A critical assessment of cross-species detection of gene duplicates using comparative genomic hybridization

Abstract

BackgroundComparison of genomic DNA among closely related strains or species is a powerful approach for identifying variation in evolutionary processes. One potent source of genomic variation is gene duplication, which is prevalent among individuals and species. Array comparative genomic hybridization (aCGH) has been successfully utilized to detect this variation among lineages. Here, beyond the demonstration that gene duplicates among species can be quantified with aCGH, we consider the effect of sequence divergence on the ability to detect gene duplicates.ResultsUsing the X chromosome genomic content difference between male D. melanogaster and female D. yakuba and D. simulans, we describe a decrease in the ability to accurately measure genomic content (copy number) for orthologs that are only 90% identical. We demonstrate that genome characteristics (e.g. chromatin environment and non-orthologous sequence similarity) can also affect the ability to accurately measure genomic content. We describe a normalization strategy and statistical criteria to be used for the identification of gene duplicates among any species group for which an array platform is available from a closely related species.ConclusionsArray CGH can be used to effectively identify gene duplication and genome content; however, certain biases are present due to sequence divergence and other genome characteristics resulting from the divergence between lineages. Highly conserved gene duplicates will be more readily recovered by aCGH. Duplicates that have been retained for a selective advantage due to directional selection acting on many loci in one or both gene copies are likely to be under-represented. The results of this study should inform the interpretation of both previously published and future work that employs this powerful technique.

Copy Number Variation in Transcriptionally Active Regions of Sexual and Apomictic Boechera Demonstrates Independently Derived Apomictic Lineages

“…Machado and Renn (Machado and Renn 2010) suggested gene duplication as an important source of functional novelty, as it has been shown to be involved in adaptive evolution in response to diet (Zhang et al 2002), chemical challenge (Labbé et al 2007), and reproductive incompatibility (Lynch and Force 2000). Our GO analyses indeed showed duplications for genes involved in both abiotic and biotic stress responses (see Supplemental Figures 2C and 2D online), potentially providing the genetic variability to rapidly respond to environmental factors in both sexual and apomictic forms.…”

Between-species differences in gene copy number are enriched among functions critical for adaptive evolution in Arabidopsis halleri

“…We employed a novel approach to correct this bias by using a signal adjustment strategy, which - unlike previous methods [42, 43] — accounts for sequence mismatches through a global adjustment of cross-species hybridization signal intensities. In brief, we implemented a two-step normalization scheme (Fig.…”

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a A. lyrata genes sharing ≥ 95% sequence identity with their closest A. thaliana homologue [68] are termed highly conserved (compare Additional file 7)

b Headers of half-columns refer to total number of CNEs predicted by Ensembl Plants (E; Vilella et al 2009) alone or additionally by A. lyrata genome analysis (E-A; Hu et al 2011), respectively, as given in parentheses here. Shown are commonalities with these two groups of genes (same column, below) or data referring to these two groups of genes (columns to the right) c True positive is a CNE detected based on array-CGH that was previously predicted to be a CNE by Ensembl Plants [68] alone, or additionally by A. lyrata genome [35] analysis d [42] e [43]

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“…Shown are commonalities with these two groups of genes (same column, below) or data referring to these two groups of genes (columns to the right) c True positive is a CNE detected based on array-CGH that was previously predicted to be a CNE by Ensembl Plants [68] alone, or additionally by A. lyrata genome [35] analysis d [42] e [43]…”

Fourteen-Genome Comparison Identifies DNA Markers for Severe-Disease-Associated Strains of Clostridium difficile

“…Given the high quality of the 3 completed genomes and 11 draft genomes used in our analyses, we were able to combine sequence comparisons and syntenic relationships to determine gene orthologs and observed that, compared to NAP1 references, the members of the NAP7-NAP8 group displayed a higher level of genetic diversity, with an average of 97% identity. We believe that in comparative genome hybridization (CGH) studies, for example, where probe mismatches can affect hybridization (41,49) and where NAP1 or strain 630 genomes have been used as the reference, even a very low number of mismatches between the probe and target DNA can increase the false-negative rate (34,58). This leads us to suggest that the C. difficile CGH arrays, which were designed using either strain 630 (R group) or NAP1 isolate QCD-32g58, may produce numerous falsenegative hybridizations when tested using more a more distantly related strain (e.g., NAP7) and have resulted in the calculation of a smaller core genome size.…”