Candidate CMS genes. (A) Genomic map surrounding the ORFs upstream of the nad6 gene that were previously shown to be associated with the CMS phenotype (Case and Willis 2008). The atp1 promoter region is shown in blue. The beginning is estimated to be 1736 bp upstream of the start of nad6 (Case and Willis 2008). (B) Genomic map surrounding the three ORFs (orf387, orf112, and orf56) identified in this study that may be alternative or additional CMS genes due to their chimeric nature. Small repeats that generate the chimeric portions of the ORFs are color coded according to the genome map in figure 2. Other small repeats are shown on the map in purple. Below each small repeat, the number of read pairs that indicate substoichiometric rearrangements with the other repeat copy is shown, and the genomic position of the other repeat copy (or copies) is given in parentheses. The large repeat R1 is shown in black. A plastid insertion site is shown in green. Additional ORFs not considered candidate CMS genes are shown as shorter boxes with hatched borders.