Novel genetic code and record-setting AT-richness in the highly reduced plastid genome of the holoparasitic plant .

Plastid genomes (plastomes) vary enormously in size and gene content among the many lineages of nonphotosynthetic plants, but key lineages remain unexplored. We therefore investigated plastome sequence and expression in the holoparasitic and morphologically bizarre Balanophoraceae. The two plastomes examined are remarkable, exhibiting features rarely if ever seen before in plastomes or in any other genomes. At 15.5 kb in size and with only 19 genes, they are among the most reduced plastomes known. They have no tRNA genes for protein synthesis, a trait found in only three other plastid lineages, and thus plastids must import all tRNAs needed for translation. plastomes are exceptionally compact, with numerous overlapping genes, highly reduced spacers, loss of all -spliced introns, and shrunken protein genes. With A+T contents of 87.8% and 88.4%, the genomes are the most AT-rich genomes known save for a single mitochondrial genome that is merely bloated with AT-rich spacer DNA. Most plastid protein genes in consist of ≥90% AT, with several between 95% and 98% AT, resulting in the most biased codon usage in any genome described to date. A potential consequence of its radical compositional evolution is the novel genetic code used by plastids, in which TAG has been reassigned from stop to tryptophan. Despite its many exceptional properties, the plastome must be functional because all examined genes are transcribed, its only intron is correctly -spliced, and its protein genes, although highly divergent, are evolving under various degrees of selective constraint.