Complicated evolutionary history of wild and cultivated Asian rice disclosed by gene tree incongruence analysis

The genus Oryza (rice) contains two cultivated and ~20 wild species with various genotypes and ecotypes. Here we attempt to elucidate the evolutionary history of rice from a genomic perspective. Oryza sativa is the Asia-originated cultivar, which is thought to be domesticated from its wild progenitor, O. rufipogon. O. sativa can be classified into diverse varietal groups including japonica and indica. In this study, to reconstruct phylogenetic trees, we utilized the genome sequences obtained from japonica and indica, and thousands of full-length cDNAs (FLcDNAs) from O. rufipogon. We expected that a large amount of high-throughput sequence data should be useful for accurate molecular evolutionary analysis. To infer phylogenetic relationship, evolutionary biologists usually reconstruct gene trees from several gene sequences, and a possible species tree is deduced from the gene trees. It is straightforward to consider that with a large number of sequences, a reliable species tree will be obtained. However, previous studies have shown that with increasing amounts of molecular data, trees from different sets could result in conflicting branching patterns, which are known as gene tree incongruence [1]. Gene tree incongruence was found in several studies of closely-related species, such as hominids, pines and fruit flies. Taking gene tree incongruence into account, we can reconstruct precise evolutionary processes of closely-related rice, which have not been examined previously because of a paucity of sequence data.