Variations in mitochondrial tRNA gene organization of reptiles as phylogenetic markers

Amplification and sequencing of mitochondrial DNA regions corresponding tothree major clusters of transfer RNA genes from a variety of speciesrepresenting major groups of birds and reptiles revealed some newvariations in tRNA gene organization. First, a gene rearrangement fromtRNA(His)-tRNA(Ser)(AGY)-tRNA(Leu)(CUN) to tRNA(Ser)(AGY)-tRNA(His)tRNA(Leu)(CUN) occurs in all three crocodilians examined(alligator, caiman, and crocodile). In addition an exceptionally longspacer region between the genes for NADH dehydrogenase subunit 4 andtRNA(Ser)(AGY) is found in caiman. Second, in congruence with a recentfinding by Seutin et al., a characteristic stem-and-loop structure for theputative light-strand replication origin located between tRNA(Asn) andtRNA(Cys) genes is absent for all the birds and crocodilians. Thisstem-and-loop structure is absent in an additional species, the Texas blindsnake, whereas the stem-and-loop structure is present in other snakes,lizards, turtles, mammals, and a frog. The disappearance of thestem-and-loop structure in the blind snake most likely occurredindependently of that on the lineage leading to birds and crocodilians.Finally, the blind snake has a novel type of tRNA gene arrangement in whichthe tRNA(Gln) gene moved from one tRNA cluster to another. Sequencesubstitution rates for the tRNA genes appeared to be somewhat higher incrocodialians than in birds and mammals. As regards the controversialphylogenetic relationship among the Aves, Crocodilia, and Mammalia, asister group relationship of birds and crocodilians relative to mammals, assuggested from the common loss of the stem-and- loop structure, wassupported with statistical significance by molecular phylogenetic analysesusing the tRNA gene sequence data.