Cell-type specific RNA-Seq reveals novel roles and regulatory programs for terminally differentiated Dictyostelium cells

Koryu Kin,Andrew Cassidy,Gillian Forbes,Pauline Schaap

doi:10.1186/s12864-018-5146-3

Abstract

BackgroundA major hallmark of multicellular evolution is increasing complexity by the evolution of new specialized cell types. During Dictyostelid evolution novel specialization occurred within taxon group 4. We here aim to retrace the nature and ancestry of the novel “cup” cells by comparing their transcriptome to that of other cell types.ResultsRNA-Seq was performed on purified mature spore, stalk and cup cells and on vegetative amoebas. Clustering and phylogenetic analyses showed that cup cells were most similar to stalk cells, suggesting that they share a common ancestor. The affinity between cup and stalk cells was also evident from promoter-reporter studies of newly identified cell-type genes, which revealed late expression in cups of many stalk genes. However, GO enrichment analysis reveal the unexpected prominence of GTPase mediated signalling in cup cells, in contrast to enrichment of autophagy and cell wall synthesis related transcripts in stalk cells. Combining the cell type RNA-Seq data with developmental expression profiles revealed complex expression dynamics in each cell type as well as genes exclusively expressed during terminal differentiation. Most notable were nine related hssA-like genes that were highly and exclusively expressed in cup cells.ConclusionsThis study reveals the unique transcriptomes of the mature cup, stalk and spore cells of D. discoideum and provides insight into the ancestry of cup cells and roles in signalling that were not previously realized. The data presented in this study will serve as an important resource for future studies into the regulation and evolution of cell type specialization.

Highlights

A major hallmark of multicellular evolution is increasing complexity by the evolution of new specialized cell types
We introduced YFP linked to the DDB_G0278537 cup specific promoter into wild type cells and confirmed that YFP fluorescence was restricted to the cup cells (Fig. 1d). (DDB_G0278537 was initially named cupB, but as the CUP acronym was already used for Dictyostelium Ca2+-upregulated genes, we replaced cup with bei, Chinese for cup, for this and three other late cup-specific genes [13], see Additional File 1: Table S6)
We found no evidence that the use of two different techniques for isolating RNA introduced systematic biases in downstream RNA-Seq analyses, such as sample clustering according to RNA isolation method

Summary

Introduction

A major hallmark of multicellular evolution is increasing complexity by the evolution of new specialized cell types. During Dictyostelid evolution novel specialization occurred within taxon group 4. Dictyostelid social amoebas are an ancient group which is thought to have diverged about six hundred million years ago and includes more than 150 known species [3]. They alternate between unicellular and multicellular stages in their life cycles, with the unicellular forms feeding on bacteria in forest soils. Molecular phylogenetic studies in the last 15 years revealed the presence of four major groups in the Dicytostelids [4,5,6]. Mapping of phenotypic characters onto the phylogeny revealed that most changes in

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