Open Access Research article

Pause-melting misalignment: a novel model for the birth and motif indel of tandem repeats in the mitochondrial genome

Wei Shi1, Xiao-Yu Kong1*, Zhong-Ming Wang1, Shan-Shan Yu1, Hai-Xia Chen2 and Elizabeth A De Stasio3

Author Affiliations

1 Key Laboratory of Marine Bio-resource Sustainable Utilization (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, Republic of China

2 Department of Biological and Environmental Sciences, University of Gothenburg, PO Box 463, SE-405 30, Gothenburg, Sweden

3 Biology Department, Lawrence University, 711 E. Boldt Way, 54911, Appleton, WI, USA

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BMC Genomics 2013, 14:103  doi:10.1186/1471-2164-14-103

Published: 15 February 2013



Tandem repeats (TRs) in the mitochondrial (mt) genome control region have been documented in a wide variety of vertebrate species. The mechanism by which repeated tracts originate and undergo duplication and deletion, however, remains unclear.


We analyzed DNA sequences of mt genome TRs (mtTRs) in the ridged-eye flounder (Pleuronichthys cornutus), and characterized DNA sequences of mtTRs from other vertebrates using the data available in GenBank. Tandem repeats are concentrated in the control regions; however, we found approximately 16.6% of the TRs elsewhere in the mt genome. The flounder mtTRs possess three motif types with hypervariable characteristics at the 3′ end of the control region (CR).


Based on our analysis of this larger dataset of mtTR sequences, we propose a novel model of Pause Melting Misalignment (PMM) to describe the birth and motif indel of tandem repeats. PMM is activated during a pause event in mitochondrial replication in which a dynamic competition between the nascent (N) heavy strand and the displaced (D) heavy strand may lead to the melting of the N-strand from the template (T) light strand. When mispairing occurs during rebinding of the N-strand, one or several motifs can be inserted or deleted in both strands during the next round of mt-replication or repair. This model can explain the characteristics of TRs in available vertebrate mt genomes.