Fig. 1

Stop codons and frameshifts in potential pseudogenes. Genes that are missing or predicted as non-functional in at least one of the five species. Solid white bars indicate the gene is present and appears functional in that species, while bars with gray shading or black lines may be pseudogenes. The structure of the protein-encoding portion of the gene is indicated within each box, with the 5′ end being at the far left and the 3′ end at the far right. The size of each box is 100% of the protein-encoding region, so they are not corrected for the different sizes of the coding regions of each gene. Gray shading indicates portions of the genes with a shifted frame, while black lines indicate stop codons. Solid black bars are genes or gene segments that are completely missing from that species. For instance, the figure shows that the 5′ end of ndhA is missing in S. forbessii and the 3′ end is missing in S. hermonthica, but the multiple stop codons and frameshifts in the 5′ end in S. hermonthica should guarantee that it is a non-functional gene