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Genetics, Vol. 179, 21-30, May 2008, Copyright © 2008
doi:10.1534/genetics.107.086025
Genomewide Analysis of Box C/D and Box H/ACA snoRNAs in Chlamydomonas reinhardtii Reveals an Extensive Organization Into Intronic Gene Clusters
Chun-Long Chen*,
,
,1,
Chong-Jian Chen*,,
,1,
Olivier Vallon**,
Zhan-Peng Huang*,
Hui Zhou* and
Liang-Hu Qu*,2
* Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Zhongshan University, Guangzhou 510275, People's Republic of China, Université Paris-Sud 11, Orsay 91405, France, Centre National de la Recherche Scientifique, UMR 8080, Orsay 91405, France, Centre National de la Recherche Scientifique, UMR 8621, Orsay 91405, France and ** Université Paris 6, Centre National de la Recherche Scientifique, UMR 7141, Institut de Biologie Physico-Chimique, Paris 75005, France
2 Corresponding author: Biotechnology Research Center, Zhongshan University, Guangzhou 510275, People's Republic of China.
E-mail: lssqlh{at}mail.sysu.edu.cn
Chlamydomonas reinhardtii is a unicellular green alga, the lineage of which diverged from that of land plants >1 billion years ago. Using the powerful small nucleolar RNA (snoRNA) mining platform to screen the C. reinhardtii genome, we identified 322 snoRNA genes grouped into 118 families. The 74 box C/D families can potentially guide methylation at 96 sites of ribosomal RNAs (rRNAs) and snRNAs, and the 44 box H/ACA families can potentially guide pseudouridylation at 62 sites. Remarkably, 242 of the snoRNA genes are arranged into 76 clusters, of which 77% consist of homologous genes produced by small local tandem duplications. At least 70 snoRNA gene clusters are found within introns of protein-coding genes. Although not exhaustive, this analysis reveals that C. reinhardtii has the highest number of intronic snoRNA gene clusters among eukaryotes. The prevalence of intronic snoRNA gene clusters in C. reinhardtii is similar to that of rice but in contrast with the one-snoRNA-per-intron organization of vertebrates and fungi and with that of Arabidopsis thaliana in which only a few intronic snoRNA gene clusters were identified. This analysis of C. reinhardtii snoRNA gene organization shows the functional importance of introns in a single-celled organism and provides evolutionary insight into the origin of intron-encoded RNAs in the plant lineage.
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