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Revisiting the Zingiberales: using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charismatic plant lineage

机译：回顾金氏龟：使用多重外显子捕获来解析具有魅力的植物谱系中的古代和最近的系统发育分裂

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摘要

The Zingiberales are an iconic order of monocotyledonous plants comprising eight families with distinctive and diverse floral morphologies and representing an important ecological element of tropical and subtropical forests. While the eight families are demonstrated to be monophyletic, phylogenetic relationships among these families remain unresolved. Neither combined morphological and molecular studies nor recent attempts to resolve family relationships using sequence data from whole plastomes has resulted in a well-supported, family-level phylogenetic hypothesis of relationships. Here we approach this challenge by leveraging the complete genome of one member of the order, Musa acuminata, together with transcriptome information from each of the other seven families to design a set of nuclear loci that can be enriched from highly divergent taxa with a single array-based capture of indexed genomic DNA. A total of 494 exons from 418 nuclear genes were captured for 53 ingroup taxa. The entire plastid genome was also captured for the same 53 taxa. Of the total genes captured, 308 nuclear and 68 plastid genes were used for phylogenetic estimation. The concatenated plastid and nuclear dataset supports the position of Musaceae as sister to the remaining seven families. Moreover, the combined dataset recovers known intra- and inter-family phylogenetic relationships with generally high bootstrap support. This is a flexible and cost effective method that gives the broader plant biology community a tool for generating phylogenomic scale sequence data in non-model systems at varying evolutionary depths.
机译：姜是单子叶植物的标志性顺序，包括八个家族，具有独特而多样的花卉形态，代表了热带和亚热带森林的重要生态元素。尽管八个家族被证明是单系的，但这些家族之间的系统发育关系仍未解决。形态学和分子学的结合研究，以及最近使用整个质体组的序列数据来解决家族关系的尝试，都没有得到充分支持的家族水平系统发育关系假说。在这里，我们通过利用该订单成员之一的完整基因组来应对这一挑战，其中包括Musa acuminata和其他七个家族的转录组信息来设计一套可以从高度分化的类群中通过一个阵列富集的核基因座。索引的基因组DNA的基于捕获。共有418个核基因的494个外显子被捕获，用于53个群内分类群。还为相同的53个分类单元捕获了整个质体基因组。在捕获的全部基因中，将308个核基因和68个质体基因用于系统发育估计。串联的质体和核数据集支持穆萨科作为其余七个科的姐妹。此外，合并后的数据集可通过通常较高的自举支持来恢复已知的家庭内部和家庭之间的系统发育关系。这是一种灵活且具有成本效益的方法，为更广泛的植物生物学界提供了一种工具，可用于在非模型系统中以不同的进化深度生成植物学尺度序列数据。

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