Phylogenomic evidence for ancient recombination between plastid genomes of the Cupressus-Juniperus-Xanthocyparis complex (Cupressaceae).
Phylogenomic evidence for ancient recombination between plastid genomes of the Cupressus-Juniperus-Xanthocyparis complex (Cupressaceae).
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DOI：
10.1186/s12862-018-1258-2
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发表时间：
2018-09-10
影响因子：
3.4
通讯作者：
Mower JP
中科院分区：
文献类型：
--
作者：
Zhu A;Fan W;Adams RP;Mower JP
东半球柏树、西半球柏树、杜松及其近亲之间的系统发育关系是有争议的，在过去的十年里，它们的属类划分一直在变化。为了解决它们之间的关系，并试图产生一个更可靠的分类，我们对这个复杂的5个不同描述的属（Callitropsis，柏树，Hesperocyparis， Juniperus和Xanthocyparis）的11个新的质体基因组（质体体）进行了测序，并将它们与来自柏科不同成员的其他质体体进行了比较。蛋白质编码基因的系统发育分析表明，杜松属柏属（Juniperus）是柏属（Cupressus）的姐妹，而基于全质体的树状结构分析表明，calitropsis - hesperocyparis - xanthocyparis （CaHX）分支是柏属（Cupressus）的姐妹。对位点特异性系统发育支持的滑动窗口分析发现了一个约15 kb的区域，横跨基因ycf1和ycf2，该区域相对于基因组的其他部分具有异常信号。在排除这些基因后，基于剩余基因和基因组的树一致地恢复了CaHX分支和柏树的拓扑结构，并具有强大的bootstrap支持。而基于ycf1和ycf2区域的树木则强烈支持柏树和杜松树之间的姐妹关系。这些结果表明，标准的系统基因组分析可以产生强烈支持但相互冲突的树。我们认为，这些相互冲突的塑料信号是由发生在该物种复合体祖先中的一个涉及ycf1和ycf2的古老渗入事件引起的。在携带不同质体单倍型的祖先异质个体中，质体重组促进了基因渗入事件，进一步证明质体之间发生了重组。最后，我们提供了强有力的支持，在该物种复合体中识别五个属：Callitropsis， Cupressus, Hesperocyparis， Juniperus和Xanthocyparis。本文的在线版本（10.1186/s12862-018-1258-2）包含补充材料，授权用户可以使用。
Phylogenetic relationships among Eastern Hemisphere cypresses, Western Hemisphere cypresses, junipers, and their closest relatives are controversial, and generic delimitations have been in flux for the past decade. To address relationships and attempt to produce a more robust classification, we sequenced 11 new plastid genomes (plastomes) from the five variously described genera in this complex (Callitropsis, Cupressus, Hesperocyparis, Juniperus, and Xanthocyparis) and compared them with additional plastomes from diverse members of Cupressaceae. Phylogenetic analysis of protein-coding genes recovered a topology in which Juniperus is sister to Cupressus, whereas a tree based on whole plastomes indicated that the Callitropsis-Hesperocyparis-Xanthocyparis (CaHX) clade is sister to Cupressus. A sliding window analysis of site-specific phylogenetic support identified a ~ 15 kb region, spanning the genes ycf1 and ycf2, which harbored an anomalous signal relative to the rest of the genome. After excluding these genes, trees based on the remainder of the genes and genome consistently recovered a topology grouping the CaHX clade and Cupressus with strong bootstrap support. In contrast, trees based on the ycf1 and ycf2 region strongly supported a sister relationship between Cupressus and Juniperus. These results demonstrate that standard phylogenomic analyses can result in strongly supported but conflicting trees. We suggest that the conflicting plastomic signals result from an ancient introgression event involving ycf1 and ycf2 that occurred in an ancestor of this species complex. The introgression event was facilitated by plastomic recombination in an ancestral heteroplasmic individual carrying distinct plastid haplotypes, offering further evidence that recombination occurs between plastomes. Finally, we provide strong support for previous proposals to recognize five genera in this species complex: Callitropsis, Cupressus, Hesperocyparis, Juniperus, and Xanthocyparis. The online version of this article (10.1186/s12862-018-1258-2) contains supplementary material, which is available to authorized users.
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影响因子：
4.1
作者：
Erixon, Per;Oxelman, Bengt
通讯作者：
Oxelman, Bengt
影响因子：
3.3
作者：
Guo W;Grewe F;Cobo-Clark A;Fan W;Duan Z;Adams RP;Schwarzbach AE;Mower JP
通讯作者：
Mower JP
影响因子：
5.3
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Takata K
影响因子：
3.3
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Yi TS
影响因子：
5.4
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通讯作者：
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