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Single-cell transcriptome sequencing atlas of cassava tuberous root
INTRODUCTION: Single-cell transcriptome sequencing (ScRNA-seq) has emerged as an effective method for examining cell differentiation and development. In non-model plants, it hasn't been employed very much, especially in sink organs that are abundant in secondary metabolites. RESULTS: In this st...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9848496/ https://www.ncbi.nlm.nih.gov/pubmed/36684718 http://dx.doi.org/10.3389/fpls.2022.1053669 |
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author | Song, Jinjia Fan, Benji Shao, Xiaodie Zang, Yuwei Wang, Dayong Min, Yi |
author_facet | Song, Jinjia Fan, Benji Shao, Xiaodie Zang, Yuwei Wang, Dayong Min, Yi |
author_sort | Song, Jinjia |
collection | PubMed |
description | INTRODUCTION: Single-cell transcriptome sequencing (ScRNA-seq) has emerged as an effective method for examining cell differentiation and development. In non-model plants, it hasn't been employed very much, especially in sink organs that are abundant in secondary metabolites. RESULTS: In this study, we sequenced the single-cell transcriptomes at two developmental phases of cassava tuberous roots using the technology known as 10x Genomics (S1, S2). In total, 14,566 cells were grouped into 15 different cell types, primarily based on the marker genes of model plants known to exist. In the pseudotime study, the cell differentiation trajectory was defined, and the difference in gene expression between the two stages on the pseudotime axis was compared. The differentiation process of the vascular tissue and cerebral tissue was identified by the trajectory. We discovered the rare cell type known as the casparian strip via the use of up-regulated genes and pseudotime analysis, and we explained how it differentiates from endodermis. The successful creation of a protoplast isolation technique for organs rich in starch was also described in our study. DISCUSSION: Together, we created the first high-resolution single-cell transcriptome atlas of cassava tuberous roots, which made significant advancements in our understanding of how these roots differentiate and develop. |
format | Online Article Text |
id | pubmed-9848496 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-98484962023-01-19 Single-cell transcriptome sequencing atlas of cassava tuberous root Song, Jinjia Fan, Benji Shao, Xiaodie Zang, Yuwei Wang, Dayong Min, Yi Front Plant Sci Plant Science INTRODUCTION: Single-cell transcriptome sequencing (ScRNA-seq) has emerged as an effective method for examining cell differentiation and development. In non-model plants, it hasn't been employed very much, especially in sink organs that are abundant in secondary metabolites. RESULTS: In this study, we sequenced the single-cell transcriptomes at two developmental phases of cassava tuberous roots using the technology known as 10x Genomics (S1, S2). In total, 14,566 cells were grouped into 15 different cell types, primarily based on the marker genes of model plants known to exist. In the pseudotime study, the cell differentiation trajectory was defined, and the difference in gene expression between the two stages on the pseudotime axis was compared. The differentiation process of the vascular tissue and cerebral tissue was identified by the trajectory. We discovered the rare cell type known as the casparian strip via the use of up-regulated genes and pseudotime analysis, and we explained how it differentiates from endodermis. The successful creation of a protoplast isolation technique for organs rich in starch was also described in our study. DISCUSSION: Together, we created the first high-resolution single-cell transcriptome atlas of cassava tuberous roots, which made significant advancements in our understanding of how these roots differentiate and develop. Frontiers Media S.A. 2023-01-04 /pmc/articles/PMC9848496/ /pubmed/36684718 http://dx.doi.org/10.3389/fpls.2022.1053669 Text en Copyright © 2023 Song, Fan, Shao, Zang, Wang and Min https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Plant Science Song, Jinjia Fan, Benji Shao, Xiaodie Zang, Yuwei Wang, Dayong Min, Yi Single-cell transcriptome sequencing atlas of cassava tuberous root |
title | Single-cell transcriptome sequencing atlas of cassava tuberous root |
title_full | Single-cell transcriptome sequencing atlas of cassava tuberous root |
title_fullStr | Single-cell transcriptome sequencing atlas of cassava tuberous root |
title_full_unstemmed | Single-cell transcriptome sequencing atlas of cassava tuberous root |
title_short | Single-cell transcriptome sequencing atlas of cassava tuberous root |
title_sort | single-cell transcriptome sequencing atlas of cassava tuberous root |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9848496/ https://www.ncbi.nlm.nih.gov/pubmed/36684718 http://dx.doi.org/10.3389/fpls.2022.1053669 |
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