Analysis of genome information for hundreds to thousands of individual trees requires bioinformatics capacity for managing and interpreting large amounts of genomics data.  We have implemented webservices and commercial software packages as well as a GALAXY workflow environment to facilitate modular development tools and pipelines.  These pipelines can be accessed by group members for high-throughput genomics analysis, and enable quality control processing of raw data and downstream analyses such as genen and genome annotation, gene expression analysis, detection of genomic variants, and discovery of genetics associations.

 

The development of specialized tools such as The Eucalyptus Genome Integrative Explorer is also actively underway.  EucGenIE is an online resource for Eucalyptus genomics and transcripts.  It allows access to all gene transcript annotations and has various search functions to isolate relevant data.  Several mRNA-Seq experiment datasets are available, providing information about expression levels in different tissues and possible co-expression of genes.  This aims to facilitate research focused on transcriptional control of gene families and metabolic pathways.  There are several visualization options, including plots, heatmaps as well as Gbrowse instances.  Another popular option for visualization and figure generation is the Circos package which provides a wide variety of track options to include data in the circular plot.  This is very useful for visualizing specific areas or characteristics in the scope of the entire genome or focusing on these areas only.  Bioinformatics capacity (both hardware and human resources) is an essential component of applied biotechnology solutions for the forestry industry.