  The ability to locate and annotate mitochondrial genes is an important
practical issue, given the rapidly increasing number of mitogenomes appearing
in the public databases. Unfortunately, tRNA genes in Metazoan mitochondria
have proved to be problematic because they often vary in number (genes missing
or duplicated) and also in the secondary structure of the transcribed tRNAs (T
or D arms missing). I have performed a series of comparative analyses of the
tRNA genes of a broad range of Metazoan mitogenomes in order to address this
issue. I conclude that no single computer program is necessarily capable of
finding all of the tRNA genes in any given mitogenome, and that use of both the
ARWEN and DOGMA programs is sometimes necessary because they produce
complementary false negatives. There are apparently a very large number of
erroneous annotations in the databased mitogenome sequences, including missed
genes, wrongly annotated locations, false complements, and inconsistent
criteria for assigning the 5' and 3' boundaries; and I have listed many of
these. The extent of overlap between genes is often greatly exaggerated due to
inconsistent annotations, although notable overlaps involving tRNAs are
apparently real. Finally, three novel hypotheses were examined and found to
have support from the comparative analyses: (1) some organisms have mitogenomic
locations that simultaneously code for multiple tRNAs; (2) some organisms have
mitogenomic locations that simultaneously code for tRNAs and proteins (but not
rRNAs); and (3) one group of nematodes has several genes that code for tRNAs
lacking both the D and T arms.
