Developmental transcriptomes of the sea star, Patiria miniata, illuminate the relationship between conservation of gene expression and morphological conservation

Abstract

Evolutionary changes in developmental gene expression lead to alteration in the embryonic body plan and biodiversity. A promising approach for linking changes in developmental gene expression to altered morphogenesis is the comparison of developmental transcriptomes of closely related and further diverged species within the same phylum. Here we generated quantitative transcriptomes of the sea star, Patiria miniata (P. miniata) of the echinoderm phylum, at eight embryonic stages. We then compared developmental gene expression between P. miniata and the sea urchin, Paracentrotus lividus (~500 million year divergence) and between Paracentrotus lividus and the sea urchin, Strongylocentrotus purpuratus (~40 million year divergence). We discovered that the interspecies correlations of gene expression level between morphologically equivalent stages decreases with increasing evolutionary distance, and becomes more similar to the correlations between morphologically distinct stages. This trend is observed for different sub-sets of genes, from various functional classes and embryonic territories, but is least severe for developmental genes sub-sets. The interspecies correlation matrices of developmental genes show a consistent peak at the onset of gastrulation, supporting the hourglass model of phylotypic stage conservation. We propose that at large evolutionary distance the conservation of relative expression levels for most sets of genes is more related to the required quantities of transcripts in a cell than to conserved morphogenesis processes. In these distances, the information about morphological similarity is reflected mostly in the interspecies correlations between the expressions of developmental control genes.\n\nAuthor summaryUnderstanding the relationship between the interspecies conservation of gene expression and morphological similarity is a major challenge in modern evolutionary and developmental biology. The Interspecies correlations of gene expression levels have been used extensively to illuminate these relationships and reveal the developmental stages that show the highest conservation of gene expression, focusing on the diagonal elements of the correlation matrices. Here we generated the developmental transcriptomes of the sea star, Patiria miniata, and used them to study the interspecies correlations between closely related and further diverged species within the echinoderm phylum. Our study reveals that the diagonal elements of the correlation matrices contain only partial information. The off-diagonal elements, that compare gene expression between distinct developmental stages, indicate whether the conservation of gene expression is indeed related to similar morphology or instead, to general cellular constraints that linger throughout development. With increasing evolutionary distances the diagonal elements decrease and become similar to the off-diagonal elements, reflecting the shift from morphological to general cellular constraints. Within this trend, the interspecies correlations of developmental control genes maintain their diagonality even at large evolutionary distance, and peak at the onset of gastrulation, supporting the hourglass model of phylotypic stage conservation.