Analysis of the Low Temperature Stress Transcriptome of the CC-Genome Oryza officinalis

The 24 species in the genus Oryza and the gradient of genome complexities they represent highlight a series of narrowly spaced evolutionary episodes that are tractable for detailed genomic analyses.  As the nature of genomic changes that occurred during speciation continue to unfold, in-depth understanding of how genome restructuring configured novel changes in regulatory network complexity is necessary in order to identify regulatory nodes with significant contributions to stress physiological variation and to harness such variation in stress tolerance breeding. The cultivated O. sativa (AA-genome) and its distant relative O. officinalis (CC-genome) produces partially fertile hybrids but the genomes of each species have clearly diverged in complexity, with O. sativa carrying a 400-Mbp genome (~40,000 protein-coding genes) and O. officinalis carrying a 650-Mbp genome (~45,000 protein-coding genes). Our earlier works established that O. sativa and O. officinalis differed substantially in their responses to low temperature (4^oC) based on a number of stress physiological parameters. Genome restructuring is a major mechanism for the evolution of alternative regulation. In this context, we hypothesized that low temperature stress physiological differences between the AA and CC genomes could be illuminated for further hypothesis-driven interrogation by reconstructing their regulatory network complexities. The RNA-SEQ data presented here is a snapshot of our on-going efforts to understand the intricacies of genetic network rewiring as an engine for the evolution of stress adaptive biochemical and physiological complexities in the genus Oryza.