Abstract
Studies of gene function are often hampered by gene-redundancy, especially in organisms with large genomes such as rice (Oryza sativa). We present an approach for using transcriptomics data to focus functional studies and address redundancy. To this end, we have constructed and validated an inexpensive and publicly available rice oligonucleotide near-whole genome array, called the rice NSF45K array. We generated expression profiles for light- vs. dark-grown rice leaf tissue and validated the biological significance of the data by analyzing sources of variation and confirming expression trends with reverse transcription polymerase chain reaction. We examined trends in the data by evaluating enrichment of gene ontology terms at multiple false discovery rate thresholds. To compare data generated with the NSF45K array with published results, we developed publicly available, web-based tools (www.ricearray.org). The Oligo and EST Anatomy Viewer enables visualization of EST-based expression profiling data for all genes on the array. The Rice Multi-platform Microarray Search Tool facilitates comparison of gene expression profiles across multiple rice microarray platforms. Finally, we incorporated gene expression and biochemical pathway data to reduce the number of candidate gene products putatively participating in the eight steps of the photorespiration pathway from 52 to 10, based on expression levels of putatively functionally redundant genes. We confirmed the efficacy of this method to cope with redundancy by correctly predicting participation in photorespiration of a gene with five paralogs. Applying these methods will accelerate rice functional genomics.
Highlights
Large genomes often contain many paralogous genes that are closely related by sequence [1,2]
In validation of the NSF45K array data collected on young above-ground tissues, we found that differentially accumulating transcripts associated with greater confidence were more likely to appear multiple times in leaf-derived expressed sequence tag (EST) collections (Figure 4A; Table S7)
To further examine whether light-responsive transcripts are likely to be associated with gene expression in leaves, we examined the representation of light- and dark-induced transcripts with an false discovery rate (FDR)#1024 among ESTs from the following diverse rice organs: leaf, seed, root, panicle, and callus
Summary
Large genomes often contain many paralogous genes that are closely related by sequence [1,2]. Eighty-three percent of the 25,193 predicted human proteins contain regions that significantly match other human proteins [3]. This genomic property is even more pronounced in plant species. The numbers of genes in sequenced plant species are greater by 2-fold or more than the predicted number of genes for the ancestral angiosperm (12,000–14,000) [4]. Edu/) recently identified 3842 rice paralogous gene families consisting of 20,729 protein sequences. Such paralogous gene families are a main source of functional redundancy in mouse and yeast [5,6,7]. With the goal of advancing functional genomics studies of rice, we have developed and validated an inexpensive, publicly available rice whole genome oligonucleotide (oligo) array
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