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GENETICS, GENOMICS, AND MOLECULAR EVOLUTION

Genomic Organization and Evolutionary Conservation of Plant D-Type Cyclins^1,[C],[W]

Institute of Biotechnology, University of Cambridge, Cambridge CB2 1QT, United Kingdom (M.M., J.A.H.M.); Department of Biomolecular Sciences and Biotechnology (G.P.), and Department of Biology (P.M.), University of Milan and Consiglio Nazionale delle Ricerche Biophysics Institute (Milan Section), 20133 Milan, Italy; and School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, United Kingdom (L.B.)

Plants contain more genes encoding core cell cycle regulators than other organisms but it is unclear whether these represent distinct functions. D-type cyclins (CYCD) play key roles in the G1-to-S-phase transition, and Arabidopsis (Arabidopsis thaliana) contains 10 CYCD genes in seven defined subgroups, six of which are conserved in rice (Oryza sativa). Here, we identify 22 CYCD genes in the poplar (Populus trichocarpa) genome and confirm that these six CYCD subgroups are conserved across higher plants, suggesting subgroup-specific functions. Different subgroups show gene number increases, with CYCD3 having three members in Arabidopsis, six in poplar, and a single representative in rice. All three species contain a single CYCD7 gene. Despite low overall sequence homology, we find remarkable conservation of intron/exon boundaries, because in most CYCD genes of plants and mammals, the first exon ends in the conserved cyclin signature. Only CYCD3 genes contain the complete cyclin box in a single exon, and this structure is conserved across angiosperms, again suggesting an early origin for the subgroup. The single CYCD gene of moss has a gene structure closely related to those of higher plants, sharing an identical exon/intron structure with several higher plant subgroups. However, green algae have CYCD genes structurally unrelated to higher plants. Conservation is also observed in the location of potential cyclin-dependent kinase phosphorylation sites within CYCD proteins. Subgroup structure is supported by conserved regulatory elements, particularly in the eudicot species, including conserved E2F regulatory sites within CYCD3 promoters. Global expression correlation analysis further supports distinct expression patterns for CYCD subgroups.

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: James A.H. Murray (j.murray{at}biotech.cam.ac.uk).

^[C] Some figures in this article are displayed in color online but in black and white in the print edition.

^[W] The online version of this article contains Web-only data.

www.plantphysiol.org/cgi/doi/10.1104/pp.107.104901

^* Corresponding author; e-mail j.murray{at}biotech.cam.ac.uk.

Received June 29, 2007; accepted October 6, 2007; published October 19, 2007.