Gymnosperms are among the most endangered groups of plant species; they include ginkgo, pines (Conifers I), cupressophytes (Conifers II), cycads, and gnetophytes. The relationships among the five extant gymnosperm groups remain equivocal. We analyzed 167 available gymnosperm plastomes and investigated their diversity and phylogeny. We found that plastome size, structure, and gene order were highly variable in the five gymnosperm groups, of which Parasitaxus usta (Vieill.) de Laub. and Macrozamia mountperriensis F.M.Bailey had the smallest and largest plastomes, respectively. The inverted repeats (IRs) of the five groups were shown to have evolved through distinctive evolutionary scenarios. The IRs have been lost in all conifers but retained in cycads and gnetophytes. A positive association between simple sequence repeat (SSR) abundance and plastome size was observed, and the SSRs with the most variation were found in Pinaceae. Furthermore, the number of repeats was negatively correlated with IR length; thus, the highest number of repeats was detected in Conifers I and II, in which the IRs had been lost. We constructed a phylogeny based on 29 shared genes from 167 plastomes. With the plastome tree and 13 calibrations, we estimated the tree height between present-day angiosperms and gymnosperms to be ∼380 million years ago (mya). The placement of Gnetales in the tree agreed with the Gnetales–other gymnosperms hypothesis. The divergence between Ginkgo and cycads was estimated as ∼284 mya; the crown age of the cycads was 251 mya. Our time-calibrated plastid-based phylogenomic tree provides a framework for comparative studies of gymnosperm evolution.

中文翻译：

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裸子植物的动态历史：结构特征、比较分析、系统基因组学和时间分歧的见解

裸子植物是最濒危的植物物种之一。它们包括银杏、松树（针叶树 I）、铜树植物（针叶树 II）、苏铁和 gnetophytes。五个现存的裸子植物群之间的关系仍然模棱两可。我们分析了 167 种可用的裸子植物，并研究了它们的多样性和系统发育。我们发现，五个裸子植物组的质体大小、结构和基因顺序高度可变，其中Parasitaxus usta (Vieill.) de Laub。和万花菜FMBailey 分别具有最小和最大的塑性体。五组的反向重复（IRs）被证明是通过独特的进化场景进化而来的。IR 已在所有针叶树中丢失，但在苏铁和 gnetophytes 中保留。观察到简单序列重复 (SSR) 丰度与质体大小之间存在正相关关系，并且在松科中发现了变异最大的 SSR。此外，重复次数与 IR 长度呈负相关；因此，在针叶树 I 和 II 中检测到的重复次数最多，其中 IR 已丢失。我们基于来自 167 个质体的 29 个共享基因构建了系统发育。通过质体树和 13 次校准，我们估计现在的被子植物和裸子植物之间的树高约为 3.8 亿年前（mya）。Gnetales 在树中的位置与 Gnetales-其他裸子植物假设一致。之间的分歧银杏和苏铁估计为~284 mya；苏铁树的冠龄为 251 岁。我们经过时间校准的基于质体的系统发育树为裸子植物进化的比较研究提供了一个框架。