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MBE Advance Access originally published online on June 29, 2005
Molecular Biology and Evolution 2005 22(10):2104-2112; 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

Research Article

Molecular Mechanisms of Extensive Mitochondrial Gene Rearrangement in Plethodontid Salamanders

Rachel Lockridge Mueller*,{dagger},1 and Jeffrey L. Boore{dagger},{ddagger}

* Museum of Vertebrate Zoology, University of California, Berkeley; {dagger} Evolutionary Genomics Department, Department of Energy Joint Genome Institute and University of California Lawrence Berkeley National Laboratory, Walnut Creek, California; and {ddagger} Department of Integrative Biology, University of California, Berkeley

E-mail: rmueller{at}uchicago.edu.

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 nontandem duplications are present in these genomes, suggesting different duplication mechanisms. In some of these mitochondrial DNAs, up to 25% of the total length is composed of tandem duplications of noncoding sequence that includes putative regulatory regions and/or pseudogenes of tRNAs and protein-coding genes along with the otherwise unassignable sequences. These data indicate that imprecise initiation and termination of replication, slipped-strand mispairing, and intramolecular recombination may all have played a role in generating repeats during the evolutionary history of plethodontid mitochondrial genomes.

Key Words: complete mitochondrial genomes • gene rearrangement • tandem duplication • pseudogenes • plethodontids


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