Gene silencing pathways found in the green alga Volvox carteri reveal insights into evolution and origins of small RNA systems in plants.

Anne Dueck,Detlef Weigel,Stefan R Henz,Eugene Berezikov,Norbert Eichner,Stephan Wenzl,Katharina Unger,Maurits Evers,Gunter Meister,Julia C Engelmann,Rainer Merkl

doi:10.1186/s12864-016-3202-4

Abstract

Background Volvox carteri (V. carteri) is a multicellular green alga used as model system for the evolution of multicellularity. So far, the contribution of small RNA pathways to these phenomena is not understood. Thus, we have sequenced V. carteri Argonaute 3 (VcAGO3)-associated small RNAs from different developmental stages.ResultsUsing this functional approach, we define the Volvox microRNA (miRNA) repertoire and show that miRNAs are not conserved in the closely related unicellular alga Chlamydomonas reinhardtii. Furthermore, we find that miRNAs are differentially expressed during different life stages of V. carteri. In addition to miRNAs, transposon-associated small RNAs or phased siRNA loci, which are common in higher land plants, are highly abundant in Volvox as well. Transposons not only give rise to miRNAs and other small RNAs, they are also targets of small RNAs.ConclusionOur analyses reveal a surprisingly complex small RNA network in Volvox as elaborate as in higher land plants. At least the identified VcAGO3-associated miRNAs are not conserved in C. reinhardtii suggesting fast evolution of small RNA systems. Thus, distinct small RNAs may contribute to multicellularity and also division of labor in reproductive and somatic cells.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3202-4) contains supplementary material, which is available to authorized users.

Highlights

Volvox carteri (V. carteri) is a multicellular green alga used as model system for the evolution of multicellularity
We found genes for an additional AGO protein, one Dicer, one RNAdependent RNA Polymerase (RdRP) and a HEN1 homolog (Additional file 2: Figure S1), suggesting that several small RNA pathways might operate in V. carteri [10]
Since we select for V. carteri Argonaute 3 (VcAGO3)-bound small RNAs only, it is very likely that we identify functional small RNAs and minimize background cloning that would contaminate our libraries

Summary

Introduction

Volvox carteri (V. carteri) is a multicellular green alga used as model system for the evolution of multicellularity. We have sequenced V. carteri Argonaute 3 (VcAGO3)-associated small RNAs from different developmental stages. V. carteri is a freshwater alga with female and male cells that can reproduce both sexually and asexually and is composed of two different cell types [1]. 2000 somatic cells and encloses several reproductive cells Each of these so called gonidia can undergo symmetric and asymmetric cell divisions to form a new colony of somatic cells and gonidia [2]. Non-coding RNAs, including small RNAs, have been associated with processes that are crucial to eukaryotic evolution. Small RNAs are processed from longer precursor molecules to their mature forms that are subsequently bound by a member of the Argonaute (AGO)

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