Abstract
Author SummaryLinking genotype to phenotype is a major undertaking in modern biological research. A variety of strategies are used but have generally failed to explain the maintenance and acquisition of new phenotypic traits in changing populations. We propose that whole-genome cross-species comparisons can be used to identify gene clusters underlying phenotypic variation. In the present study we used gene expression datasets collected during fruit fly and mosquito embryogenesis to identify temporal changes in gene expression. We found that differentially represented tissue types (such as extraembryonic serosa) were clearly manifested by clusters of local discordances in gene expression. Discordances were also observed for a suite of maternally expressed genes, consistent with the notion that the abrupt maternal-zygotic transition seen in Drosophila is an evolutionary innovation of higher Diptera. We propose that gene clustering by expression discordance can be used to determine the genetic basis of phenotypic variation.
Highlights
During the 1980s and 1990s methods of molecular genetics were used to determine the contributions of individual genes to different developmental processes, such as the segmentation of the Drosophila embryo [1]
In the present study we used gene expression datasets collected during fruit fly and mosquito embryogenesis to identify temporal changes in gene expression
We found that differentially represented tissue types were clearly manifested by clusters of local discordances in gene expression
Summary
During the 1980s and 1990s methods of molecular genetics were used to determine the contributions of individual genes to different developmental processes, such as the segmentation of the Drosophila embryo [1]. Collections of microarray data accumulated in public databases cover a variety of different conditions and sometimes even the full life cycles for a range of evolutionarily distant species. These data provide new opportunities to identify complete ensembles of genes engaged in the specification of body plans and morphological diversification. More recent studies focused on a set of fairly proximal yeast species have revealed that the regulation of even the most essential processes such as the cell cycle may not be conserved [2,3,4]. The regulation of genes, which are differentially regulated between species, was shown to be primarily driven by TATA-box containing promoters [5]
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