Replication slippage may cause parallel evolution in the secondary structures of mitochondrial transfer RNAs

Presence of the dihydrouridine (D) stem in the mitochondrial cysteine tRNAis unusually variable among lepidosaurian reptiles. Phylogenetic andcomparative analyses of cysteine tRNA gene sequences identify eightparallel losses of the D-stem, resulting in D-arm replacement loops.Sampling within the monophyletic Acrodonta provides no evidence forreversal. Slipped-strand mispairing of noncontiguous repeated sequencesduring replication or direct replication slippage can explain repeatsobserved within cysteine tRNAs that contain a D-arm replacement loop. Thesetwo mechanisms involving replication slippage can account for the loss ofthe cysteine tRNA D-stem in several lepidosaurian lineages, and mayrepresent general mechanisms by which the secondary structures ofmitochondrial tRNAs are altered.