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Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways

  • Protocol
Plant Bioinformatics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1374))

Abstract

Gramene is an integrated informatics resource for accessing, visualizing, and comparing plant genomes and biological pathways. Originally targeting grasses, Gramene has grown to host annotations for economically important and research model crops, including wheat, potato, tomato, banana, grape, poplar, and Chlamydomonas. Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data. This chapter outlines system requirements for end users and database hosting, data types and basic navigation within Gramene, and provides examples of how to (1) view a phylogenetic tree for a family of transcription factors, (2) explore genetic variation in the orthologues of a gene with a known trait association, and (3) upload, visualize, and privately share end user data into a new genome browser track.

Moreover, this is the first publication describing Gramene’s new web interface—intended to provide a simplified portal to the most complete and up-to-date set of plant genome and pathway annotations.

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Acknowledgements

The authors would like to thank all members of the Gramene Project, especially Bo Wang for going through the exercises and providing feedback for clarity in the protocols and Peter van Buren for system technolology support. We are also grateful to Gramene’s users for valuable suggestions, and our collaborators for sharing genomic-scale data sets that make Gramene an outstanding community resource. The Genomes and Pathways modules in Gramene would not have been possible without the synergistic collaborations with the Ensembl Genomes project at the EMBL-European Bioinformatics Institute, and the Reactome project at the Ontario Institute for Cancer Research, respectively.

Gramene is supported by an NSF grant (IOS-1127112).

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Authors and Affiliations

  1. Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY, 11724, USA

    Marcela Karey Tello-Ruiz, Joshua Stein, Sharon Wei, Ken Youens-Clark & Doreen Ware

  2. Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA

    Pankaj Jaiswal

  3. USDA-ARS NEA Plant, Soil & Nutrition Laboratory Research Unit, Cornell University, Ithaca, NY, 14853, USA

    Doreen Ware

Authors
  1. Marcela Karey Tello-Ruiz
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  2. Joshua Stein
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  3. Sharon Wei
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  4. Ken Youens-Clark
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  5. Pankaj Jaiswal
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  6. Doreen Ware
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Corresponding author

Correspondence to Doreen Ware .

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Editors and Affiliations

  1. School of Plant Biology, University of Western Australia, Perth, Australia

    David Edwards

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Tello-Ruiz, M.K., Stein, J., Wei, S., Youens-Clark, K., Jaiswal, P., Ware, D. (2016). Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways. In: Edwards, D. (eds) Plant Bioinformatics. Methods in Molecular Biology, vol 1374. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3167-5_7

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  • DOI: https://doi.org/10.1007/978-1-4939-3167-5_7

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3166-8

  • Online ISBN: 978-1-4939-3167-5

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