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Title: Array CGH Phylogeny: How accurate are Comparative Genomic Hybridization-based trees?

Author
item LUZ, GILBERT - University Of Toulouse
item Kasuga, Takao
item GLASS, N. LOUISE - University Of California
item TAYLOR, JOHN - University Of California

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/6/2011
Publication Date: 10/6/2011
Citation: Luz, G., Kasuga, T., Glass, N., Taylor, J. 2011. Array CGH Phylogeny: How accurate are Comparative Genomic Hybridization-based trees?. Biomed Central (BMC) Genomics. 12:487.

Interpretive Summary: Microarray hybridization has been used to infer phylogenetic (evolutionary) relationships. However, the reliability of microarray to determine evolutionary relationships has not been well established. Here, we conducted simulation study by testing the use of microarray hybridization as a phylogenetic tool with experimental hybridization data gathered using a Neurospora crassa (filamentous fungus) 70mer array and competitive hybridizations between N. crassa and other Neurospora species. In the discussion, we add to our empirical study of Neurospora by reanalyzing of data from a previous microarray phylogenetic analysis of the yeasts. Although, DNA sequence-based multilocus phylogeny gives phylogeny with higher resolution, CGH gives information on gene duplications and evolutionary rates of genes, making the method potentially powerful for the study of plant pathogens.

Technical Abstract: Array-based Comparative Genomic Hybridization (CGH) data have been used to infer phylogenetic relationships. However, the reliability of array CGH analysis to determine evolutionary relationships has not been well established. In most CGH work, all species and strains are compared to a single reference species, whose genome was used to design the array. In the accompanying work, we critically evaluated CGH-based phylogeny using simulated competitive hybridization data. This work showed that a limited number of conditions, principally concerning the tree topology and placement of the reference taxon in the tree, had a strong effect on the ability to recover the correct tree topology. Here, we add to our simulation study by testing the use of CGH as a phylogenetic tool with experimental CGH data gathered using a Neurospora crassa 70mer array and competitive hybridizations between N. crassa and other Neurospora species. In the discussion, we add to our empirical study of Neurospora by reanalyzing of data from a previous CGH phylogenetic analysis of the yeast sensu stricto complex.