Zhu Qihui, Ge Song
Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
New Phytol. 2005 Jul;167(1):249-65. doi: 10.1111/j.1469-8137.2005.01406.x.
The A-genome group in Oryza consists of eight diploid species and is distributed world-wide. Here we reconstructed the phylogeny among the A-genome species based on sequences of nuclear genes and MITE (miniature inverted-repeat transposable elements) insertions. Thirty-seven accessions representing two cultivated and six wild species from the A-genome group were sampled. Introns of four nuclear single-copy genes on different chromosomes were sequenced and analysed by both maximum parsimony (MP) and Bayesian inference methods. All the species except for Oryza rufipogon and Oryza nivara formed a monophyletic group and the Australian endemic Oryza meridionalis was the earliest divergent lineage. Two subspecies of Oryza sativa (ssp. indica and ssp. japonica) formed two separate monophyletic groups, suggestive of their polyphyletic origin. Based on molecular clock approach, we estimated that the divergence of the A-genome group occurred c. 2.0 million years ago (mya) while the two subspecies (indica and japonica) separated c. 0.4 mya. Intron sequences of nuclear genes provide sufficient resolution and are informative for phylogenetic inference at lower taxonomic levels.
稻属的A基因组组由八个二倍体物种组成，分布于全球。在此，我们基于核基因序列和微型反向重复转座元件（MITE）插入情况重建了A基因组物种间的系统发育关系。对代表A基因组组两个栽培种和六个野生种的37份材料进行了采样。对不同染色体上的四个核单拷贝基因的内含子进行了测序，并通过最大简约法（MP）和贝叶斯推断法进行了分析。除了野生稻和尼瓦拉野生稻外，所有物种形成了一个单系类群，澳大利亚特有的南方野生稻是最早分化的谱系。栽培稻的两个亚种（籼亚种和粳亚种）形成了两个独立的单系类群，表明它们具有多系起源。基于分子钟方法，我们估计A基因组组的分化发生在约200万年前，而两个亚种（籼亚种和粳亚种）的分化发生在约40万年前。核基因的内含子序列提供了足够的分辨率，对于较低分类水平的系统发育推断具有信息价值。
