Abstract
Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard features of a model organism database are provided, including genome browsers, gene list annotation, Blast homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo. We have produced an RNA-sequencing (RNA-Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the ComPlEx resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated. The PlantGenIE.org platform provides intuitive access to large-scale and genome-wide genomics data from model forest tree species, facilitating both community contributions to annotation improvement and tools supporting use of the included data resources to inform biological insight.
Highlights
Advances in genomics, developments in highthroughput sequencing, have enabled biologists to sequence the genome and transcriptome and to assay an expanding range of functional genomic processes in a rapidly expanding number of species
We provide a number of web services to allow programmatic access to the tools by external web resources, details of which are available at http://api.plantgenie.org
To provide a resource for exploring potential gene function on the basis of expression, we have developed the P. tremula Expression Atlas (Potra exAtlas) comprising 24 samples profiled using RNA-Seq (Table 1) with an average 18.4 M high-quality pairedend reads per sample, representing > 77 Gbp (441.6 M reads) in total
Summary
Developments in highthroughput sequencing, have enabled biologists to sequence the genome and transcriptome and to assay an expanding range of functional genomic processes in a rapidly expanding number of species This is an exciting liberation from previous reliance on a small number of model species, often enabling use of the most appropriate species to address a biological question rather than the best compromise model system. Populus has matured as a model system for forest tree and plant science research, with numerous genetic and genomics resources having been created (Wullschleger et al, 2002; Jansson & Douglas, 2007) Curating these disparate resources, and their subsequent community dissemination, is a challenging yet essential undertaking to ensure maximal knowledge gain and new insight. We have subsequently continued to develop the resource by integrating new tools and data, making improved versions of popular tools and removing tools that were little used or worked ineffectively in order to streamline the user experience
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