Loss of different inverted repeat copies from the chloroplast genomes of Pinaceae and cupressophytes and influence of heterotachy on the evaluation of gymnosperm phylogeny.
Loss of different inverted repeat copies from the chloroplast genomes of Pinaceae and cupressophytes and influence of heterotachy on the evaluation of gymnosperm phylogeny.
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DOI：
10.1093/gbe/evr095
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发表时间：
2011
影响因子：
3.3
通讯作者：
Chaw SM
中科院分区：
文献类型：
--
作者：
Wu CS;Wang YN;Hsu CY;Lin CP;Chaw SM
现存的五个裸子植物类群——针叶植物、松科、非松科针叶树（柏树植物）、银杏和苏铁——之间的关系仍然模棱两可。为了澄清这个问题，我们对两种铜植物（Cephalotaxus wilsoniana 和台湾杉）的叶绿体基因组 (cpDNA) 进行了测序，并对另外三种铜植物（Agathis dammara、Nageia nagi 和 Sciadopitys verticillata）以及一种非苏铁科植物的 53 个常见叶绿体蛋白编码基因进行了测序。 苏铁、锯叶鲍文尼亚。对 11 种针叶树 cpDNA 的比较分析表明，松科植物和铜植物都丢失了不同的反向重复序列 (IR)，这与所有针叶树都丢失了相同 IR 的观点形成鲜明对比。根据我们的结构发现，IR 损失的特征不再与“gnepines”假说（松科的姊妹植物）冲突。使用不同的树构建方法对氨基酸序列进行叶绿体系统发育分析，恢复不一致的拓扑结构；然而，我们证明了高异态基因（在不同谱系中具有高度不同比率的基因）导致了长分支吸引（LBA）伪影，导致系统发育基因组估计的不一致。此外，在五个裸子植物类群中，高异速基因的氨基酸组成比低异速基因的氨基酸组成显得更加异质。高异速基因的去除减轻了 LBA 伪影，并产生了一致且稳健的树拓扑，其中买麻植物和松科形成了铜植物的姐妹分支（针茅假说）和与苏铁类聚集的银杏。添加更多的铜植物类群并不能提高五个裸子植物类群叶绿体系统发育学的准确性。相比之下，从数据集中去除高异速基因很简单，并且可以增加评估裸子植物系统发育的信心。
The relationships among the extant five gymnosperm groups—gnetophytes, Pinaceae, non-Pinaceae conifers (cupressophytes), Ginkgo, and cycads—remain equivocal. To clarify this issue, we sequenced the chloroplast genomes (cpDNAs) from two cupressophytes, Cephalotaxus wilsoniana and Taiwania cryptomerioides, and 53 common chloroplast protein-coding genes from another three cupressophytes, Agathis dammara, Nageia nagi, and Sciadopitys verticillata, and a non-Cycadaceae cycad, Bowenia serrulata. Comparative analyses of 11 conifer cpDNAs revealed that Pinaceae and cupressophytes each lost a different copy of inverted repeats (IRs), which contrasts with the view that the same IR has been lost in all conifers. Based on our structural finding, the character of an IR loss no longer conflicts with the “gnepines” hypothesis (gnetophytes sister to Pinaceae). Chloroplast phylogenomic analyses of amino acid sequences recovered incongruent topologies using different tree-building methods; however, we demonstrated that high heterotachous genes (genes that have highly different rates in different lineages) contributed to the long-branch attraction (LBA) artifact, resulting in incongruence of phylogenomic estimates. Additionally, amino acid compositions appear more heterogeneous in high than low heterotachous genes among the five gymnosperm groups. Removal of high heterotachous genes alleviated the LBA artifact and yielded congruent and robust tree topologies in which gnetophytes and Pinaceae formed a sister clade to cupressophytes (the gnepines hypothesis) and Ginkgo clustered with cycads. Adding more cupressophyte taxa could not improve the accuracy of chloroplast phylogenomics for the five gymnosperm groups. In contrast, removal of high heterotachous genes from data sets is simple and can increase confidence in evaluating the phylogeny of gymnosperms.
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