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Loss of Different Inverted Repeat Copies from the Chloroplast Genomes of Pinaceae and Cupressophytes and Influence of Heterotachy on the Evaluation of Gymnosperm Phylogeny

机译:松科和柏科植物叶绿体基因组不同反向重复序列的丢失及杂种优势对裸子植物系统发育评价的影响

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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.
机译:现有的五个裸子植物群(食肉植物,松科,非松科针叶树(柏科),银杏和苏铁)之间的关系仍然模棱两可。为了阐明这个问题,我们对两个小杯藻(Cephalotaxus wilsoniana和Taiwania cryptomerioides)的叶绿体基因组(cpDNA)进行了测序,并从另外三个小杯藻(Agathis dammara,Nageia nagi和Sciadopitys verticillata)和非非小cup(Sciadopitys verticillata)中测序了53个常见的叶绿体蛋白编码基因。苏铁科苏铁科植物,波文尼亚serrulata。对11种针叶树cpDNA的比较分析表明,松科和杯状植物都丢失了不同的反向重复(IR)副本,这与所有针叶树都丢失了相同IR的观点形成了对比。根据我们的结构发现,IR损失的特征不再与“马尼平”假说(松科的灵芝姐妹)相冲突。使用不同的树木构建方法对氨基酸序列进行叶绿体系统学分析,得到不一致的拓扑结构;但是,我们证明了高异源基因(在不同谱系中具有不同比率的基因)促成了长枝吸引(LBA)伪影,从而导致系统生物学估计不一致。此外,在五个裸子植物群中,氨基酸组成在高异质性基因中的表现比低异质性基因更明显。高异源基因的去除减轻了LBA伪影,并产生了一致且健壮的树形拓扑结构,其中,触网状真菌和松科形成了杯状浮游生物的姊妹进化枝(尼尼平斯假说),银杏簇生了苏铁。对于五个裸子植物群,添加更多的杯状单核生物类群并不能提高叶绿体系统发育组学的准确性。相反,从数据集中删除高异源基因很简单,并且可以提高对裸子植物系统发育评估的信心。

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