Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Single-protoplast and single-nucleus sequencing of the leaves of two C4 species: Gynandropsis gynandra and Flaveria bidentis

ABSTRACT: In this study, we optimized protocols for single-nucleus and single-protoplast RNA sequencing (RNA-seq) to generate high-resolution transcriptome atlases for two C4 plant species, Gynandropsis gynandra and Flaveria bidentis. Using Chromium (10X Genomics) technology, we generated single-nucleus and single-protoplast RNA-seq libraries for both species and mapped raw reads to their respective genomes. After quality control, doublet removal, and batch correction, we produced gene expression matrices and performed clustering analysis. We identified major leaf cell types, confirmed the known patterns of C4 gene compartmentalization, and identified conserved and species-specific transcription factors that may contribute to C4 evolution. Our dataset provides a valuable resource for studying the regulatory dynamics of C4 photosynthesis at cellular resolution and offers insights into the evolution of C4 traits.

INSTRUMENT(S): Illumina NovaSeq X

ORGANISM(S): Flaveria bidentis

SUBMITTER: Tianshu Sun

PROVIDER: E-MTAB-15121 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The organs of multicellular species are comprised of cell types that must function together to perform specific tasks. One critical organ function is responding to internal or external change but little is known about how responses are tailored to specific cell types or coordinated among them on a global level. Here we use cellular profiling of five Arabidopsis root cell types in response to a limiting resource, nitrogen, to uncover a vast and predominantly cell-specific response that was largely undetectable using traditional methods. These methods reveal a new class of cell-specific nitrogen responses. As a proof-of-principle, we dissected one cell-specific response circuit that mediates nitrogen-induced changes in root branching from pericycle cells. Thus, cellular response profiling links gene modules to discrete functions in specific cell types. Experiment Overall Design: The whole experiment was carried out in triplicate with 84 chips in total (28 experiments). The nitrogen response in 5 FACS-sorted root cell types (LRC, lateral root cap; EpiC, epidermis and cortex; EndoP, endodermis and pericycle; Peri, pericycle; Stele, stele), protoplasts and Col-0 whole roots was assayed using microarrays. 5mM KNO3 was used as a nitrogen treatment for 2 hours. 5mM KCl was used as a control treatment for the same length of time. 1mM MSX in combination with 5mM KNO3 (or with 5mM KCl as a control) was used to block the assimilation of KNO3, and 5mM Gln added to restore it in order to separate KNO3 effects from assimilated-nitrogen effects. 5mM KNO3 was either maintained in the protoplast-generating solution (continuous treat) or not (transitory treat) to test how to best preserve the cellular nitrogen-response during the 1 hr protoplast generating procedure. As controls we used protoplasts, whole roots frozen directly after the 2hr treatment or 3.5hr treatment, or whole roots incubated in protoplast-generating solution (minus enzymes; transitory or continuous treated) and then frozen. After FACS-sorting or mock FACS-sorting cells were frozen.

Dataset Information

Single-protoplast and single-nucleus sequencing of the leaves of two C4 species: Gynandropsis gynandra and Flaveria bidentis

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