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The annotation and analysis of complex 3D plant organs using 3DCoordX

View ORCID ProfileAthul Vijayan, Soeren Strauss, Rachele Tofanelli, Tejasvinee Atul Mody, Karen Lee, Miltos Tsiantis, Richard S. Smith, View ORCID ProfileKay Schneitz
doi: https://doi.org/10.1101/2021.11.20.469364
Athul Vijayan
1Plant Developmental Biology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
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  • ORCID record for Athul Vijayan
Soeren Strauss
2Department of Comparative Developmental and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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Rachele Tofanelli
1Plant Developmental Biology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
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Tejasvinee Atul Mody
1Plant Developmental Biology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
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Karen Lee
3The John Innes Centre, Norwich Research Park, Norwich, United Kingdom
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Miltos Tsiantis
2Department of Comparative Developmental and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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Richard S. Smith
2Department of Comparative Developmental and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
3The John Innes Centre, Norwich Research Park, Norwich, United Kingdom
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Kay Schneitz
1Plant Developmental Biology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
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  • ORCID record for Kay Schneitz
  • For correspondence: kay.schneitz@tum.de
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Abstract

A fundamental question in biology concerns how molecular and cellular processes become integrated during morphogenesis. In plants, characterization of 3D digital representations of organs at single-cell resolution represents a promising approach to addressing this problem. A major challenge is to provide organ-centric spatial context to cells of an organ. We developed several general rules for the annotation of cell position and embodied them in 3DCoordX, a user-interactive computer toolbox implemented in the open-source software MorphoGraphX. It enables rapid spatial annotation of cells even in highly curved biological shapes. With the help of 3DCoordX we obtained new insight by analyzing cellular growth patterns in organs of several species. For example, the data indicated the presence of a basal cell proliferation zone in the ovule primordium of Arabidopsis thaliana. Proof-of-concept analyses suggested a preferential increase in cell length associated with neck elongation in the archegonium of Marchantia polymorpha and variations in cell volume linked to central morphogenetic features of a trap of the carnivorous plant Utricularia gibba. Our work demonstrates the broad applicability of the developed strategies as they provide organ-centric spatial context to cellular features in plant organs of diverse shape complexity.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Email addresses authors: Athul Vijayan: avijayan{at}mpipz.mpg.de, Soeren Strauss: strauss{at}mpipz.mpg.de, Rachele Tofanelli: r.tofanelli{at}tum.de, Tejasvinee Atul Mody: t.mody{at}tum.de, Karen Lee: karen.lee{at}jic.ac.uk, Miltos Tsiantis: tsiantis{at}mpipz.mpg.de, Richard Smith: Richard.Smith{at}jic.ac.uk, Kay Schneitz: kay.schneitz{at}tum.de

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted November 20, 2021.
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The annotation and analysis of complex 3D plant organs using 3DCoordX
Athul Vijayan, Soeren Strauss, Rachele Tofanelli, Tejasvinee Atul Mody, Karen Lee, Miltos Tsiantis, Richard S. Smith, Kay Schneitz
bioRxiv 2021.11.20.469364; doi: https://doi.org/10.1101/2021.11.20.469364
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The annotation and analysis of complex 3D plant organs using 3DCoordX
Athul Vijayan, Soeren Strauss, Rachele Tofanelli, Tejasvinee Atul Mody, Karen Lee, Miltos Tsiantis, Richard S. Smith, Kay Schneitz
bioRxiv 2021.11.20.469364; doi: https://doi.org/10.1101/2021.11.20.469364

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