We have developed a method for genome annotation based on evolutionary con- servation independent of transcriptomic evidence. Newly assembled genomes may be lacking comprehensive mRNA transcription data, and even when such data is available, the transcriptome may be a poor proxy for the proteome. The approach described here leverages orthology information from annotations of multiple related species to construct a pseudo-ancestral consensus protein for a given orthogroup. This consensus is then used as a guide to inform gene prediction using several existing programs. Resulting gene predictions are translated and evaluated based on their similarity to the consensus sequence. Here we discuss development of this pipeline, named GASCO (Genome Annotation by Similarity to Consensus of Orthologs), including strengths and drawbacks of several annotation methods as applied to maize, and directions for further development.