Microarrays for comparative and ecological genomics: beyond single-species applications of array technologies
Microarray technology has become an important tool to understand the biological significance of gene regulation. Microarray gene expression profiling has provided insight into development, maturation, infection and the response to pollutants and environmental stressors. However, the development of species-specific microarrays can be time consuming and costly. Therefore, where a microarray for a closely related species is available, use of a heterologous microarray platform can provide an attractive alternative. Heterologous microarray experiments are also of great interest in comparative studies where the aim is to compare gene regulation across a number of species. This review describes the principles underlying heterologous microarray experiments and discusses some examples of their use that have already helped advance the understanding of fish biology. However, sequence mismatches between the probes on the microarray and the target sequences can confound measures of gene regulation when using microarrays across species. The impact of sequence mismatches on the accurate detection of gene regulation is discussed. Interspecies genomic hybridization experiments comparing genomic DNA from different species can help identify which probes on the microarray can be used reliably to assay gene regulation across species. Finally, a number of recent advances in platform development for transcriptomics are described. These include multispecies microarrays that represent probes derived from multiple species and universal microarrays where the probes are designed to match evolutionarily conserved sequence regions. Next generation sequencing technologies are also likely to find broader application in transcriptomics in the near future.