19th International CODATA Conference
Category: Knowledge Discovery

Gene Arrangements and Branching Orders of Species Based Gene Transpositions

Takashi Kunisawa (kunisawa@rs.noda.tus.ac.jp)
Department of Applied Biological Sciences, Science University of Tokyo, Japan

Evolutionary relationships among species are frequently inferred from phylogenetic trees based on sequence alignment of homologous genes or proteins from different species. It is now known that there are many difficulties in obtaining reliable phylogenetic trees. These include reliability of sequence alignment, regions of sequences that are retained or excluded in phylogenetic analysis, variations in the substitution rate across sequence positions and/or among species, biases in base or amino acid compositions, and mutational saturation. Thus, complementary information is needed. In the previous papers (Kunisawa, J. Theor. Biol. 2001, 213, 9-19; 2003, 222,495-503), it was shown that specific gene-arrangements, namely a-x-b on one group of genomes and c-x on others, where a, b, c and stand for different genes and x is a transposed gene or gene cluster, can serve as a phylogenetic determinant. By searching for such transpositions, branching orders within Proteobacteria or Gram-positive bacteria were inferred. This method based on gene transposition provides complementary information to that derived from gene sequences, because gene rearrangements occur at different rates and by different mechanisms than gene sequences. Here, using complete genomic sequence data, which are available at NCBI (http://www.ncbi.nlm.nih.gov), a computer-search for gene transpositions is carried out to challenge an unresolved issue on the evolutionary origin of mitochondria.