Genes and genomes, an imperfect world: comparison of gene annotations of two Bos taurus draft assemblies

Results We compared the gene annotations produced with the GNOMON [1] annotation pipeline for two Bos taurus genome assemblies produced at the University of Maryland [2,3]. We find that the changes to the assembly from one release to the next, which were quite substantial, made significant differences in the gene sets and gene structures, and implicitly the predicted proteins. The annotation was affected by the availability of new gene evidence and by seemingly rare genome mis-assembly events and local sequence variations. For instance, although the later assembly is generally superior, hundreds of protein coding genes in the earlier assembly are missing from the annotation of the later genome, and ~15% (~3600) of the genes have complex structural differences between the two assemblies. In addition, 15-20% of the predicted proteins have relatively large sequence differences when compared to their Ref-seq models.