Bovine Genome Database: new annotation tools for a new reference genome

Abstract

The Bovine Genome Database (BGD) (http://bovinegenome.org) has been the key community bovine genomics database for more than a decade. To accommodate the increasing amount and complexity of bovine genomics data, BGD continues to advance its practices in data acquisition, curation, integration and efficient data retrieval. BGD provides tools for genome browsing (JBrowse), genome annotation (Apollo), data mining (BovineMine) and sequence database searching (BLAST). To augment the BGD genome annotation capabilities, we have developed a new Apollo plug-in, called the Locus-Specific Alternate Assembly (LSAA) tool, which enables users to identify and report potential genome assembly errors and structural variants. BGD now hosts both the newest bovine reference genome assembly, ARS-UCD1.2, as well as the previous reference genome, UMD3.1.1, with cross-genome navigation and queries supported in JBrowse and BovineMine, respectively. Other notable enhancements to BovineMine include the incorporation of genomes and gene annotation datasets for non-bovine ruminant species (goat and sheep), support for multiple assemblies per organism in the Regions Search tool, integration of additional ontologies and development of many new template queries. To better serve the research community, we continue to focus on improving existing tools, developing new tools, adding new datasets and encouraging researchers to use these resources.

Figure 1.

Apollo browser showing the LSAA pulldown menu and evidence for a genome assembly inversion. The BLAST hits track shows that segments of a single cDNA align to the genome in opposite directions and the Testis Iso-Seq GMAP track shows that some full-length Iso-Seq transcripts have partial alignments in opposite directions. The UMD3.1.1 Alignment (Ungapped Segments) track reveals a region without an alternate assembly alignment. In the HFD_33604_EM_bam_arcs track, connections between aligned mate pairs of a genomic read library show unusually large overlapping arcs that suggest an assembly inversion. The region of the suspected assembly inversion is highlighted using the highlight tool to the right of the navigation box, and the LSAA pulldown menu can be used to annotate the region as an inversion.

Figure 2.

LSAA track in JBrowse. Once a tentative assembly inversion has been annotated, it is viewable as a track in JBrowse. The inversion is depicted as a green bar with inverted arrowheads.