Literature DB >> 33730513

Advances and Opportunities in Single-Cell Transcriptomics for Plant Research.

Carolin Seyfferth1,2, Jim Renema1,2, Jos R Wendrich1,2, Thomas Eekhout1,2, Ruth Seurinck3,4, Niels Vandamme3,4, Bernhard Blob5,6, Yvan Saeys3,4, Yrjo Helariutta5,6, Kenneth D Birnbaum7, Bert De Rybel1,2.   

Abstract

Single-cell approaches are quickly changing our view on biological systems by increasing the spatiotemporal resolution of our analyses to the level of the individual cell. The field of plant biology has fully embraced single-cell transcriptomics and is rapidly expanding the portfolio of available technologies and applications. In this review, we give an overview of the main advances in plant single-cell transcriptomics over the past few years and provide the reader with an accessible guideline covering all steps, from sample preparation to data analysis. We end by offering a glimpse of how these technologies will shape and accelerate plant-specific research in the near future.

Entities:  

Keywords:  cell atlas; cell trajectory; plant transcriptomics; protoplast; scRNA-seq

Mesh:

Year:  2021        PMID: 33730513      PMCID: PMC7611048          DOI: 10.1146/annurev-arplant-081720-010120

Source DB:  PubMed          Journal:  Annu Rev Plant Biol        ISSN: 1543-5008            Impact factor:   26.379


  68 in total

1.  Casparian strip diffusion barrier in Arabidopsis is made of a lignin polymer without suberin.

Authors:  Sadaf Naseer; Yuree Lee; Catherine Lapierre; Rochus Franke; Christiane Nawrath; Niko Geldner
Journal:  Proc Natl Acad Sci U S A       Date:  2012-06-04       Impact factor: 11.205

2.  Accounting for technical noise in single-cell RNA-seq experiments.

Authors:  Philip Brennecke; Simon Anders; Jong Kyoung Kim; Aleksandra A Kołodziejczyk; Xiuwei Zhang; Valentina Proserpio; Bianka Baying; Vladimir Benes; Sarah A Teichmann; John C Marioni; Marcus G Heisler
Journal:  Nat Methods       Date:  2013-09-22       Impact factor: 28.547

3.  Molecular Mechanisms Driving Switch Behavior in Xylem Cell Differentiation.

Authors:  Gina M Turco; Joel Rodriguez-Medina; Stefan Siebert; Diane Han; Miguel Á Valderrama-Gómez; Hannah Vahldick; Christine N Shulse; Benjamin J Cole; Celina E Juliano; Diane E Dickel; Michael A Savageau; Siobhan M Brady
Journal:  Cell Rep       Date:  2019-07-09       Impact factor: 9.423

4.  Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation.

Authors:  Sebastian Preissl; Rongxin Fang; Hui Huang; Yuan Zhao; Ramya Raviram; David U Gorkin; Yanxiao Zhang; Brandon C Sos; Veena Afzal; Diane E Dickel; Samantha Kuan; Axel Visel; Len A Pennacchio; Kun Zhang; Bing Ren
Journal:  Nat Neurosci       Date:  2018-02-12       Impact factor: 24.884

5.  MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices.

Authors:  Christopher S McGinnis; David M Patterson; Juliane Winkler; Daniel N Conrad; Marco Y Hein; Vasudha Srivastava; Jennifer L Hu; Lyndsay M Murrow; Jonathan S Weissman; Zena Werb; Eric D Chow; Zev J Gartner
Journal:  Nat Methods       Date:  2019-06-17       Impact factor: 28.547

6.  Comprehensive single-cell transcriptional profiling of a multicellular organism.

Authors:  Junyue Cao; Jonathan S Packer; Vijay Ramani; Darren A Cusanovich; Chau Huynh; Riza Daza; Xiaojie Qiu; Choli Lee; Scott N Furlan; Frank J Steemers; Andrew Adey; Robert H Waterston; Cole Trapnell; Jay Shendure
Journal:  Science       Date:  2017-08-18       Impact factor: 47.728

7.  High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation.

Authors:  Song Li; Masashi Yamada; Xinwei Han; Uwe Ohler; Philip N Benfey
Journal:  Dev Cell       Date:  2016-11-10       Impact factor: 12.270

Review 8.  Review: imaging technologies for flow cytometry.

Authors:  Yuanyuan Han; Yi Gu; Alex Ce Zhang; Yu-Hwa Lo
Journal:  Lab Chip       Date:  2016-11-29       Impact factor: 6.799

9.  Resolving cellular systems by ultra-sensitive and economical single-cell transcriptome filtering.

Authors:  Andres F Vallejo; James Davies; Amit Grover; Ching-Hsuan Tsai; Robert Jepras; Marta E Polak; Jonathan West
Journal:  iScience       Date:  2021-02-05

10.  The regulatory landscape of Arabidopsis thaliana roots at single-cell resolution.

Authors:  Michael W Dorrity; Cristina M Alexandre; Morgan O Hamm; Anna-Lena Vigil; Stanley Fields; Christine Queitsch; Josh T Cuperus
Journal:  Nat Commun       Date:  2021-06-07       Impact factor: 14.919

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  21 in total

1.  On the origin of lateral roots from a single cell perspective.

Authors:  Dorota Kawa
Journal:  Plant Cell       Date:  2021-08-13       Impact factor: 11.277

Review 2.  Omics-Facilitated Crop Improvement for Climate Resilience and Superior Nutritive Value.

Authors:  Tinashe Zenda; Songtao Liu; Anyi Dong; Jiao Li; Yafei Wang; Xinyue Liu; Nan Wang; Huijun Duan
Journal:  Front Plant Sci       Date:  2021-12-01       Impact factor: 5.753

3.  An in situ sequencing approach maps PLASTOCHRON1 at the boundary between indeterminate and determinate cells.

Authors:  Reinout Laureyns; Jessica Joossens; Denia Herwegh; Julie Pevernagie; Benjamin Pavie; Kirin Demuynck; Kevin Debray; Griet Coussens; Laurens Pauwels; Tom Van Hautegem; Michiel Bontinck; Josh Strable; Hilde Nelissen
Journal:  Plant Physiol       Date:  2022-02-04       Impact factor: 8.340

4.  Mathematical model and genomics construction of developmental biology patterns using digital image technology.

Authors:  Shiwei Ni; Fei Chen; Guolong Chen; Yufeng Yang
Journal:  Front Genet       Date:  2022-08-10       Impact factor: 4.772

5.  Transcriptional landscapes of de novo root regeneration from detached Arabidopsis leaves revealed by time-lapse and single-cell RNA sequencing analyses.

Authors:  Wu Liu; Yuyun Zhang; Xing Fang; Sorrel Tran; Ning Zhai; Zhengfei Yang; Fu Guo; Lyuqin Chen; Jie Yu; Madalene S Ison; Teng Zhang; Lijun Sun; Hongwu Bian; Yijing Zhang; Li Yang; Lin Xu
Journal:  Plant Commun       Date:  2022-02-25

6.  Trafficking and localization of KNOTTED1 related mRNAs in shoot meristems.

Authors:  Munenori Kitagawa; Xiaosa Xu; David Jackson
Journal:  Commun Integr Biol       Date:  2022-07-06

7.  The maize single-nucleus transcriptome comprehensively describes signaling networks governing movement and development of grass stomata.

Authors:  Guiling Sun; Mingzhang Xia; Jieping Li; Wen Ma; Qingzeng Li; Jinjin Xie; Shenglong Bai; Shanshan Fang; Ting Sun; Xinlei Feng; Guanghui Guo; Yanli Niu; Jingyi Hou; Wenling Ye; Jianchao Ma; Siyi Guo; Hongliang Wang; Yu Long; Xuebin Zhang; Junli Zhang; Hui Zhou; Baozhu Li; Jiong Liu; Changsong Zou; Hai Wang; Jinling Huang; David W Galbraith; Chun-Peng Song
Journal:  Plant Cell       Date:  2022-04-26       Impact factor: 12.085

8.  Profiling the endosperm, one nucleus at a time.

Authors:  Miloš Tanurdžić
Journal:  Nat Plants       Date:  2021-06       Impact factor: 15.793

Review 9.  Single-cell analysis of cell identity in the Arabidopsis root apical meristem: insights and opportunities.

Authors:  Rachel Shahan; Trevor M Nolan; Philip N Benfey
Journal:  J Exp Bot       Date:  2021-10-13       Impact factor: 7.298

Review 10.  Fruity, sticky, stinky, spicy, bitter, addictive, and deadly: evolutionary signatures of metabolic complexity in the Solanaceae.

Authors:  Paul D Fiesel; Hannah M Parks; Robert L Last; Cornelius S Barry
Journal:  Nat Prod Rep       Date:  2022-07-20       Impact factor: 15.111

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