Abstract
BackgroundMitochondrial tRNAs have been the subject of study for structural biologists interested in their secondary structure characteristics, evolutionary biologists have researched patterns of compensatory and structural evolution and medical studies have been directed towards understanding the basis of human disease. However, an up to date, manually curated database of mitochondrially encoded tRNAs from higher animals is currently not available.DescriptionWe 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.ConclusionWe 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.
Highlights
Mitochondrial tRNAs have been the subject of study for structural biologists interested in their secondary structure characteristics, evolutionary biologists have researched patterns of compensatory and structural evolution and medical studies have been directed towards understanding the basis of human disease
In the course of re-annotation and the compilation of a secondary-structure based multiple alignment, we have modified the annotation of the mt-tRNA gene location for 13% of all mt-tRNAs presented in our database
We suggest for researchers reporting novel mitochondrial genome sequences to check their tRNA gene annotations against our database to ensure a higher level of fidelity of their annotation
Summary
We report a secondary structure based multiple alignment of 6060 mt-tRNAs from 277 tetrapod species. FTarhiygeusstrereucco2tnudraeryfosrtrsuecletcutreedosfptehceietsheofnminte--tbRaNndAeCdysa(rbm, ca)dillo mt-tRNACys (a), and the multiple alignment with annotated secondThe secondary structure of the the nine-banded armadillo mt-tRNACys (a), and the multiple alignment with annotated secondary structure for selected species of mt-tRNACys (b, c). Http://www.biomedcentral.com/1471-2105/8/441 on mammalian mt-tRNAs. prediction of pathogenic mutations in mt-tRNAs relies heavily on evolutionary conservation [13,14] and the availability of a secondary structure-based alignment of an expanded set of species may contribute to a more accurate prediction of the phenotypic consequences of mt-tRNA mutations. KYuP, LAM and FAK conceived the construction of the database, and participated in the construction of the initial and final alignments, corrected erroneously annotated tRNAs and were involved in secondary structure prediction. FAK drafted the paper, and all authors read and approved the final manuscript
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