A molecular phylogenetic analysis of Oryza L. based on chloroplast DNA sequences.

摘要

In the most taxonomically comprehensive study on this group to date, several molecular phylogenetic reconstructions were generated in an analysis of the grass genus Oryza L. (rice relatives). The objectives of the phylogenies were: (1) to inspect the relationships among the species and genomes, elucidating the origin of the alloploids; (2) to investigate the impact of indels on the resolution power; and (3) to describe the distribution and type of sequence changes in the genome region studied, and their effect on the secondary structure of the RNA. The transition/transversion and indel size distribution are typical. Phylogenies were based on the sequences of the trnTLF non-coding region of the chloroplast and were reconstructed both with maximum parsimony and maximum likelihood. A Principal Components Analysis based on the comparative morphometry of the spikelet contour was performed and discussed in the light of the phylogenetic relationships. Secondary structure has a few conserved motifs and a reasonable amount of variation in loop number and length. The inclusion of indels always enhanced resolution. Oryza is composed of 4 clades in different evolutionary stages (from basal to apical): the exclusively diploid GG, the mixed-ploidy O. schlechteri/O. brachyantha, the exclusively tetraploid HHJJ and the mixed-ploidy, large Euoryza, structured in 3 subclades (AA, BB and CC). The Asian BBCC species received the chloroplast from the BB maternal parent, while the African BBCC species had the CC genome as the maternal parent. The CCDD species are monophyletic and, similarly to the African BBCC species, received the CC genome from the maternal parent. Since a diploid DD is unknown, CC species are absent from the Neotropic, and Africa and S. America were close in the past, we hypothesize parsimoniously that the CCDD ancestor evolved by anagenesis in the Neotropic after dispersal of a BBCC-like tetraploid from Africa. BB and AA are sister genomes and CC is basal to them. The AA species had a very recent radiation and, due to their unusually long awns, spread quickly throughout the tropics, but remained poorly differentiated morphologically. Older clades, as CCDD, BB, BBCC, GG, showed much less overlapping, BBCC being intermediate between CC and BB.