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Plant phenomics: Data integration and analyses

Edited by Dr. Rubén Rellán Álvarez, Dr. Guillaume Lobet, Dr. Malia Gehan, and Dr. Srikant Srinivasan

GigaScience is proud to present this cutting-edge series, with the aim to shed light on new advances, applications, and challenges, and to improve data sharing, integration, analyses and reproducibility in plant phenomics. Recent improvements in phenomics has created a lot of new opportunities to understand and predict dynamic phenotypic responses to genotypic variation. However, problems and opportunities begin to emerge, such as the ability to collect phenotypic data in a way that can be combined with different datasets for meta-analyses, the generation of models or as ground-truth datasets.

We encourage the submission of Research Articles and Technical Notes, as well as Data Notes, which are papers that focus on the description of interesting plant phenomic datasets, curated and hosted in our database, GigaDB. We also consider Commentaries and thought provoking Reviews in this area.

Potential topics include, but are not limited to:


New methods in phenotype data collection e.g. Drones, imaging techniques
New tools in phenotype data integration and analyses
Morphometrics
Organ-scale phenomics
Databases, management and workflows
Research or Data wrapped in a containerized form e.g. Docker, BioBox, VMs


This collection of articles has not been sponsored and articles have undergone the journal’s standard peer-review process. The Guest Editors declare no competing interests.

View all collections published in GigaScience


RESEARCH

Morphometric analysis of Passiflora leaves: the relationship between landmarks of the vasculature and elliptical Fourier descriptors of the blade

Leaf shape among Passiflora species is spectacularly diverse. Underlying this diversity in leaf shape are profound changes in the patterning of the primary vasculature and laminar outgrowth. Each of these aspects of leaf morphology—vasculature and blade—provides different insights into leaf patterning.

Daniel H. Chitwood, Wagner C. Otoni

GigaScience
Published on: 07 January 2017

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Plant specimen contextual data consensus

The Compliance and Interoperability Working Group of the Genomic Standards Consortium facilitates the establishment of a community of experts and the development of recommendations to describe genomic data and associated information. Here we present our ongoing conation to harmonise the reporting of contextual plant specimen data associated with genomics and functional genomics. This commentary summarises the current state of our plant sample contextual data harmonisation efforts to engage a broad plant science community.

Petra ten Hoopen, Ramona L. Walls, Ethalinda KS Cannon, Guy Cochrane, James Cole, Anjanette Johnston, Ilene Karsch-Mizrachi, Pelin Yilmaz

GigaScience 2016 5:1
Published on: 29 December 2016

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Circadian rhythms have significant effects on leaf-to-canopy scale gas exchange under field conditions

Molecular clocks drive oscillations in leaf photosynthesis, stomatal conductance, and other cell and leaf-level processes over ~24 h under controlled laboratory conditions. The influence of such circadian regulation over whole-canopy fluxes remains uncertain.

Víctor Resco de Dios, Arthur Gessler, Juan Pedro Ferrio, Josu G. Alday, Michael Bahn, Jorge del Castillo, Sébastien Devidal, Sonia García-Muñoz, Zachary Kayler, Damien Landais, Paula Martín-Gómez, Alexandru Milcu, Clément Piel, Karin Pirhofer-Walzl, Olivier Ravel, Serajis Salekin…

GigaScience 2016 5:43
Published on: 20 October 2016

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