Discovery and Visualisation of Homologous Genes and Gene Families Using Galaxy

The phylogenetic information inferred from the study of homologous genes helps us to understand the evolution of gene families and plays a vital role in finding ancestral gene duplication events as well as identifying regions that are under positive selection within species.

The Ensembl GeneTrees pipeline generates gene trees based on coding sequences and provides details about exon conservation, and is used in the Ensembl Compara project to discover homologous gene families. Since expertise is required to configure and run the pipeline via the command-line, we created GeneSeqToFamily, an open-source Galaxy workflow based on Ensembl GeneTrees. GeneSeqToFamily helps users to run potentially large-scale gene family analyses without requiring the command-line while still allowing tool parameters, configurations, and the tools themselves to be modified.

We have also developed two additional sub-workflows: one to output orphan genes from the GeneSeqToFamily workflow itself, i.e. genes that are represented in no gene families; the other is to query SwissProt and Ensembl for genes of interest (or orphan genes from GeneSeqToFamily) in order to retrieve genomic information. The results from both these sub-workflows can be subsequently imported back into GeneSeqToFamily for familial analysis.

At present, we are using these workflows on grasses (wheat, rice, Brachypodium, Arabidopsis, and barley) and vertebrates (human, dog, chicken, kangaroo, macropod, opossum, mouse, platypus, and tasmanian devil), with some analyses comprising more than 13000 gene families. Gene families discovered with GeneSeqToFamily can be visualised using the Aequatus.js interactive tool, integrated within Galaxy as a visualisation plugin.

Availability: https://github.com/TGAC/earlham-galaxytools