Abstract
BackgroundVertebrates share the same general body plan and organs, possess related sets of genes, and rely on similar physiological mechanisms, yet show great diversity in morphology, habitat and behavior. Alteration of gene regulation is thought to be a major mechanism in phenotypic variation and evolution, but relatively little is known about the broad patterns of conservation in gene expression in non-mammalian vertebrates.ResultsWe measured expression of all known and predicted genes across twenty tissues in chicken, frog and pufferfish. By combining the results with human and mouse data and considering only ten common tissues, we have found evidence of conserved expression for more than a third of unique orthologous genes. We find that, on average, transcription factor gene expression is neither more nor less conserved than that of other genes. Strikingly, conservation of expression correlates poorly with the amount of conserved nonexonic sequence, even using a sequence alignment technique that accounts for non-collinearity in conserved elements. Many genes show conserved human/fish expression despite having almost no nonexonic conserved primary sequence.ConclusionsThere are clearly strong evolutionary constraints on tissue-specific gene expression. A major challenge will be to understand the precise mechanisms by which many gene expression patterns remain similar despite extensive cis-regulatory restructuring.
Highlights
Vertebrates share the same general body plan and organs, possess related sets of genes, and rely on similar physiological mechanisms, yet show great diversity in morphology, habitat and behavior
Our analyses demonstrate that core tissue-specific gene expression patterns are conserved across all major vertebrate lineages, but that the correspondence between conservation of expression and amount of conserved nonexonic sequence is weak overall, at least at a level that is detectable by current alignment approaches
To ask whether tissue-specific gene expression patterns are conserved among vertebrates, we focused on 1-1-1-1-1 orthologs, because genes that have undergone duplication events are subject to different constraints from singletons [45,46]
Summary
Vertebrates share the same general body plan and organs, possess related sets of genes, and rely on similar physiological mechanisms, yet show great diversity in morphology, habitat and behavior. Alteration of gene regulation is thought to be a major mechanism in phenotypic variation and evolution, but relatively little is known about the broad patterns of conservation in gene expression in non-mammalian vertebrates. Changes that benefit fitness (for example, under new ecological pressures) may become fixed: changes in gene expression are believed to underlie many differences in morphology, physiology and behavior and, subtle differences in gene regulation can result in spatial and temporal alterations in transcript levels, with phenotypic consequences at the cell, tissue and organismal levels [5,25]. The degree to which stabilizing selection constrains directional selection and neutral drift across the full vertebrate subphylum is, to our knowledge, unknown
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