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Phylogenetic Analysis of AA-genome Oryza Species (Poaceae) Based on Chloroplast, Mitochondrial, and Nuclear DNA Sequences

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Species in the genus Oryza (Poaceae) contain 10 genomic types and are distributed in pan-tropics of the world. To explore phylogenetic relationships of Oryza species having the AA-genome, DNA sequences of the chloroplast trnL intron and trnL-trnF spacer, mitochondrial nad1 intron 2, and nuclear internal transcribed spacer were analyzed, based on materials from 6 cultivated (O. sativa and O. glaberrima) and 13 wild accessions, in addition to a CC-genome species (O. officinalis) that was used as an outgroup. Analyses of the combined sequence data set from different sources provide a much better resolution of the AA-genome species than the individual data set, indicating the limitation of a single gene in phylogenetic reconstruction. The phylogeny based on the combined data set demonstrated an apparent grouping of the AA-genome Oryza species that was well associated with their geographic origin, although the Australian O. meridionalis showed its affinity with the African species. The geographic pattern of the phylogenetic relationship was probably attributed to the frequent genetic exchange and introgression among the AA-genome species from the same continents. In addition, Asian cultivated rice O. sativa showed its close relation to O. rufipogon and O. nivara, whereas African cultivated rice O. glaberrima was closely linked to O. barthii and O. longistaminata, indicating the independent domestication of the two cultivated species in different geographic locations.

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ACKNOWLEDGMENTS

We thank Dr. N. R. Sackville Hamilton of the International Rice Research Institute (Manila, Philippines) for providing plant material for this study. This research was supported by the National Natural Science Foundation of China (30270149) and Chinese Ministry of Science and Technology (2006CB100205).

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  1. Ministry of Education Key Laboratory for Plant Developmental Biology, College of Life Science, Wuhan University, Wuhan, 430072, P.R. China

    Shihua Duan, Zhong Li, Jiping Tong, Jin Kong, Wen Yao, Shaoqing Li & Yingguo Zhu

  2. Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, 200433, P.R. China

    Baorong Lu

  3. College of Life Science, Jinggangshan University, Ji’an, Jiangxi 343009, P.R. China

    Shihua Duan

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  1. Shihua Duan
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Duan, S., Lu, B., Li, Z. et al. Phylogenetic Analysis of AA-genome Oryza Species (Poaceae) Based on Chloroplast, Mitochondrial, and Nuclear DNA Sequences. Biochem Genet 45, 113–129 (2007). https://doi.org/10.1007/s10528-006-9062-x

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