Agriculture and Agri-Food Canada, Eastern Cereal and Oilseed Research Centre, Neatby Building, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada.
Genome. 2013 May;56(5):245-66. doi: 10.1139/gen-2012-0195. Epub 2013 May 3.
We have investigated the complex relationships among the annual genera within the tribe Triticeae through phylogenetic analyses of the 5S rRNA multigene family. Cloned sequences were assigned to groups of orthologous sequences, called unit classes, that were subjected to several analyses including BLAST (Basic Local Alignment Search Tool) searches to assess possible ancestral relationships with perennial genera; phylogenetic analyses using parsimony (Pars), maximum likelihood (ML), and Bayesian methods; and minimum reticulation networks from the Pars, ML, and Bayesian trees. In this study, we included genera with both annual and perennial species, such as Dasypyrum, Hordeum, and Secale. BLAST pointed to Pseudoroegneria (carrier of the St genome) and possibly Thinopyrum (carrier of the J genome) as the potential next of kin. However, Thinopyrum and Pseudoroegneria have never fallen together on the individual trees with the former generally associated with Crithopsis, Aegilops, Triticum, and Dasypyrum, while the latter is usually associated with the rest of the genera within Triticeae. The "long" unit classes placed Dasypyrum breviaristatum together with Dasypyrum villosum, whereas the "short" unit classes put them far apart on the trees. None of the gene trees alone was able to summarize the complex relationships among the genera, in line with previous results in the Triticeae. However, the application of tools designed to display phylogenetic networks was able to depict the complex links among the genera based on the short and the long gene trees, including the close link between Thinopyrum and Pseudoroegneria suggested by the phylogenetic analyses. In addition, our analyses provide support for the hypothesis that at least some annual Triticeae taxa are derived from their perennial relatives.
我们通过对小麦族 5S rRNA 多基因家族的系统发育分析，研究了年度属间的复杂关系。克隆序列被分配到称为同源序列单元类的同源序列组中，这些单元类进行了多项分析，包括与多年生属可能的祖先关系的 BLAST（基本局部比对搜索工具）搜索；使用简约法（Pars）、最大似然法（ML）和贝叶斯法进行系统发育分析；以及从 Pars、ML 和贝叶斯树中得出的最小网状网络。在本研究中，我们包括了一年生和多年生物种的属，如 Dasypyrum、Hordeum 和 Secale。BLAST 指出 Pseudoroegneria（St 基因组的携带者）和可能的 Thinopyrum（J 基因组的携带者）是潜在的近亲。然而，Thinopyrum 和 Pseudoroegneria 从未在个体树上一起出现，前者通常与 Crithopsis、Aegilops、Triticum 和 Dasypyrum 相关，而后者通常与小麦族内的其余属相关。“长”单元类将 Dasypyrum breviaristatum 与 Dasypyrum villosum 放在一起，而“短”单元类将它们在树上分得很远。没有一个基因树能够单独概括属间的复杂关系，这与小麦族的先前结果一致。然而，应用旨在显示系统发育网络的工具能够根据短基因树和长基因树描绘属间的复杂联系，包括系统发育分析中暗示的 Thinopyrum 和 Pseudoroegneria 之间的密切联系。此外，我们的分析支持了这样的假设，即至少一些一年生小麦族类群是从它们的多年生亲缘关系中衍生而来的。
