title: A hotspot of gene order rearrangement by tandem duplication and random loss in the vertebrate mitochondrial genome.
abstract: Most reported examples of change in vertebrate mitochondrial (mt) gene order could be explained by a tandem duplication followed by random loss of redundant genes (tandem duplication-random loss [TDRL] model). Under this model of evolution, independent loss of genes arising from a single duplication in an ancestral species are predicted, and remnant pseudogenes expected, intermediate states that may remain in rearranged genomes. However, evidence for this is rare and largely scattered across vertebrate lineages. Here, we report new derived mt gene orders in the vertebrate "WANCY" region of four closely related caecilian amphibians. The novel arrangements found in this genomic region (one of them is convergent with the derived arrangement of marsupials), presence of pseudogenes, and positions of intergenic spacers fully satisfy predictions from the TDRL model. Our results, together with comparative data for the available vertebrate complete mt genomes, provide further evidence that the WANCY genomic region is a hotspot for gene order rearrangements and support the view that TDRL is the dominant mechanism of gene order rearrangement in vertebrate mt genomes. Convergent gene rearrangements are not unlikely in hotspots of gene order rearrangement by TDRL.
authors.affiliation: Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain. diegos@mncn.csic.es
authors.forename: Diego
authors.initials: D
authors.lastname: San Mauro
authors.forename: David J
authors.initials: DJ
authors.lastname: Gower
authors.forename: Rafael
authors.initials: R
authors.lastname: Zardoya
authors.forename: Mark
authors.initials: M
authors.lastname: Wilkinson
mesh_terms: D000663:Amphibians / Q000235:genetics*; D000818:Animals; D001483:Base Sequence; D001499:Bayes Theorem; D001938:Brazil; D021901:DNA, Intergenic / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics*; D017353:Gene Deletion; D020440:Gene Duplication; D023061:Gene Order / Q000235:genetics*; D015321:Gene Rearrangement / Q000235:genetics*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D011544:Pseudogenes / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D021901:DNA, Intergenic; D004272:DNA, Mitochondrial