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Tello-Ruiz MK, Jaiswal P, Ware D. Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways. Methods Mol Biol. 2022;2443:101-131doi: 10.1007/978-1-0716-2067-0_5.
Tello-Ruiz, M. K., Jaiswal, P., & Ware, D. (2022). Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways. Methods in molecular biology (Clifton, N.J.), 2443101-131. https://doi.org/10.1007/978-1-0716-2067-0_5
Tello-Ruiz, Marcela Karey, et al. "Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways." Methods in molecular biology (Clifton, N.J.) vol. 2443 (2022): 101-131. doi: https://doi.org/10.1007/978-1-0716-2067-0_5
Tello-Ruiz MK, Jaiswal P, Ware D. Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways. Methods Mol Biol. 2022;2443:101-131. doi: 10.1007/978-1-0716-2067-0_5. PMID: 35037202.
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Methods Mol Biol. 2022;2443:101-131. doi: 10.1007/978-1-0716-2067-0_5.

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

Methods in molecular biology (Clifton, N.J.)

Marcela Karey Tello-Ruiz, Pankaj Jaiswal, Doreen Ware

Affiliations

  1. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
  2. Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.
  3. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA. [email protected].
  4. USDA-ARS NAA Plant, Soil & Nutrition Laboratory Research Unit, Cornell University, Ithaca, NY, USA. [email protected].

PMID: 35037202 DOI: 10.1007/978-1-0716-2067-0_5

Abstract

Gramene is an integrated bioinformatics resource for accessing, visualizing, and comparing plant genomes and biological pathways. Originally targeting grasses, Gramene has grown to host annotations for over 90 plant genomes including agronomically important cereals (e.g., maize, sorghum, wheat, teff), fruits and vegetables (e.g., apple, watermelon, clementine, tomato, cassava), specialty crops (e.g., coffee, olive tree, pistachio, almond), and plants of special or emerging interest (e.g., cotton, tobacco, cannabis, or hemp). For some species, the resource includes multiple varieties of the same species, which has paved the road for the creation of species-specific pan-genome browsers. The resource also features plant research models, including Arabidopsis and C4 warm-season grasses and brassicas, as well as other species that fill phylogenetic gaps for plant evolution studies. 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) explore Gramene's search results, (2) explore gene-centric comparative genomics data visualizations in Gramene, and (3) explore genetic variation associated with a gene locus. This is the first publication describing in detail Gramene's integrated search interface-intended to provide a simplified entry portal for the resource's main data categories (genomic location, phylogeny, gene expression, pathways, and external references) to the most complete and up-to-date set of plant genome and pathway annotations.

© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Keywords: Comparative genomics; Gene homology; Gene trees; Genetic variation; Genomes; Orthologs; Paralogs; Pathways; Phylogenetics; Structural variation; Synteny

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