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A gene co-expression network representing clusters of rice genes with similar expression patterns across four nitrogen conditions and two tissue types was generated.
This phylogenetic analysis, led to the definition of four clusters of rice and Arabidopsis orthologous genes and to identify the minimum complement of Dof genes that were present in the angiosperm common ancestor.
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Clustering of rice data was performed using EPICLUST, a module of Expression Profiler.
At least 99 pseudogenes for 328 functional cytochrome P450s were identified in rice [ 37], and on a smaller scale Itoh et al. [ 38] identified a pseudogene in a cluster of rice ent-kaurene oxidase genes.
A cluster of rice transcripts are up-regulated at early stage of germination, and reach its peak in their abundance at 1 or 3 hours after imbibition, and then decreased to low levels again at 12 hours after imbibition [ 55].
But the hot spicy shrimp with sizzling rice was a platter of awesome: deep-fried shrimp with clusters of puffed rice, sliced green onions, garlic and, of course, chiles.
Interestingly, the cluster on rice chr8 was composed of five MIR169 gene copies, whereas the orthologous cluster on sorghum chr7 contained only three annotated MIR169 gene copies.
The principal component analysis (PCA) also revealed significant variation among the samples (See additional file 5: Principal component analysis clustering of 13 rice cultivars and 18 wild rice accessions).
(A) Clustering of expressed rice genes.
Although clustering of weedy rice groups with cultivated relatives could also be due to common descent from a shared ancestral founding gene pool, the pattern of shared polymorphisms among weedy and cultivated groups is more consistent with direct descent from domesticated ancestors.
The integrated transcriptome results indicated that specific clusters of co-expressed rice WRKY genes are involved in response to a range of applied stress conditions.
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