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



Using 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.



Our 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.
Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany.
Anne
A
Dueck
Department of Statistical Bioinformatics, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany.|Present address: The John Curtin School of Medical Research, The Australian National University, Canberra, Australia.
Maurits
M
Evers
Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany.|Present address: Intomics A/S, Diplomvej 377, 2800, Lyngby, Denmark.
Stefan R
SR
Henz
Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany.
Katharina
K
Unger
Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany.
Norbert
N
Eichner
Biochemistry Center Regensburg (BZR), Biochemistry II, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany.
Rainer
R
Merkl
European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AV, Groningen, The Netherlands.
Eugene
E
Berezikov
Department of Statistical Bioinformatics, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany.
Julia C
JC
Engelmann
Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany.
Detlef
D
Weigel
Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany.
Stephan
S
Wenzl
Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany. gunter.meister@vkl.uni-regensburg.de.
Gunter
G
Meister
D060565:Argonaute Proteins / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods; D004251:DNA Transposable Elements; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D020868:Gene Silencing; D035683:MicroRNAs / Q000235:genetics; D058977:Molecular Sequence Annotation; D059372:Nucleotide Motifs; D011485:Protein Binding; D058727:RNA, Small Untranslated / Q000235:genetics*; D015203:Reproducibility of Results; D059467:Transcriptome; D044446:Volvox / Q000235:genetics*
D060565:Argonaute Proteins; D004251:DNA Transposable Elements; D035683:MicroRNAs; D058727:RNA, Small Untranslated
Argonaute; Evolution; Gene silencing; Small RNAs; Transposons; Volvox carteri; microRNAs