Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture

Lei Li,Ning Su,Viktor Stolc,Zhiyu Peng,Songgang Li,Xing Deng,Jun Wang,Xiangfeng Wang,Xiping Wang,Mian Xia

doi:10.1186/gb-2005-6-6-r52

Abstract

A transcriptome analysis of chromosome 10 of 2 rice subspecies identifies 549 new gene models and gives experimental evidence for around 75% of the previously unsupported predicted genes.

Highlights

Sequencing and annotation of the genome of rice (Oryza sativa) have generated gene models in numbers that top all other fully sequenced species, with many lacking recognizable sequence homology to known genes
Hybridized with a mixed pool of cDNA targets, these tiling microarrays detected over 80% of the annotated nonredundant gene models in both japonica and indica, and identified a large number of transcriptionally active intergenic regions. These results, coupled with comparative gene model mapping and reverse transcription PCR (RT-PCR) analysis, allowed the first comprehensive identification and analysis of a rice chromosomal transcriptome. These results further revealed an association of chromosome 10 transcriptome regulation with the euchromatinheterochromatin organization at the chromosomal level
Rice chromosome 10 oligonucleotide tiling microarrays Based on recent studies using maskless array synthesizer (MAS) oligonucleotide tiling microarrays to obtain gene expression and structure information [24,26,28,29], we designed two independent sets of 36mer probes, with 10-nucleotide intervals, tiled throughout both strands of japonica and indica chromosome 10, respectively

Summary

Introduction

Sequencing and annotation of the genome of rice (Oryza sativa) have generated gene models in numbers that top all other fully sequenced species, with many lacking recognizable sequence homology to known genes. Experimental evaluation of these gene models and identification of new models will facilitate rice genome annotation and the application of this knowledge to other more complex cereal genomes. Available rice sequences have been subjected to extensive annotation using ab initio gene prediction, comparative genomics, and a variety of other methods. These analyses revealed abundant compositional and structural features of the predicted rice genes that deviate from genes in other model organisms. The abundance and diversity of transposable elements (TEs) within the rice genome that possess a coding capacity pose an additional challenge to accurate annotation of the rice genome [10,12,13]

Methods

Results

Discussion

Conclusion