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Phylogenetic study of Oryzoideae species and related taxa of the Poaceae based on atpB-rbcL and ndhF DNA sequences

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Abstract

Oryzoideae (Poaceae) plants have economic and ecological value. However, the phylogenetic position of some plants is not clear, such as Hygroryza aristata (Retz.) Nees. and Porteresia coarctata (Roxb.) Tateoka (syn. Oryza coarctata). Comprehensive molecular phylogenetic studies have been carried out on many genera in the Poaceae. The different DNA sequences, including nuclear and chloroplast sequences, had been extensively employed to determine relationships at both higher and lower taxonomic levels in the Poaceae. Chloroplast DNA ndhF gene and atpB-rbcL spacer were used to construct phylogenetic trees and estimate the divergence time of Oryzoideae, Bambusoideae, Panicoideae, Pooideae and so on. Complete sequences of atpB-rbcL and ndhF were generated for 17 species representing six species of the Oryzoideae and related subfamilies. Nicotiana tabacum L. was the outgroup species. The two DNA datasets were analyzed, using Maximum Parsimony and Bayesian analysis methods. The molecular phylogeny revealed that H. aristata (Retz.) Nees was the sister to Chikusichloa aquatica Koidz. Moreover, P. coarctata (Roxb.) Tateoka was in the genus Oryza. Furthermore, the result of evolution analysis, which based on the ndhF marker, indicated that the time of origin of Oryzoideae might be 31 million years ago.

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Acknowledgments

This work was funded by National Natural Science Foundation of China (81102746), Beijing Natural Science Foundation (5113033), Scientific Research Foundation of the State Human Resource Ministry and the Education Ministry for Returned Chinese Scholars, New Star Project of Peking Union Medical College, Youth Foundation of Peking Union Medical College, the Research Fund for the Doctoral Program of Higher Education (20111106120028), “Major Drug Discovery” major science and technology research “12nd Five-Year Plan” (2012ZX09301-002-001) China Medical Board of New York (A2009001) granted to Zhihua Liu.

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Authors and Affiliations

  1. Center for Computational Biology and Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China

    Xu Zeng, Zhengrong Yuan, Xin Tong, Qiushi Li, Weiwei Gao & Zhihua Liu

  2. Department of Resources Science of Traditional Chinese Medicines, China Pharmaceutical University, Nanjing, 210009, China

    Xu Zeng & Minjian Qin

  3. Indiana University School of Medicine, Indianapolis, IN, 46202, USA

    Xin Tong

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  1. Xu Zeng
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  2. Zhengrong Yuan
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  3. Xin Tong
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  4. Qiushi Li
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  5. Weiwei Gao
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  7. Zhihua Liu
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Correspondence to Zhihua Liu.

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X. Zeng, Z. Yuan and X. Tong have contributed equally to this work.

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Zeng, X., Yuan, Z., Tong, X. et al. Phylogenetic study of Oryzoideae species and related taxa of the Poaceae based on atpB-rbcL and ndhF DNA sequences. Mol Biol Rep 39, 5737–5744 (2012). https://doi.org/10.1007/s11033-011-1383-0

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  • DOI: https://doi.org/10.1007/s11033-011-1383-0

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