EucGenIE is an online resource for Eucalyptus genomics and transcriptomics. The Eucalyptus grandis V1.0 genome sequence was released in January 2011 and an updated annotation (V1.1) by Jan 2012. Subsequently, in 2015, an updated assembly (V2.0) was released, but with minimal effect on the V1.1 gene model annotations. The genome sequence and annotation are available in the Joint Genome Institute (JGI) Phytozome (V12.1) genome browser.
We previously made available several Illumina mRNA-Seq datasets, which were used to perform a de novo transcriptome assembly of a Eucalyptus grandis x Eucalyptus urophylla F1 clonal genotype (Mizrachi et al., 2010, BMC Genomics & Vining et al., 2015, New Phytologist ). The mRNA-Seq datasets were used to determine transcript expression in xylem, immature xylem, mature and young leaf, phloem and shoot tip tissues. With the release of the Eucalyptus grandis genome sequence (Myburg et al.,2014, Nature) and associated gene models, we have re-calculated the transcript expression in these tissues.
We have since sequenced several other transcriptomes of Eucalyptus, that range from mature, xylogenic tissues to young photosynthetic and reproductive tissues, as well as several disease challenged tissue datasets. We therefore started the development of the EucGenIE online portal, which enables researchers involved in Eucalyptus research to have access to published and private (password protected) gene expression datasets.
We have implemented standard protocols (identical to that used in the rest of PlantGenIE) to follow when calculating the gene expression values of the Eucalyptus grandis V1.1 and V2.0 gene models and aim to provide comparative transcript expression values analysis across the datasets in order to facilitate research focused on transcriptional control of genes, gene families and metabolic pathways involved in growth, development and defense.
There is scope to add a new dimension to the PlantGenIE resource that focuses on how traits and genes co-vary among individuals within populations. We are developing and implementing tools for the visual exploration of expression quantitative trait locus (eQTL) datasets, from both Eucalyptus (EucGenIE) and aspen (PopGenIE). We expect that our genetic variation module (qtlXplorer) will provide a platform for systems genetics modelling and high-resolution dissection of the molecular basis of complex trait variation in plants.
Development of EucGenIE is in progress. You can expect new features, especially new data visualisation tools to be made available in time.