Spooner David M, Ruess Holly, Iorizzo Massimo, Senalik Douglas, Simon Philipp
U. S. Department of Agriculture, Agricultural Research Service, Vegetable Crops Research Unit; and Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, Wisconsin 53706-1590 USA
U. S. Department of Agriculture, Agricultural Research Service, Vegetable Crops Research Unit; and Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, Wisconsin 53706-1590 USA.
Am J Bot. 2017 Feb;104(2):296-312. doi: 10.3732/ajb.1600415. Epub 2017 Feb 15.
We explored the phylogenetic utility of entire plastid DNA sequences in and compared the results with prior phylogenetic results using plastid and nuclear DNA sequences.
We used Illumina sequencing to obtain full plastid sequences of 37 accessions of 20 taxa and outgroups, analyzed the data with phylogenetic methods, and examined evidence for mitochondrial DNA transfer to the plastid (MP).
Our phylogenetic trees of the entire data set were highly resolved, with 100% bootstrap support for most of the external and many of the internal clades, except for the clade of and its most closely related species . Subsets of the data, including regions traditionally used as phylogenetically informative regions, provide various degrees of soft congruence with the entire data set. There are areas of hard incongruence, however, with phylogenies using nuclear data. We extended knowledge of a mitochondrial to plastid DNA insertion sequence previously named MP and identified the first instance in flowering plants of a sequence of potential nuclear genome origin inserted into the plastid genome. There is a relationship of inverted repeat junction classes and repeat DNA to phylogeny, but no such relationship with nonsynonymous mutations.
Our data have allowed us to (1) produce a well-resolved plastid phylogeny of , (2) evaluate subsets of the entire plastid data for phylogeny, (3) examine evidence for plastid and nuclear DNA phylogenetic incongruence, and (4) examine mitochondrial and nuclear DNA insertion into the plastid.
我们探索了整个质体DNA序列在[研究对象]中的系统发育效用，并将结果与先前使用质体和核DNA序列的系统发育结果进行了比较。
我们使用Illumina测序获得了20个[分类群]的37个材料及外类群的完整质体序列，用系统发育方法分析数据，并检查线粒体DNA转移到质体（MP）的证据。
我们整个数据集的系统发育树分辨率很高，除了[分类群]及其最密切相关的物种[分类群]的分支外，大多数外部和许多内部分支都有100%的自展支持率。数据子集，包括传统上用作系统发育信息区域的区域，与整个数据集呈现出不同程度的软一致性。然而，与使用核数据的系统发育树存在硬不一致的区域。我们扩展了先前命名为MP的线粒体到质体DNA插入序列的知识，并在开花植物中鉴定出了第一个插入到质体基因组中的潜在核基因组起源序列的实例。倒位重复连接类和重复DNA与系统发育存在关系，但与非同义突变没有这种关系。
我们的数据使我们能够（1）构建一个分辨率良好的[研究对象]质体系统发育树，（2）评估整个质体数据的子集用于系统发育分析，（3）检查质体和核DNA系统发育不一致的证据，以及（4）检查线粒体和核DNA插入到质体中的情况。
