compared to Arabidopsis and/or maize. Differential expression of genes associated with DNA methylation and chromatin modification were identified between vascular and non-vascular cell types, implying that changes in DNA methylation may be a feature of sorghum root vascularization. To profile DNA methylation in these tissues, sodium bisulfite sequencing of laser capture microdissected tissue was performed. DNA methylation was enriched in genic regions of genes demonstrating higher expression in non-vascular tissues. Methylation in genic and intergenic regions varied by tissue type and gene expression level. Furthermore, genes involved in cell elongation showed differences in methylation levels concomitant with expression between non-vascular and vascular tissue types suggesting a novel mode by which root growth in distinct tissues may be modulated. Our results provide both a genetic and epigenetic framework for studying vascularization and secondary cell wall development in sorghum.

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A pan-grass transcriptome reveals patterns of cellular divergence in crops

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