Comparing the development of cortex-wide gene expression patterns between two species in a common reference frame

Advances in sequencing techniques have made comparative studies of gene expression a current focus for understanding evolutionary and developmental processes. How-ever, insights into the spatial expression of genes have been limited by a lack of robust methodology. To overcome this obstacle, we developed methods and software tools for quantifying and comparing tissue-wide spatial patterns of gene expression within and between species. Here, we compare cortex-wide expression of RZR beta and Id2 mRNA across early postnatal development in mice and voles. We show that patterns of RZR beta expression in neocortical layer 4 are highly conserved between species but develop rapidly in voles and much more gradually in mice, who show a marked expansion in the relative size of the putative primary visual area across the first post-natal week. Patterns of Id2 expression, by contrast, emerge in a dynamic and layer -specific sequence that is consistent between the two species. We suggest that these differences in the development of neocortical patterning reflect the independent evo-lution of brains, bodies, and sensory systems in the 35 million years since their last common ancestor.

Automated summary

Advances in sequencing techniques have allowed for comparative studies of gene expression, but spatial expression has remained limited due to a lack of robust methodology. In this study, methods and software tools were developed to quantify and compare tissue-wide spatial patterns of gene expression within and between species. The expression patterns of RZR beta and Id2 mRNA in the cortex were compared across early postnatal development in mice and voles. The results showed that RZR beta expression patterns were highly conserved between species, while Id2 expression patterns emerged in a consistent manner across layers in both species. These differences in neocortical patterning development were suggested to reflect the independent evolution of brains, bodies, and sensory systems since their common ancestor 35 million years ago.