Vision, challenges and opportunities for a plant cell atlas

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; Luigif 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

doi:10.7554/eLife.66877

Vision, challenges and opportunities for a plant cell atlas

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, Luigif Di Costanzo, Moises Exposito-Alonso, Stefania GiacomelloFabio 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

Biology and Genomics

Research output: Contribution to journal › Article › peer-review

Abstract

With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.

Original language	English (US)
Article number	e66877
Journal	eLife
Volume	10
DOIs	https://doi.org/10.7554/eLife.66877
State	Published - 2021

ASJC Scopus subject areas

Neuroscience(all)
Biochemistry, Genetics and Molecular Biology(all)
Immunology and Microbiology(all)

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10.7554/eLife.66877

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Jha, S. G., Borowsky, A. T., Cole, B. J., Fahlgren, N., Farmer, A., Huang, S. S. C., Karia, P., Libault, M., Provart, N. J., Rice, S. L., Saura-Sanchez, M., Agarwal, P., Ahkami, A. H., Anderton, C. R., Briggs, S. P., Brophy, J. A., Denolf, P., Di Costanzo, L., Exposito-Alonso, M., ... Rhee, S. Y. (2021). Vision, challenges and opportunities for a plant cell atlas. eLife, 10, [e66877]. https://doi.org/10.7554/eLife.66877

Vision, challenges and opportunities for a plant cell atlas. / Jha, Suryatapa Ghosh; Borowsky, Alexander T.; Cole, Benjamin J.; Fahlgren, Noah; Farmer, Andrew; Huang, Shao Shan Carol; Karia, Purva; Libault, Marc; Provart, Nicholas J.; Rice, Selena L.; Saura-Sanchez, Maite; Agarwal, Pinky; Ahkami, Amir H.; Anderton, Christopher R.; Briggs, Steven P.; Brophy, Jennifer An; Denolf, Peter; Di Costanzo, Luigif; Exposito-Alonso, Moises; Giacomello, Stefania; Gomez-Cano, Fabio; Kaufmann, Kerstin; Ko, Dae Kwan; Kumar, Sagar; Malkovskiy, Andrey V.; Nakayama, Naomi; Obata, Toshihiro; Otegui, Marisa S.; Palfalvi, Gergo; Quezada-Rodríguez, Elsa H.; Singh, Rajveer; Uhrig, R. Glen; Waese, Jamie; VAN WIJK, Klaas; Wright, R. Clay; Ehrhardt, David W.; Birnbaum, Kenneth D.; Rhee, Seung Y.

In: eLife, Vol. 10, e66877, 2021.

Research output: Contribution to journal › Article › peer-review

Jha, SG, Borowsky, AT, Cole, BJ, Fahlgren, N, Farmer, A, Huang, SSC, Karia, P, Libault, M, Provart, NJ, Rice, SL, Saura-Sanchez, M, Agarwal, P, Ahkami, AH, Anderton, CR, Briggs, SP, Brophy, JA, Denolf, P, Di Costanzo, L, Exposito-Alonso, M, Giacomello, S, Gomez-Cano, F, Kaufmann, K, Ko, DK, Kumar, S, Malkovskiy, AV, Nakayama, N, Obata, T, Otegui, MS, Palfalvi, G, Quezada-Rodríguez, EH, Singh, R, Uhrig, RG, Waese, J, VAN WIJK, K, Wright, RC, Ehrhardt, DW, Birnbaum, KD & Rhee, SY 2021, 'Vision, challenges and opportunities for a plant cell atlas', eLife, vol. 10, e66877. https://doi.org/10.7554/eLife.66877

Jha, Suryatapa Ghosh ; Borowsky, Alexander T. ; Cole, Benjamin J. ; Fahlgren, Noah ; Farmer, Andrew ; Huang, Shao Shan Carol ; Karia, Purva ; Libault, Marc ; Provart, Nicholas J. ; Rice, Selena L. ; Saura-Sanchez, Maite ; Agarwal, Pinky ; Ahkami, Amir H. ; Anderton, Christopher R. ; Briggs, Steven P. ; Brophy, Jennifer An ; Denolf, Peter ; Di Costanzo, Luigif ; Exposito-Alonso, Moises ; Giacomello, Stefania ; Gomez-Cano, Fabio ; Kaufmann, Kerstin ; Ko, Dae Kwan ; Kumar, Sagar ; Malkovskiy, Andrey V. ; Nakayama, Naomi ; Obata, Toshihiro ; Otegui, Marisa S. ; Palfalvi, Gergo ; Quezada-Rodríguez, Elsa H. ; Singh, Rajveer ; Uhrig, R. Glen ; Waese, Jamie ; VAN WIJK, Klaas ; Wright, R. Clay ; Ehrhardt, David W. ; Birnbaum, Kenneth D. ; Rhee, Seung Y. / Vision, challenges and opportunities for a plant cell atlas. In: eLife. 2021 ; Vol. 10.

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title = "Vision, challenges and opportunities for a plant cell atlas",

abstract = "With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.",

author = "Jha, {Suryatapa Ghosh} and Borowsky, {Alexander T.} and Cole, {Benjamin J.} and Noah Fahlgren and Andrew Farmer and Huang, {Shao Shan Carol} and Purva Karia and Marc Libault and Provart, {Nicholas J.} and Rice, {Selena L.} and Maite Saura-Sanchez and Pinky Agarwal and Ahkami, {Amir H.} and Anderton, {Christopher R.} and Briggs, {Steven P.} and Brophy, {Jennifer An} and Peter Denolf and {Di Costanzo}, Luigif and Moises Exposito-Alonso and Stefania Giacomello and Fabio Gomez-Cano and Kerstin Kaufmann and Ko, {Dae Kwan} and Sagar Kumar and Malkovskiy, {Andrey V.} and Naomi Nakayama and Toshihiro Obata and Otegui, {Marisa S.} and Gergo Palfalvi and Quezada-Rodr{\'i}guez, {Elsa H.} and Rajveer Singh and Uhrig, {R. Glen} and Jamie Waese and {VAN WIJK}, Klaas and Wright, {R. Clay} and Ehrhardt, {David W.} and Birnbaum, {Kenneth D.} and Rhee, {Seung Y.}",

note = "Funding Information: The PCA community-building activities are funded in part by the National Science Foundation grant numbers MCB-1916797 and MCB-2052590, Carnegie Institution for Science, and BASF. We thank Emily Fryer, Nick Melosh, Heather Meyer, Jason Thomas, Terri Tippets, Renate Weizbauer, Zhiyong Wang and Kangmei Zhao for helping with organizing the first work-shop. We thank Emily Fryer and Julie Gosse at the Science Editors Network for developing the PCA website. We are grateful to the first PCA workshop steering committee members Jim Haseloff, David Jackson, Edward Marcotte, John Marioni, Marisa Otegui, Alberto Salleo, Waltraud Schulze, Edgar Spalding, Michael Suss-man, Marja Timmermans and HS Philip Wong for their guidance and support. We thank Rachel Shahan, Shouling Xu, Kevin Cox and Erin Zess for their input in developing the manuscript. Some images in the figures were created with BioRender.com. National Science Foundation- 1916797- David W Ehrhardt, Kenneth D, Birnbaum, Seung Yon Rhee; National Science Foundation- 2052590- Seung Yon Rhee. Funding Information: Industry is another potential source of funding. Over 70% of applied research and development in the US is funded by industry (Khan et al., 2020). A thorough understanding of plant systems is essential for designing effective agro-biotech solutions leading to new crop varieties, and to innovative crop protection products that can leverage sustainable food production. A partnership with the PCA initiative would accelerate development of new solutions for customers of the agbiotech industry. Thus, funding and collaborations, ranging over multiple disciplines and countries, and multiway interactions amongst academia, industry and philanthropy will be essential to realize the vision of the PCA. Publisher Copyright: {\textcopyright} Jha et al.",

year = "2021",

doi = "10.7554/eLife.66877",

language = "English (US)",

volume = "10",

journal = "eLife",

issn = "2050-084X",

publisher = "eLife Sciences Publications",

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T1 - Vision, challenges and opportunities for a plant cell atlas

AU - Jha, Suryatapa Ghosh

AU - Borowsky, Alexander T.

AU - Cole, Benjamin J.

AU - Fahlgren, Noah

AU - Farmer, Andrew

AU - Huang, Shao Shan Carol

AU - Karia, Purva

AU - Libault, Marc

AU - Provart, Nicholas J.

AU - Rice, Selena L.

AU - Saura-Sanchez, Maite

AU - Agarwal, Pinky

AU - Ahkami, Amir H.

AU - Anderton, Christopher R.

AU - Briggs, Steven P.

AU - Brophy, Jennifer An

AU - Denolf, Peter

AU - Di Costanzo, Luigif

AU - Exposito-Alonso, Moises

AU - Giacomello, Stefania

AU - Gomez-Cano, Fabio

AU - Kaufmann, Kerstin

AU - Ko, Dae Kwan

AU - Kumar, Sagar

AU - Malkovskiy, Andrey V.

AU - Nakayama, Naomi

AU - Obata, Toshihiro

AU - Otegui, Marisa S.

AU - Palfalvi, Gergo

AU - Quezada-Rodríguez, Elsa H.

AU - Singh, Rajveer

AU - Uhrig, R. Glen

AU - Waese, Jamie

AU - VAN WIJK, Klaas

AU - Wright, R. Clay

AU - Ehrhardt, David W.

AU - Birnbaum, Kenneth D.

AU - Rhee, Seung Y.

N1 - Funding Information: The PCA community-building activities are funded in part by the National Science Foundation grant numbers MCB-1916797 and MCB-2052590, Carnegie Institution for Science, and BASF. We thank Emily Fryer, Nick Melosh, Heather Meyer, Jason Thomas, Terri Tippets, Renate Weizbauer, Zhiyong Wang and Kangmei Zhao for helping with organizing the first work-shop. We thank Emily Fryer and Julie Gosse at the Science Editors Network for developing the PCA website. We are grateful to the first PCA workshop steering committee members Jim Haseloff, David Jackson, Edward Marcotte, John Marioni, Marisa Otegui, Alberto Salleo, Waltraud Schulze, Edgar Spalding, Michael Suss-man, Marja Timmermans and HS Philip Wong for their guidance and support. We thank Rachel Shahan, Shouling Xu, Kevin Cox and Erin Zess for their input in developing the manuscript. Some images in the figures were created with BioRender.com. National Science Foundation- 1916797- David W Ehrhardt, Kenneth D, Birnbaum, Seung Yon Rhee; National Science Foundation- 2052590- Seung Yon Rhee. Funding Information: Industry is another potential source of funding. Over 70% of applied research and development in the US is funded by industry (Khan et al., 2020). A thorough understanding of plant systems is essential for designing effective agro-biotech solutions leading to new crop varieties, and to innovative crop protection products that can leverage sustainable food production. A partnership with the PCA initiative would accelerate development of new solutions for customers of the agbiotech industry. Thus, funding and collaborations, ranging over multiple disciplines and countries, and multiway interactions amongst academia, industry and philanthropy will be essential to realize the vision of the PCA. Publisher Copyright: © Jha et al.

PY - 2021

Y1 - 2021

N2 - With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.

AB - With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.

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SN - 2050-084X

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ER -

Vision, challenges and opportunities for a plant cell atlas

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