Annotating the New Bovine Reference Genome Assembly

We are preparing to annotate the new ARS-UCD bovine genome assembly, and to seek annotation input from the bovine research community. The Bovine Genome Database (http://BovineGenome.org) provides Apollo2.0, a web-based gene annotation system that allows users to view and edit gene annotations. Changes to genes are updated in real time so that they are immediately visible in Apollo, allowing for an unprecedented level of collaboration. Bovine gene evidence tracks will include automated gene predictions, genes transferred from the UMD3.1 assembly using UCSC liftOver, and alignments of Illumina RNAseq and PacBio Iso-Seq transcript sequences. Given that genome assembly discrepancies are major sources of gene annotation errors, we have also developed a plugin to Apollo that allows users to manually correct local assembly errors or provide localized information about genomic structural variants. We call these alternate sequences “Locus Specific Alternate Assemblies” (LSAA). The tool enables gene annotators to correct putative assembly errors they identify in the process of annotating genes. JBrowse visualizations of genomic read alignments that display arcs between read pairs and highlight discordant read pairs help users pinpoint assembly errors. Users may create insertions, deletions and inversions. Although the reference genome is not modified in our database or genome viewer, the submitted LSAA information is maintained and searchable. LSAA locations are highlighted in JBrowse, and LSAA sequences can be exported. We will present the bovine gene and assembly annotation tools using the UMD3.1 assembly as an example, in anticipation of a community annotation project for the ARS-UCD bovine genome assembly.