A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures

We obtained the complete mitochondrial sequence for 277 tetrapod species from GenBank and re-annotated all of the tRNAs based on a multiple alignment of each tRNA gene and secondary structure prediction made independently for each tRNA. The mitochondrial (mt) tRNA sequences and the secondary structure based multiple alignments are freely available as Supplemental Information online.We compiled a manually curated database of mitochondrially encoded tRNAs from tetrapods with completely sequenced genomes. In the course of our work, we reannotated more than 10% of all tetrapod mt-tRNAs and subsequently predicted the secondary structures of 6060 mitochondrial tRNAs. This carefully constructed database can be utilized to enhance our knowledge in several different fields including the evolution of mt-tRNA secondary structure and prediction of pathogenic mt-tRNA mutations. In addition, researchers reporting novel mitochondrial genome sequences should check their tRNA gene annotations against our database to ensure a higher level of fidelity of their annotation.Mitochondrially encoded tRNAs (mt-tRNAs) are an excellent object of study for researchers in several fields for a variety of reasons. The primary reason is the wide variety of available completely sequenced mitochondrial genomes, which provides a large data sample from a broad phylogenetic background. Besides the obvious availability factor, mt-tRNAs show several unusual properties. mt-tRNAs are of particular interest to structural biologists, since the secondary structure of the mt-tRNAs is not as conserved as that of their nuclear encoded counterparts [1], and some mt-tRNAs in several lineages show accelerated rates of secondary structure evolution [2]. Although some changes of the secondary structure may be of limited use as a phylogenetic marker the observation of parallel loss of the D-loop structure [1-3] may lead to our understanding of the broader issues associated with parallel evolution of secondary structur