Molecular Systematics Of The Tribe Oryzeae (Poaceae)

Oryzeae is a tribe belonging to Poaceae and consists of about 12 genera. This tribe includes many economically important species, and is distributed in tropical and temperate regions worldwide. Recently, investigation on the genus Oryza and its related genera in the Oryzeae has attracted much attention for their important economic value and representative in the study of plant biology in general. Although evidence shows that the tribe Oryzeae is a monophyletic group, there are still many unsolved questions to be answered. In this study, the phylogeny and evolutionary history of Oryzeae were explored using sequences of seven DNA fragments from chloroplast (matK and trnL), mitochondrial (nad1) and nuclear genomes (Adh1, Adh2, GPA1, and Waxy). Additionally, the phylogeny and evolutionary history of the rice genus (Oryza) were constructed based on sequences of six DNA fragments (matK, trnL, nad1, Adh1, Adh2, GPA1). On these basis, we estimated the divergence times of the main lineages of Oryzeae and provided implication for the biogeographic history of the tribe. 1. Phylogenetic reconstruction of Oryzeae Phylogenetic analyses implemented by both maximum parsimony and Bayesian inference methods indicate that: (1) Oryzeae is monophyletic and falls into two main clades corresponding to the traditionally recognized subtribes (Oryzinae and Zizaniinae); The first clade includes Oryza, Leersia and Porteresia while the second clade consists of the remaining eight genera. Close affinities of the monoecious genera are not supported, suggesting the multiple origins of unisexual florets, and the bisexual florets was the ancestral state of the tribe. (2) Zizania is closely related with monoecious genus Rhynchoryza. (3) Previous recognition of three monotypic genera (Hydrochloa, Porteresia and Prosphytochloa) is not justified. (4) The morphological analysis suggests four species of Zizania formed a clade with the eastern Asian species Zizania latifolia as the basal clade. 2. Phylogenetic relationship of the basal lineages in Oryza Multiple gene phylogenies indicate that: 1) the genus Oryza is monophyletic; 2) All the data sets support the monophyly of each genome group; 3) the F genome is most closely related to the H-genome progenitor that give rise to the HK or HJ genome just as E genome to D genome of CD genome; 4) the previous recognition of the HK genome is justified, and Porteresia coarctata should be treated as an Oryza species; 5) the maternal origin of the HHJJ species is the H genome, while the maternal donor of the HHKK species is the K genome. Of the three genomes K, J and H, K is the relatively recent diverged genome type, and the H genome diverged relatively earlier; 6) the subdivision of four complexes of the genus Oryza is evidently supported, and Porteresia coarctata, O. brachyantha and O. schlechteri should be treated as members of the O. ridleyi complex. 3. The divergence times and biogeography of the main lineages in Oryzeae Using molecular clock approach, we estimated that the tribe Oryzeae origins at ~36 million years ago (MYA) and then diverged into two clades. A divergence time of 1200 MYA is obtained for the most basal split within the genus Oryza, and a divergence time of 700 MYA is obtained for the genome clade of A/B/C/E genomes. Within the first clade of Oryzeae (Oryzinae), Oryza and Leersia separated from each other ~14 MYA. Long distance dispersal would be the main factor to form the present distribution of these two genera. The genus Oryza is most likely to originate from eastern Asia and disperse to Africa, Australia, and America; while Leersia probably originated from Africa and dispersed to tropical and temperate regions. The second clade of Oryzeae (Zizaniinae) includes eight genera that form three subclades. In the Zizania/Rhynchoryza subclade, Zizania is the only genus with a distribution pattern of eastern Asian-eastern North America disjunction, which is diverged from its sister genus Rhynchoryza ~25.54 MYA. The subclade mainly dispersed from South America to eastern Asia, then dispersal from eastern Asia to North America. In the Zizaniopsis/Luziola subclade, the two genera diverged from each other ~21.80 MYA and are both distributed in South America and North America. The distribution pattern of Zizaniopsis/Luziola clade is mainly due to the disperse of the two genera from Northern America to Southern America across Panamanian land bridge as aresult of the rise of the Panamanian land bridge at the end of the Pliocene Epoch. In the third subclade, Chikusichola and Potamophila/Prosphytochloa diverged ~22.70 MYA and the three genera (Potamophila, Prosphytochloa, and Chikusichola), are distributed in Australia, Africa, and eastern Asia, respectively. The geographic distribution of this subclade may be related with long distance and even trans-oceanic dispersion.