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Open Access Research article

A scenario of mitochondrial genome evolution in maize based on rearrangement events

Aude Darracq123, Jean-Stéphane Varré23 and Pascal Touzet1*

Author Affiliations

1 Laboratoire de Genetique et Evolution des Populations Vegetales, UMR CNRS 8016, Universite Lille 1, 59655 Villeneuve d'Ascq Cedex, France

2 Laboratoire d'Informatique Fondamentale de Lille, UMR CNRS 8022, Universite Lille 1, 59655 Villeneuve d'Ascq Cedex, France

3 INRIA Lille-Nord Europe, 59650 Villeneuve d'Ascq, France

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BMC Genomics 2010, 11:233  doi:10.1186/1471-2164-11-233

Published: 9 April 2010

Abstract

Background

Despite their monophyletic origin, animal and plant mitochondrial genomes have been described as exhibiting different modes of evolution. Indeed, plant mitochondrial genomes feature a larger size, a lower mutation rate and more rearrangements than their animal counterparts. Gene order variation in animal mitochondrial genomes is often described as being due to translocation and inversion events, but tandem duplication followed by loss has also been proposed as an alternative process. In plant mitochondrial genomes, at the species level, gene shuffling and duplicate occurrence are such that no clear phylogeny has ever been identified, when considering genome structure variation.

Results

In this study we analyzed the whole sequences of eight mitochondrial genomes from maize and teosintes in order to comprehend the events that led to their structural features, i.e. the order of genes, tRNAs, rRNAs, ORFs, pseudogenes and non-coding sequences shared by all mitogenomes and duplicate occurrences. We suggest a tandem duplication model similar to the one described in animals, except that some duplicates can remain. This model enabled us to develop a manual method to deal with duplicates, a recurrent problem in rearrangement analyses. The phylogenetic tree exclusively based on rearrangement and duplication events is congruent with the tree based on sequence polymorphism, validating our evolution model.

Conclusions

This study suggests more similarity than usually reported between plant and animal mitochondrial genomes in their mode of evolution. Further work will consist of developing new tools in order to automatically look for signatures of tandem duplication events in other plant mitogenomes and evaluate the occurrence of this process on a larger scale.