Schematic of analysis pipeline. The expected location of genes with no BLASTP hit was scrutinized for any evidence of a homologous protein-coding gene. The expected location of a gene is indicated by green shading and was defined as a 10 gene window on either side of the gene of interest projected onto the syntenic location in the other genome. Candidate genes were excluded if there was a sequencing gap in the expected location (or local inversions that rendered the expected location ambiguous) or similar sequence at the expected location with no clear exclusion from producing a protein.