Orthology-Based Genome Annotation and Interpretation

The OrthoDB [Kriventseva, et al. 2015] catalog of orthologs, www.orthodb.org, represents a comprehensive resource of comparative genomics data to help researchers make the most of their newly-sequenced genomes. OrthoDB’s sets of Benchmarking Universal Single-Copy Orthologs, BUSCO [Simão, et al. 2015], provide a rich source of data to assess the quality and completeness of these genome assemblies and their gene annotations. These resources and tools enable improved and extended orthology-based genome annotation and interpretation in a comparative genomics framework that incorporates the rapidly growing numbers of newly-sequenced plant and animal genomes. Such comparative approaches are well-established as immensely valuable for gene discovery and characterization, helping to build resources to support biological research. Orthology delineation is a cornerstone of comparative genomics, offering evolutionarily-qualified hypotheses on gene function by identifying “equivalent” genes in different species, as well as highlighting shared and unique genes that offer clues to understanding species diversity and provide the means to begin to investigate key biological traits – for both large-scale evolutionary biology research and targeted gene and gene family studies. The success of such interpretative analyses relies on the comprehensiveness and accuracy of the input data, making BUSCO quality assessment an important part of the process of genome sequencing, assembly, and annotation. Orthology-based approaches therefore offer not only a vital means by which to begin to interpret the increasing quantities of genomic data, but also to help prioritize improvements, and to ensure that initial “draft” genomes develop into high-quality resources that benefit the entire research community.