Characterization of ribosomal DNA clones from rice

Abstract

A 3,699 base pairs long nucleotide sequence of an indica rice (KDML105) DNA clone, called GX3.6, was determined. Five additional DNA clones, designated as C13, C14, C32, C35 and C76, were also isolated from a KDML105 rice cDNA library and DNA sequences determined. The 5 new clones showed approximately 5777 % sequence matching with that of GX3.6. Identity searching from DNA data banks showed that the GX3.6 and the new DNA clones had high sequence identities with large subunit rRNA genes of plant organelles. Nucleotide sequence comparison between GX3.6 and known rRNA genes revealed the presence of three conserved regions in GX3.6 which showed 50-60 % sequence identities with 23S rRNA gene (2808 bp in length), 4.5S rRNA gene (95 bp in length) and 5S rRNA gene (118 bp in length) of plant chloroplasts. The structural and arrangement of 3 putative genes in GX3.6 were similar to those of plant chloroplast rRNA genes. However, a copy of GX3.6 DNA could not be detected in rice chloroplast DNA and nuclear DNA based on Southern hybridization of total DNAs from rice leaves. Many data available indicated the clone GX3.6 was likely from rice mitochondrial origin. However, the DNA clones C32, C35 and C76 were identified as parts of indica rice chloroplast 23S rRNA gene.