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Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements
- Source :
- Nucleic acids research, 40(7): 2833–2845, Nucleic Acids Research
- Publication Year :
- 2011
- Publisher :
- Oxford University Press (OUP), 2011.
-
Abstract
- Transfer RNAs (tRNAs) are present in all types of cells as well as in organelles. tRNAs of animal mitochondria show a low level of primary sequence conservation and exhibit 'bizarre' secondary structures, lacking complete domains of the common cloverleaf. Such sequences are hard to detect and hence frequently missed in computational analyses and mitochondrial genome annotation. Here, we introduce an automatic annotation procedure for mitochondrial tRNA genes in Metazoa based on sequence and structural information in manually curated covariance models. The method, applied to re-annotate 1876 available metazoan mitochondrial RefSeq genomes, allows to distinguish between remaining functional genes and degrading 'pseudogenes', even at early stages of divergence. The subsequent analysis of a comprehensive set of mitochondrial tRNA genes gives new insights into the evolution of structures of mitochondrial tRNA sequences as well as into the mechanisms of genome rearrangements. We find frequent losses of tRNA genes concentrated in basal Metazoa, frequent independent losses of individual parts of tRNA genes, particularly in Arthropoda, and wide-spread conserved overlaps of tRNAs in opposite reading direction. Direct evidence for several recent Tandem Duplication-Random Loss events is gained, demonstrating that this mechanism has an impact on the appearance of new mitochondrial gene orders.
- Subjects :
- 0106 biological sciences
Mitochondrial DNA
RNA, Mitochondrial
Pseudogene
Computational biology
Biology
Mitochondrion
010603 evolutionary biology
01 natural sciences
Genome
Evolution, Molecular
03 medical and health sciences
RNA, Transfer
Gene Order
Genetics
Animals
Gene
030304 developmental biology
0303 health sciences
Computational Biology
Molecular Sequence Annotation
Gene Annotation
Genes, Mitochondrial
Genome, Mitochondrial
Transfer RNA
RNA
Pseudogenes
Subjects
Details
- ISSN :
- 13624962 and 03051048
- Volume :
- 40
- Database :
- OpenAIRE
- Journal :
- Nucleic Acids Research
- Accession number :
- edsair.doi.dedup.....a4826d1225f0de01b1e535e108d3c2cb