Vision, challenges and opportunities for a Plant Cell Atlas

Author:

,Ahmed Jahed1,Alaba Oluwafemi2,Ameen Gazala3,Arora Vaishali4,Arteaga-Vazquez Mario A5,Arun Alok6,Bailey-Serres Julia7,Bartley Laura E3,Bassel George W8,Bergmann Dominique C9,Bertolini Edoardo10,Bhati Kaushal Kumar11,Blanco-Touriñán Noel12,Briggs Steven P13,Brumos Javier14,Buer Benjamin15,Burlaocot Adrien16,Cervantes-Pérez Sergio Alan17,Chen Sixue18,Contreras-Moreira Bruno19,CORPAS Francisco J20,Cruz-Ramirez Alfredo21,Cuevas-Velazquez Cesar L22,Cuperus Josh T23,David Lisa I24,de Folter Stefan25,Denolf Peter H26,Ding Pingtao27,Dwyer William P28,Evans Matthew MS28,George Nancy29,Handakumbura Pubudu P30,Harrison Maria J31,Haswell Elizabeth S32,Herath Venura33,Jiao Yuling34,Jinkerson Robert E35,John Uwe36,Joshi Sanjay37,Joshi Abhishek38,Joubert Lydia-Marie39,Katam Ramesh40,Kaur Harmanpreet41,Kazachkova Yana42,Raju Sunil K Kenchanmane43,Khan Mather A44,Khangura Rajdeep45,Kumar Ajay46,Kumar Arun47,Kumar Pankaj48,Kumar Pradeep49,Lavania Dhruv50,Lew Tedrick Thomas Salim51,Lewsey Mathew G52,Lin Chien-Yuan53,Liu Dianyi54,Liu Le55,Liu Tie56,Lokdarshi Ansul57,My Luong Ai58,Macaulay Iain C59,Mahmud Sakil60,Mähönen Ari Pekka61,Malukani Kamal Kumar62,Marand Alexandre P63,Martin Carly A64,McWhite Claire D65,Mehta Devang50,Martín Miguel Miñambres66,Mortimer Jenny C67,Nikolov Lachezar A68,Nobori Tatsuya69,Nolan Trevor M70,Ogden Aaron J71,Otegui Marisa S72,Ott Mark-Christoph15,Palma José M73,Paul Puneet74,Rehman Atique U75,Romera-Branchat Maida76,Romero Luis C77,Roth Ronelle78,Sah Saroj K79,Shahan Rachel70,Solanki Shyam3,Song Bao-Hua80,Sozzani Rosangela24,Stacey Gary81,Stepanova Anna N24,Taylor Nicolas L82,Tello-Ruiz Marcela K83,Tran Tuan M84,Tripathi Rajiv Kumar85,Vadde Batthula Vijaya Lakshmi Vadde86,Varga Tamas87,Vidovic Marija88,Walley Justin W89,Wang Zhiyong90,Weizbauer Renate A90,Whelan James91,Wijeratne Asela J92,Xiang Tingting80,Xu Shouling93,Yadegari Ramin94,Yu Houlin95,Yuan Hai Ying96,Zanini Fabio97,Zhao Feng98,Zhu Jie99,Zhuang Xiaohong100,Jha Suryatapa Ghosh28ORCID,Borowsky Alexander T101ORCID,Cole Benjamin J102ORCID,Fahlgren Noah10ORCID,Farmer Andrew103ORCID,Huang Shao-shan Carol104,Karia Purva28105ORCID,Libault Marc106ORCID,Provart Nicholas J107ORCID,Rice Selena L28ORCID,Saura-Sanchez Maite108ORCID,Agarwal Pinky109,Ahkami Amir H30ORCID,Anderton Christopher R30,Briggs Steven P110ORCID,Brophy Jennifer AN111ORCID,Denolf Peter112ORCID,Di Costanzo Luigi F113ORCID,Exposito-Alonso Moises28114ORCID,Giacomello Stefania115ORCID,Gomez-Cano Fabio116ORCID,Kaufmann Kerstin117ORCID,Ko Dae Kwan118ORCID,Kumar Sagar119ORCID,Malkovskiy Andrey V28ORCID,Nakayama Naomi120,Obata Toshihiro121ORCID,Otegui Marisa S122ORCID,Palfalvi Gergo123,Quezada-Rodríguez Elsa H124ORCID,Singh Rajveer125ORCID,Uhrig R Glen126ORCID,Waese Jamie127ORCID,Van Wijk Klaas128ORCID,Wright R Clay129,Ehrhardt David W28,Birnbaum Kenneth D104,Rhee Seung Y28ORCID

Affiliation:

1. Louvain Institute of Biomolecular Science and Technology, UCLouvain, Louvain La Neuve, Belgium

2. School of Biology and Ecology, University of Maine, Orono, United States

3. Washington State University, Pullman, United States

4. University of Delhi, Delhi, India

5. Universidad Veracruzana, Xalapa, Mexico

6. Inter American University of Puerto Rico, Barranquitas, United States

7. Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, Riverside, United States

8. University of Warwick, Coventry, United Kingdom

9. Stanford University and Howard Hughes Medical Institute, Stanford, United States

10. Donald Danforth Plant Science Center, St. Louis, United States

11. Louvain Institute of Biomolecular Sciences, Catholic University of Louvain, Louvain La Neuve, Belgium

12. Plant Vascular Development Group, ETH Zürich, Zurich, Switzerland

13. University of California San Diego, La Jolla, United States

14. Instituto de Biologia Molecular y Celular de Plantas (IBMCP) Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain

15. Bayer AG, Monheim am Rhein, Germany

16. HHMI, Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States

17. LANGEBIO-CINVESTAV, Irapuato, Mexico

18. Department of Biology, University of Florida, Gainesville, United States

19. European Bioinformatics Institute - EMBL, Hinxton, United Kingdom

20. Estación Experimental del Zaidin (CSIC), Granada, Spain

21. National Laboratory of Genomics for Biodiversity CINVESTAV, Irapuato, Mexico

22. Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Cd., Irapuato, Mexico

23. University of Washington, Seattle, United States

24. North Carolina State University, Raleigh, United States

25. Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Mexico

26. BASF Innovation Center Gent, Zwijnaarde, Belgium

27. Institute of Biology Leiden, Leiden University, Leiden, Netherlands

28. Department of Plant Biology, Carnegie Institution for Science, Stanford, United States

29. European Bioinformatics Institute, Cambridge, United Kingdom

30. Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, United States

31. Boyce Thompson Institute, Ithaca, United States

32. Washington University in St. Louis, St. Louis, United States

33. University of Peradeniya, Peradeniya, Sri Lanka

34. Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China

35. University of California, Riverside, Riverside, United States

36. Alfrd-Wegener-Institute Helmholtz centre for Polar and Marine Research, Bremerhaven, Germany

37. University of Kentucky, Lexington, United States

38. Mohanlal Sukhadia University, Udaipur, India

39. Stanford University, Stanford, United States

40. Florida A&M University, Tallahassee, United States

41. Punjab Agricultural University, Ludhiana, India

42. Weizmann Institute of Science, Rehovot, Israel

43. Michigan State University, East Lansing, United States

44. Heinrich Heine University, Dusseldorf, Germany

45. Purdue University, West Lafayette, United States

46. ICAR-NIPB, New Delhi, India

47. Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India

48. Dr Yashwant Singh Parmar University of Horticulture and Forestry Nauni Solan Himachal Pradesh, Solan, India

49. Centre for Cellular & Molecular Biology, Hyderabad, India

50. University of Alberta, Edmonton, Canada

51. Institute of Materials Research and Engineering, Singapore, Singapore

52. La Trobe University, Bundoora, Australia

53. Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, United States

54. Donald Danforth Plant Science Center, Saint Louis, United States

55. Department of Biology, University of Massachusetts Amherst, Amherst, United States

56. University of Florida, Gainesville, United States

57. University of Tennessee, Knoxville, United States

58. Louvain Institute of Biomolecular Science and Technology, Louvain-la-Neuve, Belgium

59. Earlham Institute, Norwich, United Kingdom

60. Plant Cell Biology, IZMB, University of Bonn, Bonn, Germany

61. Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland

62. Molecular Biology, Hyderabad, India

63. University of Georgia, Athens, United States

64. MIT, Cambridge, United States

65. Princeton University, Princeton, United States

66. Heinrich Heine University, Düsseldorf, Germany

67. University of Adelaide, Adelaide, Australia

68. University of California, Los Angeles, Los, Angeles, United States

69. Salk Institute for Biological Studies, San, Diego, United States

70. Duke University, Durham, United States

71. Pacific Northwest National Laboratory, Richland, United States

72. University of Wisconsin-Madison, Madison, United States

73. Estación Experimental del Zaidín, CSIC, Granada, Spain

74. University of Nebraska-Lincoln, Lincoln, United States

75. Department of Agronomy, Bahauddin Zakariya University Multan, Multan, Pakistan

76. Institute of Plant Biology and Biotechnology, University of Münster, Muenster (Germany), Germany

77. Instituto de Bioquimica Vegetal y Fotosintesis, CSIC-US, Seville, Spain

78. Department of Plant Sciences, University of Oxford, Oxford, United Kingdom

79. The Pennsylvania State University, University Park, United States

80. University of North Carolina at Charlotte, Charlotte, United States

81. University of Missouri, Columbia, United States

82. The University of Western Australia, Perth, Australia

83. Cold Spring Harbor Laboratory, Cold Spring Harbor, United States

84. Nanyang Technological University, Singapore, Singapore

85. University of Manitoba, Winnipeg, Canada

86. Cornell University, Ithaca, United States

87. Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, (PNNL), Richland, United States

88. Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia

89. Iowa State University, Ames, United States

90. Carnegie Institution for Science, Dept. of Plant Biology, Stanford, United States

91. La Trobe University, Melbourne, Australia

92. Arkansas State University, Jonesboro, United States

93. Carnegie Institution for Science, Stanford, United States

94. University of Arizona, Tucson, United States

95. Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, United States

96. University of Saskatchewan, Saskatoon, Canada

97. UNSW, Sydney, Australia

98. Laboratoire Reproduction et Développement des Plantes, Université de Lyon, Lyon, France

99. University of California, Davis, Davis, United States

100. Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, Shatin, Hong Kong

101. Department of Botany and Plant Sciences, University of California, Riverside, Riverside, United States

102. Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, United States

103. National Center for Genome Resources, Santa Fe, United States

104. Center for Genomics and Systems Biology, New York University, New York, United States

105. Department of Cell and Systems Biology, University of Toronto, Toronto, Canada

106. Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, United States

107. Department of Cell and Systems Biology and the Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada

108. Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina

109. National Institute of Plant Genome Research, New Delhi, India

110. Department of Biological Sciences, University of California, San Diego, San Diego, United States

111. Department of Biology, Stanford University, Stanford, United States

112. BASF Seeds & Traits, Ghent, Belgium

113. Department of Agricultural Sciences, University of Naples Federico II, Napoli, Italy

114. Department of Plant Biology, Carnegie Institution for Science, Tübingen, Germany

115. SciLifeLab, KTH Royal Institute of Technology, Solna, Sweden

116. Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States

117. Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universitaet zu Berlin, Berlin, Germany

118. Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, United States

119. Department of Plant Breeding & Genetics, Mata Gujri College, Fatehgarh Sahib, Punjabi University, Patiala, India

120. Department of Bioengineering, Imperial College London, London, United Kingdom

121. Department of Biochemistry, University of Nebraska-Lincoln, Madison, United States

122. Department of Botany, University of Wisconsin-Madison, Madison, United States

123. Division of Evolutionary Biology, National Institute for Basic Biology, Okazaki, Japan

124. Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México, León, Mexico

125. School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India

126. Department of Science, University of Alberta, Edmonton, Canada

127. Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada

128. School of Integrated Plant Science, Plant Biology Section, Cornell University, Ithaca, United States

129. Department of Biological Systems Engineering, Virginia Tech, Blacksburg, United States

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.

Funder

National Science Foundation

Publisher

eLife Sciences Publications, Ltd

Subject

General Immunology and Microbiology,General Biochemistry, Genetics and Molecular Biology,General Medicine,General Neuroscience

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