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This article is part of the Research Topic The Brassica Genome

Original Research ARTICLE

Front. Plant Sci., 29 August 2012 | http://dx.doi.org/10.3389/fpls.2012.00192

A phylogenetic analysis of the Brassicales clade based on an alignment-free sequence comparison method

  • Abteilung NMR-Basierte Strukturbiologie, Max-Planck-Institut für Biophysikalische Chemie, Göttingen, Germany

Phylogenetic analyses reveal the evolutionary derivation of species. A phylogenetic tree can be inferred from multiple sequence alignments of proteins or genes. The alignment of whole genome sequences of higher eukaryotes is a computational intensive and ambitious task as is the computation of phylogenetic trees based on these alignments. To overcome these limitations, we here used an alignment-free method to compare genomes of the Brassicales clade. For each nucleotide sequence a Chaos Game Representation (CGR) can be computed, which represents each nucleotide of the sequence as a point in a square defined by the four nucleotides as vertices. Each CGR is therefore a unique fingerprint of the underlying sequence. If the CGRs are divided by grid lines each grid square denotes the occurrence of oligonucleotides of a specific length in the sequence (Frequency Chaos Game Representation, FCGR). Here, we used distance measures between FCGRs to infer phylogenetic trees of Brassicales species. Three types of data were analyzed because of their different characteristics: (A) Whole genome assemblies as far as available for species belonging to the Malvidae taxon. (B) EST data of species of the Brassicales clade. (C) Mitochondrial genomes of the Rosids branch, a supergroup of the Malvidae. The trees reconstructed based on the Euclidean distance method are in general agreement with single gene trees. The Fitch–Margoliash and Neighbor joining algorithms resulted in similar to identical trees. Here, for the first time we have applied the bootstrap re-sampling concept to trees based on FCGRs to determine the support of the branchings. FCGRs have the advantage that they are fast to calculate, and can be used as additional information to alignment based data and morphological characteristics to improve the phylogenetic classification of species in ambiguous cases.

Keywords: Chaos game representation, Brassicales, Brassica rapa, phylogenetic tree, bootstrap re-sampling, frequency Chaos game representation

Citation: Hatje K and Kollmar M (2012) A phylogenetic analysis of the Brassicales clade based on an alignment-free sequence comparison method. Front. Plant Sci. 3:192. doi: 10.3389/fpls.2012.00192

Received: 25 May 2012; Accepted: 06 August 2012;
Published online: 29 August 2012.

Edited by:

Xiaowu Wang, Chinese Academy of Agricultural Sciences, China

Reviewed by:

Ruiqiang Li, Peking University, China
Bernhard Haubold, Max-Planck-Society, Germany

Copyright: © 2012 Hatje and Kollmar. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and subject to any copyright notices concerning any third-party graphics etc.

*Correspondence: Martin Kollmar, Abteilung NMR-Basierte Strukturbiologie, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, D-37077 Göttingen, Germany. e-mail: mako@nmr.mpibpc.mpg.de