Automatic Workflow to Compare Variants Between Genomes

In this work we present the automatic workflow creation tool in the CLC Genomics Workbench. We describe the workflow allowing for mapping and comparison of variants between different species.  As the test dataset for this workflow we used the sequencing data from three bovine genomes published by Cosart et al. (2011).

This workflow consists of the following steps:

• Mapping the sequencing reads from each of the three cattle species (zebu, taurine, and bison) separately to the reference genome
• SNV calling
• Filtering for variants present in known transcripts and genes
• Filtering for variants found in zebu only
• Annotation of variants with amino acid changes
• Annotation of variants with known variation IDs from dbSNP
• GO term enrichment analysis for genes having non-synonymous SNVs in zebu only

From almost 20,000 single nucleotide variations identified in zebu, bison and taurine, over 2,500 variations were identified to be present in zebu only, and over 600 of them were found to be the non-synonymous variations. An enrichment analysis of all genes overlapping these variations showed that they are linked to the pathways for immune and defense responses. Considering only the genes with non-synonymous variations, immune response pathways were ranked as the most divergent in zebu. This matches previous findings showing that zebu responds differently to some infections and also has a better innate immune response compared to taurine and bison species (Freeman et al. 2008).

We also will discuss the performance of the workflow in terms of speed, and suggest the possible extension capabilities.