Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray

Abstract

Rice (Oryza sativa L.) is a model organism for the functional genomics of monocotyledonous plants since the genome size is considerably smaller than those of other monocotyledonous plants. Although highly accurate genome sequences of indica and japonica rice are available, additional resources such as full-length complementary DNA (FL-cDNA) sequences are also indispensable for comprehensive analyses of gene structure and function. We cross-referenced 28.5K individual loci in the rice genome defined by mapping of 578K FL-cDNA clones with the 56K loci predicted in the TIGR genome assembly. Based on the annotation status and the presence of corresponding cDNA clones, genes were classified into 23K annotated expressed (AE) genes, 33K annotated non-expressed (ANE) genes, and 5.5K non-annotated expressed (NAE) genes. We developed a 60mer oligo-array for analysis of gene expression from each locus. Analysis of gene structures and expression levels revealed that the general features of gene structure and expression of NAE and ANE genes were considerably different from those of AE genes. The results also suggested that the cloning efficiency of rice FL-cDNA is associated with the transcription activity of the corresponding genetic locus, although other factors may also have an effect. Comparison of the coverage of FL-cDNA among gene families suggested that FL-cDNA from genes encoding rice- or eukaryote-specific domains, and those involved in regulatory functions were difficult to produce in bacterial cells. Collectively, these results indicate that rice genes can be divided into distinct groups based on transcription activity and gene structure, and that the coverage bias of FL-cDNA clones exists due to the incompatibility of certain eukaryotic genes in bacteria.

Figure 1. Gene structure analysis in rice.

(a) The length distribution of FL-cDNA for FL-AE (black) and FL-NAE (white). (b) The distribution of open reading frame (ORF) proportions for FL-AE (black) and FL-NAE (white). (c) The distribution of FL-cDNA locus lengths for FL-AE (black) and FL-NAE (white). (d) The distribution of locus lengths for CDS-AE (black) and CDS-ANE (white) in TIGR4. (e) The distribution of the number of exons for FL-AE (black) and FL-NAE (white). (f) The distribution of exon (black) and intron (white) lengths for the respective locus types. (g) The distribution of the number of FL-cDNA clones mapped per single FL-AE (black) and FL-NAE (white) locus.

Figure 2. Strategy for mapping of FL-cDNA clones and FL-ESTs, and for definition of FL-cDNA loci.