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The ability to locate and annotate mitochondrial genes is an importantpractical issue, given the rapidly increasing number of mitogenomes appearingin the public databases. Unfortunately, tRNA genes in Metazoan mitochondriahave proved to be problematic because they often vary in number (genes missingor duplicated) and also in the secondary structure of the transcribed tRNAs (Tor D arms missing). I have performed a series of comparative analyses of thetRNA genes of a broad range of Metazoan mitogenomes in order to address thisissue. I conclude that no single computer program is necessarily capable offinding all of the tRNA genes in any given mitogenome, and that use of both theARWEN and DOGMA programs is sometimes necessary because they producecomplementary false negatives. There are apparently a very large number oferroneous annotations in the databased mitogenome sequences, including missedgenes, wrongly annotated locations, false complements, and inconsistentcriteria for assigning the 5' and 3' boundaries; and I have listed many ofthese. The extent of overlap between genes is often greatly exaggerated due toinconsistent annotations, although notable overlaps involving tRNAs areapparently real. Finally, three novel hypotheses were examined and found tohave support from the comparative analyses: (1) some organisms have mitogenomiclocations that simultaneously code for multiple tRNAs; (2) some organisms havemitogenomic locations that simultaneously code for tRNAs and proteins (but notrRNAs); and (3) one group of nematodes has several genes that code for tRNAslacking both the D and T arms.

How and where to look for tRNAs in Metazoan mitochondrial genomes, and what you might find when you get there