Comparative Transcriptomics Reveals Distinct Patterns of Gene Expression Conservation through Vertebrate Embryogenesis

Despitelife's diversity, studies of variation often remindus of our shared evolutionarypast. Abundantgenomesequencingandanalyses of gene regulatory networks illustrate that genes and entire pathways are conserved, reused, and elaborated in the evolution of diversity. Predating these discoveries, 19th-century embryologists observed that though morphology at birth varies tremendously, certain stages of vertebrate embryogenesis appear remarkably similar across vertebrates. In the mid to late 20th century, anatomical variabilityofearlyandlate-stage embryosandconservationofmid-stagesembryos (thephylotypic stage) wasnamedthehourglass model of diversification. Thismodel has found mixed support in recent analyses comparing gene expression across species possibly owing to differences in species, embryonic stages, and gene sets compared. We compare 186 microarray and RNA-seq data sets covering embryogenesis in six vertebrate species. We use an unbiased clustering approach to group stages of embryogenesis by transcriptomic similarity and ask whether gene expression similarity of clustere dembryonic stages deviates from a null expectation. We characterize expression conservation patterns of each gene at each evolutionary node after correcting for phylogenetic nonindependence. We find significant enrichment of genes exhibiting early conservation, hourglass, late conservation patterns in both microarray and RNA-seq data sets. Enrichment of genes showing patterned conservation through embryogenesis indicates diversification of embryogenesismay be temporally constrained. However, the circumstances under which each pattern emerges remain unknown and require both broad evolutionary sampling and systematic examination of embryogenesis across species.

Automated summary

Studies have shown that genes and entire pathways are often conserved, reused, and elaborated in the evolution of diversity. Observations in embryology suggest similarities in certain stages of vertebrate embryogenesis across species. Genes exhibiting conservation patterns through embryogenesis, including early conservation, hourglass, and late conservation, are significantly enriched in both microarray and RNA-seq data sets.