In cytoplasmic male-sterile Petunia lines, NADH dehydrogenase subunit 3 (nad3) and ribosomal protein S12 (rps12) are cotranscribed with the chimeric gene pcf and located in the region of the mitochondrial genome associated with cytoplasmic male sterility (CMS) in Petunia. In fertile Petunia line 3704, the genes for nad3 and rps12 are cotranscribed with an unidentified open reading frame (orf143). In the homologous region of fertile line 3699, there is an ORF that lacks a genomic DNA-encoded stop codon; instead an RNA editing event creates a stop codon, resulting in an ORF of 161 codons. While expressed sequences homologous to this open reading frame can be detected in sterile lines, a contiguous orf143/orf161 gene does not exist in the CMS-encoding mitochondrial genome. Transcription at the CMS-associated pcf locus and the fertile orf143/nad3/rps12 locus is complex, with multiple 5′ and 3′ termini. The presence of the nuclear fertility restorer gene affects the abundance of a transcript class with 5′ termini - 121 nucleotides before the pcf start codon, and greatly reduces the abundance of a pcf gene product with apparent molecular mass of 25 kDa which is present in both vegetative and reproductive tissues of CMS plants. In addition to the 25 kDa protein product, small amounts of precursor and processed pcf products with higher molecular mass have been detected; their possible role in the CMS phenotype is unknown. Current hypotheses for the mechanism of action of CMS-associated and fertility restorer genes are discussed.