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Background  One of evolution’s most important achievements is the development and radiation of multicellular organisms with different types of cells. Complex multicellularity has evolved several times in eukaryotes; yet, in most lineages, an investigation of its molecular background is considerably challenging since the transition occurred too far in the past and, in addition, these lineages evolved a large number of cell types. However, for volvocine green algae, such as  Volvox carteri , multicellularity is a relatively recent innovation. Furthermore,  V. carteri  shows a complete division of labor between only two cell types – small, flagellated somatic cells and large, immotile reproductive cells. Thus,  V. carteri  provides a unique opportunity to study multicellularity and cellular differentiation at the molecular level.    Results  This study provides a whole transcriptome RNA-Seq analysis of separated cell types of the multicellular green alga  V. carteri  f.  nagariensis  to reveal cell type-specific components and functions. To this end, 246 million quality filtered reads were mapped to the genome and valid expression data were obtained for 93% of the 14,247 gene loci. In the subsequent search for protein domains with assigned molecular function, we identified 9435 previously classified domains in 44% of all gene loci. Furthermore, in 43% of all gene loci we identified 15,254 domains that are involved in biological processes. All identified domains were investigated regarding cell type-specific expression. Moreover, we provide further insight into the expression pattern of previously described gene families (e.g., pherophorin, extracellular matrix metalloprotease, and  VARL  families). Our results demonstrate an extensive compartmentalization of the transcriptome between cell types: More than half of all genes show a clear difference in expression between somatic and reproductive cells.    Conclusions  This study constitutes the first transcriptome-wide RNA-Seq analysis of separated cell types of  V. carteri  focusing on gene expression. The high degree of differential expression indicates a strong differentiation of cell types despite the fact that  V. carteri  diverged relatively recently from its unicellular relatives. Our expression dataset and the bioinformatic analyses provide the opportunity to further investigate and understand the mechanisms of cell type-specific expression and its transcriptional regulation.    Electronic supplementary material  The online version of this article (doi:10.1186/s12915-017-0450-y) contains supplementary material, which is available to authorized users.

Whole transcriptome RNA-Seq analysis reveals extensive cell type-specific compartmentalization in Volvox carteri