ArticleBMC genomics2010
Using comparative genomic hybridization to survey genomic sequence divergence across species: a proof-of-concept from Drosophila.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers, 1 of them a synthesis that pooled it.
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Who cites it
13 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Dissecting the Transcriptional Patterns of Social Dominance across Teleosts.Integrative and comparative biology · 2016Pooled it
- Correspondence of aCGH and long-read genome assembly for detection of copy number differences: A proof-of-concept with cichlid genomes.PloS one · 2021Article
- The Genomic Substrate for Adaptive Radiation: Copy Number Variation across 12 Tribes of African Cichlid Species.Genome biology and evolution · 2019Article
- Population genomics of parallel evolution in gene expression and gene sequence during ecological adaptation.Scientific reports · 2018Article
- Between-species differences in gene copy number are enriched among functions critical for adaptive evolution in Arabidopsis halleri.BMC genomics · 2016Article
- Optimization of next-generation sequencing transcriptome annotation for species lacking sequenced genomes.Molecular ecology resources · 2016Article
- A Systems Biology Interpretation of Array Comparative Genomic Hybridization (aCGH) Data through Phylogenetics.Omics : a journal of integrative biology · 2016Article
- Gene duplication in an African cichlid adaptive radiation.BMC genomics · 2014Article
- Replication-timing boundaries facilitate cell-type and species-specific regulation of a rearranged human chromosome in mouse.Human molecular genetics · 2012Article
- Evolutionary insights into scleractinian corals using comparative genomic hybridizations.BMC genomics · 2012Article
- Fourteen-genome comparison identifies DNA markers for severe-disease-associated strains of Clostridium difficile.Journal of clinical microbiology · 2011Article
- Normalization and centering of array-based heterologous genome hybridization based on divergent control probes.BMC bioinformatics · 2011Article
- A critical assessment of cross-species detection of gene duplicates using comparative genomic hybridization.BMC genomics · 2010Article
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6 authors.
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Abstract
backgroundGenome-wide analysis of sequence divergence among species offers profound insights into the evolutionary processes that shape lineages. When full-genome sequencing is not feasible for a broad comparative study, we propose the use of array-based comparative genomic hybridization (aCGH) in order to identify orthologous genes with high sequence divergence. Here we discuss experimental design, statistical power, success rate, sources of variation and potential confounding factors. We used a spotted PCR product microarray platform from Drosophila melanogaster to assess sequence divergence on a gene-by-gene basis in three fully sequenced heterologous species (D. sechellia, D. simulans, and D. yakuba). Because complete genome assemblies are available for these species this study presents a powerful test for the use of aCGH as a tool to measure sequence divergence.
resultsWe found a consistent and linear relationship between hybridization ratio and sequence divergence of the sample to the platform species. At higher levels of sequence divergence (< 92% sequence identity to D. melanogaster) approximately 84% of features had significantly less hybridization to the array in the heterologous species than the platform species, and thus could be identified as "diverged". At lower levels of divergence (>or= 97% identity), only 13% of genes were identified as diverged. While approximately 40% of the variation in hybridization ratio can be accounted for by variation in sequence identity of the heterologous sample relative to D. melanogaster, other individual characteristics of the DNA sequences, such as GC content, also contribute to variation in hybridization ratio, as does technical variation.
conclusionsHere we demonstrate that aCGH can accurately be used as a proxy to estimate genome-wide divergence, thus providing an efficient way to evaluate how evolutionary processes and genomic architecture can shape species diversity in non-model systems. Given the increased number of species for which microarray platforms are available, comparative studies can be conducted for many interesting lineages in order to identify highly diverged genes that may be the target of natural selection.
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