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Codage et traitement phylogénétique de caractères structuraux de génomes entiers


By Cyril - Posted on 17 April 2014

TitleCodage et traitement phylogénétique de caractères structuraux de génomes entiers
Publication TypeMiscellaneous
Year of Publication2001
AuthorsGallut C
Keywordschromosome, Cladistic, coding, evolution, gene order, genomic, mitochondrial genome., phylogeny
AbstractAn original approach of phylogenetic reconstruction from whole genomes' organization in a cladistic framework is proposed. This approach is based on global comparison of genomes' organization with no a priori assumptions about rearrangements. Two codings are proposed: "Relative position" and "Junctions", with two different options. These coding possibilities are analyzed and compared along with the "Signed junctions" coding of Cosner et al.; they allow to represent the functional units order along the chromosome, as an example, functional units can be gene or homologous chromosomal segments. The "Relative position" coding is composed of three different kinds of characters: position characters, polarity and units presence/absence characters. The "Junctions" coding is based on binary characters: units' polarity, units and units junctions presence/absence. The "Signed junctions" coding is only composed of signed junctions presence/absence characters. This coding has the advantage of considering polarity and position simultaneously. On the other hand, the "Relative position" coding allows reconstituting ancestral genomes a posteriori, which is of great interest to interpreting genome evolution. The metazoan mitochondrial genome and Mastomys genus chromosomes have been successfully analyzed with the three coding approaches.