Literature DB >> 32388018

The promise of single-cell genomics in plants.

José L McFaline-Figueroa1, Cole Trapnell2, Josh T Cuperus3.   

Abstract

Single-cell genomic approaches have the potential to revolutionize the study of plant systems. Here, we highlight newly developed techniques to analyze transcriptomes at single-cell resolution. We focus on the rigorous standards necessary to generate and compare these data sets introducing analysis methods that can be applied to interpret their results. Lastly, we discuss the inherent limitations of single-cell studies and address future directions for plant single-cell genomics.
Copyright © 2020 Elsevier Ltd. All rights reserved.

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Year:  2020        PMID： 32388018      PMCID： PMC7971421          DOI： 10.1016/j.pbi.2020.04.002

Source DB:  PubMed          Journal:  Curr Opin Plant Biol        ISSN： 1369-5266            Impact factor:   7.834


  62 in total

1.  A Single-Cell RNA Sequencing Profiles the Developmental Landscape of Arabidopsis Root.

Authors:  Tian-Qi Zhang; Zhou-Geng Xu; Guan-Dong Shang; Jia-Wei Wang
Journal:  Mol Plant       Date:  2019-04-17       Impact factor: 13.164

2.  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

3.  Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis.

Authors:  Jacob H Levine; Erin F Simonds; Sean C Bendall; Kara L Davis; El-ad D Amir; Michelle D Tadmor; Oren Litvin; Harris G Fienberg; Astraea Jager; Eli R Zunder; Rachel Finck; Amanda L Gedman; Ina Radtke; James R Downing; Dana Pe'er; Garry P Nolan
Journal:  Cell       Date:  2015-06-18       Impact factor: 41.582

4.  Cell type-specific transcriptome analysis in the early Arabidopsis thaliana embryo.

Authors:  Daniel Slane; Jixiang Kong; Kenneth W Berendzen; Joachim Kilian; Agnes Henschen; Martina Kolb; Markus Schmid; Klaus Harter; Ulrike Mayer; Ive De Smet; Martin Bayer; Gerd Jürgens
Journal:  Development       Date:  2014-11-19       Impact factor: 6.868

5.  Differential effects of sucrose and auxin on localized phosphate deficiency-induced modulation of different traits of root system architecture in Arabidopsis.

Authors:  Ajay Jain; Michael D Poling; Athikkattuvalasu S Karthikeyan; Joshua J Blakeslee; Wendy A Peer; Boosaree Titapiwatanakun; Angus S Murphy; Kashchandra G Raghothama
Journal:  Plant Physiol       Date:  2007-03-16       Impact factor: 8.340

6.  The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.

Authors:  Cole Trapnell; Davide Cacchiarelli; Jonna Grimsby; Prapti Pokharel; Shuqiang Li; Michael Morse; Niall J Lennon; Kenneth J Livak; Tarjei S Mikkelsen; John L Rinn
Journal:  Nat Biotechnol       Date:  2014-03-23       Impact factor: 54.908

7.  Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics.

Authors:  Kelly Street; Davide Risso; Russell B Fletcher; Diya Das; John Ngai; Nir Yosef; Elizabeth Purdom; Sandrine Dudoit
Journal:  BMC Genomics       Date:  2018-06-19       Impact factor: 3.969

Review 8.  An Introduction to the Analysis of Single-Cell RNA-Sequencing Data.

Authors:  Aisha A AlJanahi; Mark Danielsen; Cynthia E Dunbar
Journal:  Mol Ther Methods Clin Dev       Date:  2018-08-02       Impact factor: 6.698

9.  High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types.

Authors:  Christine N Shulse; Benjamin J Cole; Doina Ciobanu; Junyan Lin; Yuko Yoshinaga; Mona Gouran; Gina M Turco; Yiwen Zhu; Ronan C O'Malley; Siobhan M Brady; Diane E Dickel
Journal:  Cell Rep       Date:  2019-05-14       Impact factor: 9.423

10.  CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq.

Authors:  Tamar Hashimshony; Naftalie Senderovich; Gal Avital; Agnes Klochendler; Yaron de Leeuw; Leon Anavy; Dave Gennert; Shuqiang Li; Kenneth J Livak; Orit Rozenblatt-Rosen; Yuval Dor; Aviv Regev; Itai Yanai
Journal:  Genome Biol       Date:  2016-04-28       Impact factor: 13.583
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  10 in total

Review 1.  The biology of time: dynamic responses of cell types to developmental, circadian and environmental cues.

Authors:  Joseph Swift; Kathleen Greenham; Joseph R Ecker; Gloria M Coruzzi; C Robertson McClung
Journal:  Plant J       Date:  2021-12-06       Impact factor: 7.091

Review 2.  Single-Cell RNA Sequencing for Plant Research: Insights and Possible Benefits.

Authors:  George Bawa; Zhixin Liu; Xiaole Yu; Aizhi Qin; Xuwu Sun
Journal:  Int J Mol Sci       Date:  2022-04-19       Impact factor: 6.208

Review 3.  Potentials of single-cell genomics in deciphering cellular phenotypes.

Authors:  Abbas Shojaee; Michelle Saavedra; Shao-Shan Carol Huang
Journal:  Curr Opin Plant Biol       Date:  2021-06-08       Impact factor: 9.396

4.  A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants.

Authors:  Rachel Shahan; Che-Wei Hsu; Trevor M Nolan; Benjamin J Cole; Isaiah W Taylor; Laura Greenstreet; Stephen Zhang; Anton Afanassiev; Anna Hendrika Cornelia Vlot; Geoffrey Schiebinger; Philip N Benfey; Uwe Ohler
Journal:  Dev Cell       Date:  2022-02-07       Impact factor: 13.417

5.  High expression of the MADS-box gene VRT2 increases the number of rudimentary basal spikelets in wheat.

Authors:  Anna E Backhaus; Ashleigh Lister; Melissa Tomkins; Nikolai M Adamski; James Simmonds; Iain Macaulay; Richard J Morris; Wilfried Haerty; Cristobal Uauy
Journal:  Plant Physiol       Date:  2022-06-27       Impact factor: 8.005

6.  Vision, challenges and opportunities for a Plant Cell Atlas.

Authors:  Suryatapa Ghosh Jha; Alexander T Borowsky; Benjamin J Cole; Noah Fahlgren; Andrew Farmer; Shao-Shan Carol Huang; Purva Karia; Marc Libault; Nicholas J Provart; Selena L Rice; Maite Saura-Sanchez; Pinky Agarwal; Amir H Ahkami; Christopher R Anderton; Steven P Briggs; Jennifer An Brophy; Peter Denolf; Luigi F Di Costanzo; Moises Exposito-Alonso; Stefania Giacomello; Fabio Gomez-Cano; Kerstin Kaufmann; Dae Kwan Ko; Sagar Kumar; Andrey V Malkovskiy; Naomi Nakayama; Toshihiro Obata; Marisa S Otegui; Gergo Palfalvi; Elsa H Quezada-Rodríguez; Rajveer Singh; R Glen Uhrig; Jamie Waese; Klaas Van Wijk; R Clay Wright; David W Ehrhardt; Kenneth D Birnbaum; Seung Y Rhee
Journal:  Elife       Date:  2021-09-07       Impact factor: 8.140

7.  Single-cell genomics in plants: current state, future directions, and hurdles to overcome.

Authors:  Josh T Cuperus
Journal:  Plant Physiol       Date:  2022-02-04       Impact factor: 8.340

Review 8.  A Sight on Single-Cell Transcriptomics in Plants Through the Prism of Cell-Based Computational Modeling Approaches: Benefits and Challenges for Data Analysis.

Authors:  Aleksandr Bobrovskikh; Alexey Doroshkov; Stefano Mazzoleni; Fabrizio Cartenì; Francesco Giannino; Ulyana Zubairova
Journal:  Front Genet       Date:  2021-05-21       Impact factor: 4.599

9.  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

10.  Single-cell RNA-seq describes the transcriptome landscape and identifies critical transcription factors in the leaf blade of the allotetraploid peanut (Arachis hypogaea L.).

Authors:  Hao Liu; Dongxiu Hu; Puxuan Du; Liping Wang; Xuanqiang Liang; Haifen Li; Qing Lu; Shaoxiong Li; Haiyan Liu; Xiaoping Chen; Rajeev K Varshney; Yanbin Hong
Journal:  Plant Biotechnol J       Date:  2021-07-19       Impact factor: 9.803
  10 in total

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