A genome at the brink of extinction: the mitochondrial genome of Chromera velia encodes a single gene

Mitochondrial genomes have all degenerated from the same bacterial ancestor, but to greatly different degrees. The most reduced genomes known are in apicomplexan parasites and dinoflagellates, where only three protein-coding and truncated rRNA genes have been found in a variety of unusual organizations. Here we characterize the mitochondrial genome of Chromera velia, a recently described photosynthetic relative of apicomplexans, and find this genome to be reduced to a single complete gene. Analysis of 1 Gbp of sequence data obtained from both total DNA and mitochondrial DNA-enriched CsCl fraction revealed hundreds of linear, partially overlapping molecules varying in length. These molecules encode a single protein-coding gene, cox1, as well as small independently transcribed fragments of ribosomal RNA genes. Cox1 genes were found in hundreds of different genetic contexts and, although many of them are pseudogenes, full-length functional genes are transcribed into oligoadenylated mRNA. Overall, the C. velia mitochondrial genome appears to have reached the lower limit of coding capacity, since the loss of the last remaining functional gene would presumably lead to the outright extinction of the genome altogether.