Gramene 2018: unifying comparative genomics and pathway resources for plant research

Abstract

Gramene (http://www.gramene.org) is a knowledgebase for comparative functional analysis in major crops and model plant species. The current release, #54, includes over 1.7 million genes from 44 reference genomes, most of which were organized into 62,367 gene families through orthologous and paralogous gene classification, whole-genome alignments, and synteny. Additional gene annotations include ontology-based protein structure and function; genetic, epigenetic, and phenotypic diversity; and pathway associations. Gramene's Plant Reactome provides a knowledgebase of cellular-level plant pathway networks. Specifically, it uses curated rice reference pathways to derive pathway projections for an additional 66 species based on gene orthology, and facilitates display of gene expression, gene-gene interactions, and user-defined omics data in the context of these pathways. As a community portal, Gramene integrates best-of-class software and infrastructure components including the Ensembl genome browser, Reactome pathway browser, and Expression Atlas widgets, and undergoes periodic data and software upgrades. Via powerful, intuitive search interfaces, users can easily query across various portals and interactively analyze search results by clicking on diverse features such as genomic context, highly augmented gene trees, gene expression anatomograms, associated pathways, and external informatics resources. All data in Gramene are accessible through both visual and programmatic interfaces.

Figure 1.

Visualization of query results in the new Gramene database search interface. (A) Species tree of 44 plant reference genomes available in Gramene build 54. Blue, red, black and green lines correspond respectively to 21 monocots, 15 dicots, the basal angiosperm Amborella and 7 lower plant species. New genome assemblies are marked with a red asterisk (*), and updated assemblies are highlighted in violet font (see also Table 1 and Supplementary Table S1). (B) Customized gene tree alignment views, color coded by InterPro domain. Filtered query results and gene tree branches are shown for selected species. Filter query results and gene tree branches are shown for selected species. (C) Detailed DNA sequence alignment. (D) Oryza sativa QTLs, SSRs, and RFLPs from legacy sets reincorporated to the IRGSP1 assembly (mapping courtesy of KeyGene). QTLs from Q-TARO (Yonemaru et al, 2010) are also available.

Figure 2.

Plant Reactome pathway views and functionalities. (A) The ‘Fireworks’ pathway visualization platform displays a navigation panel (left) and a hierarchical graph of pathways in a pathway viewer window with various associated features, such as summation, download options, and links to external public resources providing complementary information on various pathway entities. (B) A view of the Plant Reactome pathway displaying an overlay of gene–gene interaction data. Two common interactors of the MADS15 and MADS14 transcription factors (MAD1 ORYS and MAD6 ORYS, shown in red boxes) were imported via web services from the IntAct database. (C) Analysis and visualization of user-uploaded gene expression data on the pathway browser, with options to explore full expression profiles of the homologs and download results.