Finding All Sorting Tandem Duplication Random Loss Operations

Bernt, Matthias; Chen, Ming-Chiang; Merkle, Daniel; Wang, Hung-Lung; Chao, Kun-Mao; Middendorf, Martin

doi:10.1007/978-3-642-02441-2_27

Cited by 1 publication

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“…While the standard model, i.e. a tandem duplication followed by a complete loss of one of the redundant copies, is well understood from a formal/bioinformatic point of view (76,77), our results motivate also for further studies of the TDRL model. In particular, this includes multiplications, cases with inverse duplications and especially the possibility of partial loss.…”

Section: Resultsmentioning

confidence: 63%

Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements

Jühling

Pütz²,

Bernt³

et al. 2011

Nucleic Acids Research

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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.

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Section: Resultsmentioning

confidence: 63%