Gramene: a resource for comparative analysis of plants genomes and pathways

Authors: TELLO-RUIZ, MARCELA - COLD SPRING HARBOR LABORATORY; JAISWAL, PANKAJ - OREGON STATE UNIVERSITY; Ware, Doreen

Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: 11/12/2020
Publication Date: 1/16/2022
Citation: Tello-Ruiz, M.K., Jaiswal, P., Ware, D. 2022. Gramene: a resource for comparative analysis of plants genomes and pathways. In: Edwards, D. Plant Bioinformatics Methods and Protocols. 3rd edition. Hertfordshire, UK:Humana Press. p.101-131. https://doi.org/10.1007/978-1-0716-2067-0_5#DOI
DOI: https://doi.org/10.1007/978-1-0716-2067-0_5#DOI

Interpretive Summary: In this book chapter, the authors provide step-wise instructions to accomplish three practical exercises to explore the Gramene website: 1) understand the results of Gramene’s search interface, 2) explore comparative genomics data visualizations, and 3) assess the genetic variation associated with a gene locus.

Technical 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 provide 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.