Differentiation of the two rice subspecies indica and japonica: a Gene Ontology perspective.

Cultivated rice (Oryza sativa) is comprised of two subspecies: japonica and indica. Polymorphism levels between putative homologues were determined for genes whose japonica homologue had been classified into functional categories using the Gene Ontology (GO) system. Genes were partitioned into below-average and above-average polymorphism groups, and then the set of genes having each GO term was checked for the randomness of its distribution into these polymorphism groups using a series of False Discovery Rate (FDR) tests. The robustness of the conclusions was enhanced by employing different cutoff values and sequence samplings in the FDR tests. Significant nonrandom polymorphism distributions were found for protein-coding sequences in many GO categories. In contrast, a random distribution for nearly all GO terms was seen with intron sequences. These results were extended by measuring the nonsynonymous to synonymous codon usage ratio (dN/dS) using a permutation test, which showed that some above-average polymorphism GO categories also had a high proportion of genes with a dN/dS ratio greater than one, suggesting positive selection on these GO categories during indica-japonica differentiation. An analysis of predominant gene names in the significant GO categories divided them into four functional classes: production of defense-related compounds, cell wall, cell signaling, and transcription factors.