Dataset Information

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.

SUBMITTER: Tello-Ruiz MK

PROVIDER: S-EPMC5753211 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

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Publications

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

Tello-Ruiz Marcela K MK Naithani Sushma S Stein Joshua C JC Gupta Parul P Campbell Michael M Olson Andrew A Wei Sharon S Preece Justin J Geniza Matthew J MJ Jiao Yinping Y Lee Young Koung YK Wang Bo B Mulvaney Joseph J Chougule Kapeel K Elser Justin J Al-Bader Noor N Kumari Sunita S Thomason James J Kumar Vivek V Bolser Daniel M DM Naamati Guy G Tapanari Electra E Fonseca Nuno N Huerta Laura L Iqbal Haider H Keays Maria M Munoz-Pomer Fuentes Alfonso A Tang Amy A Fabregat Antonio A D'Eustachio Peter P Weiser Joel J Stein Lincoln D LD Petryszak Robert R Papatheodorou Irene I Kersey Paul J PJ Lockhart Patti P Taylor Crispin C Jaiswal Pankaj P Ware Doreen D

Nucleic acids research 20180101 D1

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 path ...[more]

PMID: 29165610

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Project description:In a local environment, plant networks include interactions among individuals of different species and among genotypes of the same species. While interspecific interactions are recognized as main drivers of plant community patterns, intraspecific interactions have recently gained attention in explaining plant community dynamics. However, an overview of intraspecific genotype-by-genotype interaction patterns within wild plant species is still missing. From the literature, we identified 91 experiments that were mainly designed to investigate the presence of positive interactions based on two contrasting hypotheses. Kin selection theory predicts partisan help given to a genealogical relative. The rationale behind this hypothesis relies on kin/non-kin recognition, with the positive outcome of kin cooperation substantiating it. On the other hand, the elbow-room hypothesis supports intraspecific niche partitioning leading to positive outcome when genetically distant genotypes interact. Positive diversity-productivity relationship rationalizes this hypothesis, notably with the outcome of overyielding. We found that both these hypotheses have been highly supported in experimental studies despite their opposite predictions between the extent of genetic relatedness among neighbors and the level of positive interactions. Interestingly, we identified a highly significant effect of breeding system, with a high proportion of selfing species associated with the presence of kin cooperation. Nonetheless, we identified several shortcomings regardless of the species considered, such as the lack of a reliable estimate of genetic relatedness among genotypes and ecological characterization of the natural habitats from which genotypes were collected, thereby impeding the identification of selective drivers of positive interactions. We therefore propose a framework combining evolutionary ecology and genomics to establish the eco-genomic landscape of positive GxG interactions in wild plant species.

Dataset Information

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

Publications

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

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