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MBE Advance Access published online on June 29, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msi204
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© The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oupjournals.org
Accepted June 21, 2005

Research Article

Molecular Mechanisms of Extensive Mitochondrial Gene Rearrangement in Plethodontid Salamanders

Rachel Lockridge Mueller 1* and Jeffrey L. Boore 2

1 Museum of Vertebrate Zoology, 3101 Valley Life Sciences Bldg., University of California, Berkeley, CA 94720-3160; Evolutionary Genomics Department, DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, 2800 Mitchell Dr., Walnut Creek, CA 94598; Current address: Department of Organismal Biology and Anatomy, University of Chicago, 1027 E. 57th St, Chicago, IL 60637
2 Evolutionary Genomics Department, DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, 2800 Mitchell Dr., Walnut Creek, CA 94598; Department of Integrative Biology, 3060 Valley Life Sciences Bldg., University of California, Berkeley, CA 94720-3160

* To whom correspondence should be addressed.
Rachel Lockridge Mueller, E-mail: rmueller{at}uchicago.edu


  Abstract

Extensive gene rearrangement is reported in the mitochondrial genomes of lungless salamanders (Plethodontidae). In each genome with a novel gene order, there is evidence that the rearrangement was mediated by duplication of part of the mitochondrial genome, including the presence of both pseudogenes and additional, presumably functional, copies of duplicated genes. All rearrangement-mediating duplications include either the origin of light strand replication and the nearby tRNA genes or the regions flanking the origin of heavy strand replication. The latter regions comprise nad6, trnE, cob, trnT, an intergenic spacer between trnT and trnP and, in some genomes, trnP, the control region, trnF, rrnS, trnV, rrnL, trnL1, and nad1. In some cases, two copies of duplicated genes, presumptive regulatory regions, and/or sequences with no assignable function have been retained in the genome following the initial duplication; in other genomes, only one of the duplicated copies has been retained. Both tandem and non-tandem duplications are present in these genomes, suggesting different duplication mechanisms. In some of these mtDNAs, up to 25% of the total length is composed of tandem duplications of non-coding sequence that includes putative regulatory regions and/or pseudogenes of tRNAs and protein-coding genes along with otherwise unassignable sequences. These data indicate that imprecise initiation and termination of replication, slipped-strand mispairing, and intra-molecular recombination may all have played a role in generating repeats during the evolutionary history of plethodontid mitochondrial genomes.

Keywords: complete mitochondrial genomes; gene rearrangement; tandem duplication; pseudogenes; plethodontids.
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