The organization of cytoplasmic ribosomal protein genes in the arabidopsisgenome

Eukaryotic ribosomes are made of two components, four ribosomal RNAs, and a pproximately 80 ribosomal proteins (r-proteins). The exact number of r-prot eins and r-protein genes in higher plants is not known. The strong conserva tion in eukaryotic r-protein primary sequence allowed us to use the well-ch aracterized rat (Rattus norvegicus) r-protein set to identify orthologues o n the five haploid chromosomes of Arabidopsis. By use of the numerous expre ssed sequence tag (EST) accessions and the complete genomic sequence of thi s species, we identified 249 genes (including some pseudogenes) correspondi ng to 80 (32 small subunit and 48 large subunit) cytoplasmic r-protein type s. None of the r-protein genes are single copy and most are encoded by thre e or four expressed genes, indicative of the internal duplication of the Ar abidopsis genome. The r-proteins are distributed throughout the genome. Ins pection of genes in the vicinity of r-protein gene family members confirms extensive duplications of large chromosome fragments and sheds light on the evolutionary history of the Arabidopsis genome. Examination of large dupli cated regions indicated that a significant fraction of the r-protein genes have been either lost from one of the duplicated fragments or inserted afte r the initial duplication event. Only 52 r-protein genes lack a matching ES T accession, and 19 of these contain incomplete open reading frames, confir ming that most genes are expressed. Assessment of cognate EST numbers sugge sts that r-protein gene family members are differentially expressed.