Abstract
BackgroundUsing gene order as a phylogenetic character has the potential to resolve previously unresolved species relationships. This character was used to resolve the evolutionary history within the genus Prochlorococcus, a group of marine cyanobacteria.Methodology/Principal FindingsOrthologous gene sets and their genomic positions were identified from 12 species of Prochlorococcus and 1 outgroup species of Synechococcus. From this data, inversion and breakpoint distance-based phylogenetic trees were computed by GRAPPA and FastME. Statistical support of the resulting topology was obtained by application of a 50% jackknife resampling technique. The result was consistent and congruent with nucleotide sequence-based and gene-content based trees. Also, a previously unresolved clade was resolved, that of MIT9211 and SS120.Conclusions/SignificanceThis is the first study to use gene order data to resolve a bacterial phylogeny at the genus level. It suggests that the technique is useful in resolving the Tree of Life.
Highlights
Comparisons of genomes reveal difference in the order of genes
Gene order data has been used in phylogenetic reconstructions of mitochondrion and chloroplast genomes [4,5,6] as well as bacterial genomes [7]
The BLASTCLUST procedure revealed 1131 orthologous genes which are shared by all 13 genomes, the 12 Prochlorococcus and the outgroup Synechococcus WH8102
Summary
Comparisons of genomes reveal difference in the order of genes. This provides a phylogenetic character to resolve species relationships and complements the standard approach of using the nucleotide as the character of interest. We use inversion and breakpoint distances to reconstruct the phylogeny of the genus Prochlorococcus and to resolve a controversial node with statistical confidence. Gene order phylogenetic reconstruction GRAPPA [1,15] was used to compute the pairwise inversion and breakpoint distances from the gene order data.
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