A New Tool for Annotating Locus-Specific Alternate Assemblies and its Application to the Bovine Genome

Genome assembly discrepancies are major sources of gene annotation errors. A discrepancy can arise due to errors in the assembly process or due to structural variations among individuals or breeds. To address the issue, we have created a tool that allows users to manually correct local assembly errors or provide localized information about genomic structural variants in a genome browser environment. The tool is built on JBrowse and WebApollo2.0, a community gene annotation tool. Our tool allows users to create “locus-specific alternate assembly” (LSAA) annotations, which provide the locations and alternative sequences to correct assembly errors or describe variants. To help users identify assembly issues, the LSAA tool includes visualizations of genomic read alignments that display arcs between read pairs or show discordant read pairs. The LSAA tool provides report pages showing the alternate loci. It provides easy navigation, and allows the results to be searched with BLAT in the WebApollo environment. Future goals are to provide viewing of gene annotations and evidence with updated genome coordinates and to allow users to export LSAA and alternate genome assemblies in FASTA and GFF format for downstream analyses.

We demonstrate the LSAA annotation procedure with examples showing correction of assembly errors in the Bos taurus genome. The LSAA tool can also be used early in genome projects to allow annotators to provide feedback on the assembly. We encourage bovine researchers to use the LSAA tool available at the Bovine Genome Database (http://BovineGenome.org) to provide feedback on new bovine reference genome assemblies.