Transcriptional landscape of highly lignified poplar stems at single-cell resolution

Abstract Background Plant secondary growth depends on the activity of the vascular cambium, which produces xylem and phloem. Wood derived from xylem is the most abundant form of biomass globally and has played key socio-economic and subsistence roles throughout human history. However, despite intens...

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Autores principales:	Yang Chen, Shaofei Tong, Yuanzhong Jiang, Fandi Ai, Yanlin Feng, Junlin Zhang, Jue Gong, Jiajia Qin, Yuanyuan Zhang, Yingying Zhu, Jianquan Liu, Tao Ma
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Biology (General) QH301-705.5 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/0317262ca22f41619fce426ec55aa705
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spelling	oai:doaj.org-article:0317262ca22f41619fce426ec55aa7052021-11-28T12:40:53ZTranscriptional landscape of highly lignified poplar stems at single-cell resolution10.1186/s13059-021-02537-21474-760Xhttps://doaj.org/article/0317262ca22f41619fce426ec55aa7052021-11-01T00:00:00Zhttps://doi.org/10.1186/s13059-021-02537-2https://doaj.org/toc/1474-760XAbstract Background Plant secondary growth depends on the activity of the vascular cambium, which produces xylem and phloem. Wood derived from xylem is the most abundant form of biomass globally and has played key socio-economic and subsistence roles throughout human history. However, despite intensive study of vascular development, the full diversity of cell types and the gene networks engaged are still poorly understood. Results Here, we have applied an optimized protoplast isolation protocol and RNA sequencing to characterize the high-resolution single-cell transcriptional landscape of highly lignified poplar stems. We identify 20 putative cell clusters with a series of novel cluster-specific marker genes and find that these cells are highly heterogeneous based on the transcriptome. Analysis of these marker genes’ expression dynamics enables reconstruction of the cell differentiation trajectories involved in phloem and xylem development. We find that different cell clusters exhibit distinct patterns of phytohormone responses and emphasize the use of our data to predict potential gene redundancy and identify candidate genes related to vascular development in trees. Conclusions These findings establish the transcriptional landscape of major cell types of poplar stems at single-cell resolution and provide a valuable resource for investigating basic principles of vascular cell specification and differentiation in trees.Yang ChenShaofei TongYuanzhong JiangFandi AiYanlin FengJunlin ZhangJue GongJiajia QinYuanyuan ZhangYingying ZhuJianquan LiuTao MaBMCarticleBiology (General)QH301-705.5GeneticsQH426-470ENGenome Biology, Vol 22, Iss 1, Pp 1-22 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5 Genetics QH426-470
spellingShingle	Biology (General) QH301-705.5 Genetics QH426-470 Yang Chen Shaofei Tong Yuanzhong Jiang Fandi Ai Yanlin Feng Junlin Zhang Jue Gong Jiajia Qin Yuanyuan Zhang Yingying Zhu Jianquan Liu Tao Ma Transcriptional landscape of highly lignified poplar stems at single-cell resolution
description	Abstract Background Plant secondary growth depends on the activity of the vascular cambium, which produces xylem and phloem. Wood derived from xylem is the most abundant form of biomass globally and has played key socio-economic and subsistence roles throughout human history. However, despite intensive study of vascular development, the full diversity of cell types and the gene networks engaged are still poorly understood. Results Here, we have applied an optimized protoplast isolation protocol and RNA sequencing to characterize the high-resolution single-cell transcriptional landscape of highly lignified poplar stems. We identify 20 putative cell clusters with a series of novel cluster-specific marker genes and find that these cells are highly heterogeneous based on the transcriptome. Analysis of these marker genes’ expression dynamics enables reconstruction of the cell differentiation trajectories involved in phloem and xylem development. We find that different cell clusters exhibit distinct patterns of phytohormone responses and emphasize the use of our data to predict potential gene redundancy and identify candidate genes related to vascular development in trees. Conclusions These findings establish the transcriptional landscape of major cell types of poplar stems at single-cell resolution and provide a valuable resource for investigating basic principles of vascular cell specification and differentiation in trees.
format	article
author	Yang Chen Shaofei Tong Yuanzhong Jiang Fandi Ai Yanlin Feng Junlin Zhang Jue Gong Jiajia Qin Yuanyuan Zhang Yingying Zhu Jianquan Liu Tao Ma
author_facet	Yang Chen Shaofei Tong Yuanzhong Jiang Fandi Ai Yanlin Feng Junlin Zhang Jue Gong Jiajia Qin Yuanyuan Zhang Yingying Zhu Jianquan Liu Tao Ma
author_sort	Yang Chen
title	Transcriptional landscape of highly lignified poplar stems at single-cell resolution
title_short	Transcriptional landscape of highly lignified poplar stems at single-cell resolution
title_full	Transcriptional landscape of highly lignified poplar stems at single-cell resolution
title_fullStr	Transcriptional landscape of highly lignified poplar stems at single-cell resolution
title_full_unstemmed	Transcriptional landscape of highly lignified poplar stems at single-cell resolution
title_sort	transcriptional landscape of highly lignified poplar stems at single-cell resolution
publisher	BMC
publishDate	2021
url	https://doaj.org/article/0317262ca22f41619fce426ec55aa705
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Transcriptional landscape of highly lignified poplar stems at single-cell resolution

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