Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/21/2011
Publication Date: 9/21/2011
Publication URL: http://www.biomedcentral.com/1471-2164/12/456
Citation: Luz, G., Lee, C., Kasuga, T., Taylor, J. 2011. Array Comparative Genomic Hybridizations: Assessing the ability to recapture evolutionary relationships using an in silico approach. Biomed Central (BMC) Genomics. 12:456. Interpretive Summary: Comparative Genomic Hybridization (CGH) with DNA microarrays has many biological applications including surveys of copy number changes in cancer biology, species detection and identification, and gene function study among related organisms. Array CGH has also been used to infer phylogenetic (evolutionary) relatedness among species or strains. The use of the entire genome can be seen as a considerable advantage for use in phylogenetic analysis. The method can also be used to highlight genome deviation between two organisms. A potential use of CGH for plant pathology would be for the identification of genome differences associated with ecological differences between pathogens.
Technical Abstract: Comparative Genomic Hybridization (CGH) with DNA microarrays has many biological applications including surveys of copy number changes in tumorigenesis, species detection and identification, and functional genomics studies among related organisms. Array CGH has also been used to infer phylogenetic relatedness among species or strains. Although the use of the entire genome can be seen as a considerable advantage for use in phylogenetic analysis, few such studies have questioned the reliability of array CGH to correctly determine evolutionary relationships. A potential flaw in this application lies in the fact that all comparisons are made to a single reference species. This situation differs from traditional DNA sequence, distance-based phylogenetic analyses where all possible pairwise comparisons are made for the isolates in question. By simulating array data based on the Neurospora crassa genome, we address this potential flaw and other questions regarding array CGH phylogeny.