RESUMO
Despite their monophyletic origin, mitochondrial (mt) genomes of plants and animals have developed contrasted evolutionary paths over time. Animal mt genomes are generally small, compact, and exhibit high mutation rates, whereas plant mt genomes exhibit low mutation rates, little compactness, larger sizes, and highly rearranged structures. We present the (nearly) whole sequences of five new mt genomes in the Beta genus: four from Beta vulgaris and one from B. macrocarpa, a sister species belonging to the same Beta section. We pooled our results with two previously sequenced genomes of B. vulgaris and studied genome diversity at the species level with an emphasis on cytoplasmic male-sterilizing (CMS) genomes. We showed that, contrary to what was previously assumed, all three CMS genomes belong to a single sterile lineage. In addition, the CMSs seem to have undergone an acceleration of the rates of substitution and rearrangement. This study suggests that male sterility emergence might have been favored by faster rates of evolution, unless CMS itself caused faster evolution.
Assuntos
Beta vulgaris/genética , DNA Mitocondrial/genética , Variação Genética , Genoma Mitocondrial/genética , Sequência de Bases , Beta vulgaris/classificação , Mapeamento Cromossômico , Cromossomos de Plantas/genética , DNA de Cloroplastos/química , DNA de Cloroplastos/genética , DNA Mitocondrial/química , DNA de Plantas/química , DNA de Plantas/genética , Evolução Molecular , Genes Mitocondriais/genética , Genoma de Planta/genética , Genômica/métodos , Dados de Sequência Molecular , Mutação , Filogenia , Análise de Sequência de DNA , Homologia de Sequência de Aminoácidos , Especificidade da Espécie , SinteniaRESUMO
MOTIVATION: Evolution acts in several ways on DNA: either by mutating a base, or by inserting, deleting or copying a segment of the sequence (Ruddle, 1997; Russell, 1994; Li and Grauer, 1991). Classical alignment methods deal with point mutations (Waterman, 1995), genome-level mutations are studied using genome rearrangement distances (Bafna and Pevzner, 1993, 1995; Kececioglu and Sankoff, 1994; Kececioglu and Ravi, 1995). The latter distances generally operate, not on the sequences, but on an ordered list of genes. To our knowledge, no measure of distance attempts to compare sequences using a general set of segment-based operations. RESULTS: Here we define a new family of distances, called transformation distances, which quantify the dissimilarity between two sequences in terms of segment-based events. We focus on the case where segment-copy, -reverse-copy and -insertion are allowed in our set of operations. Those events are weighted by their description length, but other sets of weights are possible when biological information is available. The transformation distance from sequence S to sequence T is then the Minimum Description Length among all possible scripts that build T knowing S with segment-based operations. The underlying idea is related to Kolmogorov complexity theory. We present an algorithm which, given two sequences S and T, computes exactly and efficiently the transformation distance from S to T. Unlike alignment methods, the method we propose does not necessarily respect the order of the residues within the compared sequences and is therefore able to account for duplications and translocations that cannot be properly described by sequence alignment. A biological application on Tnt1 tobacco retrotransposon is presented. AVAILABILITY: The algorithm and the graphical interface can be downloaded at http://www.lifl.fr/ approximately varre/TD
