B chromosomes (Bs) are supernumerary, dispensable parts of the nuclear genome, which appear in many different species of eukaryote. So far, Bs have been considered to be genetically inert elements without any functional genes. Our comparative transcriptome analysis and the detection of active RNA polymerase II (RNAPII) in the proximity of B chromatin demonstrate that the Bs of rye (Secale cereale) contribute to the transcriptome. In total, 1954 and 1218 B-derived transcripts with an open reading frame were expressed in generative and vegetative tissues, respectively. In addition to B-derived transposable element transcripts, a high percentage of short transcripts without detectable similarity to known proteins and gene fragments from A chromosomes (As) were found, suggesting an ongoing gene erosion process. In vitro analysis of the A- and B-encoded AGO4B protein variants demonstrated that both possess RNA slicer activity. These data demonstrate unambiguously the presence of a functional AGO4B gene on Bs and that these Bs carry both functional protein coding genes and pseudogene copies. Thus, B-encoded genes may provide an additional level of gene control and complexity in combination with their related A-located genes. Hence, physiological effects, associated with the presence of Bs, may partly be explained by the activity of B-located (pseudo)genes.

Department of Biochemistry Institute of Biochemistry and Biophysics University of Tehran PO Box 13145 1384 Tehran Iran

Institute of Biochemistry and Biotechnology Section Microbial Biotechnology Faculty of Life Sciences Martin Luther University Halle Wittenberg Kurt Mothes Str 3 06120 Halle Saale Germany

Institute of Bioinformatics and Systems Biology Munich Information Center for Protein Sequences Helmholtz Center Munich German Research Center for Environmental Health 85764 Neuherberg Germany

Institute of Experimental Botany Center of the Region Haná for Biotechnological and Agricultural Research Šlechtitelů 31 78371 Olomouc Czech Republic

Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben Corrensstrasse 3 06466 Stadt Seeland Germany

National Bioinformatics Infrastructure Sweden Department of Clinical and Experimental Medicine Linköping University SE 558185 Linköping Sweden

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