title: Phylogenetic study of Oryzoideae species and related taxa of the Poaceae based on atpB-rbcL and ndhF DNA sequences.
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.
authors.affiliation: Center for Computational Biology and Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
authors.forename: Xu
authors.initials: X
authors.lastname: Zeng
authors.forename: Zhengrong
authors.initials: Z
authors.lastname: Yuan
authors.forename: Xin
authors.initials: X
authors.lastname: Tong
authors.forename: Qiushi
authors.initials: Q
authors.lastname: Li
authors.forename: Weiwei
authors.initials: W
authors.lastname: Gao
authors.forename: Minjian
authors.initials: M
authors.lastname: Qin
authors.forename: Zhihua
authors.initials: Z
authors.lastname: Liu
mesh_terms: D001483:Base Sequence; D021901:DNA, Intergenic / Q000235:genetics; D030561:Databases, Nucleic Acid; D019143:Evolution, Molecular; D061125:Genes, Chloroplast / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics; D014644:Genetic Variation; D005843:Geography; D009245:NADH Dehydrogenase / Q000235:genetics*; D009711:Nucleotides / Q000235:genetics; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D006109:Poaceae / Q000145:classification* / Q000201:enzymology / Q000235:genetics*; D012273:Ribulose-Bisphosphate Carboxylase / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D013997:Time Factors
chemical_list: D021901:DNA, Intergenic; D009711:Nucleotides; D010940:Plant Proteins; C489904:NdhF protein, plant; D009245:NADH Dehydrogenase; D012273:Ribulose-Bisphosphate Carboxylase