Genome Assembly Consequences For Gene Annotation

Gene annotation is the first and most important step in analyzing a genome. As a growing number of species are being sequenced and assembled to various degrees of completion, a key question is: How does the quality of the assembled sequence affect gene annotations? We compared the gene annotations produced with the GNOMON annotation pipeline for two successive Bos taurus genome assemblies generated at the University of Maryland. We found that even between high-quality draft assemblies such as these there were significant changes in the annotations, due primarily to genome mis-assembly events and local sequence variation. We illustrate with a comparison of annotations in assemblies produced with different methods, from reads generated by diverse sequencing technologies, and undergoing various amounts of curation.