Mangroves is an umbrella term for plants located across the tropics and sub‐tropics that live in the coastal region, between the sea and the land. All mangroves evolved from terrestrial plants, providing the opportunity to assess convergence, as well as the lineage‐specific features, at the genetic level. In this study, we compared chloroplast genomes from 21 mangrove species, covering main phylogenetic clades. We demonstrate that chloroplast gene order, content, and genome size is largely conserved in mangroves. The exceptions are loss of the photosystem I gene psaZ in Acanthus ilicifolius and inversion of the ribosomal protein gene rpl23 in Avicennia germinans. The repeat content of mangrove chloroplast varied between species, but was conserved within species of the same order. Sequence diversity analysis revealed that the IR (invert repeat) region was highly conserved compared to the SC (single‐copy) region in most phylogenetic clades, except clade core leptosporangiates (ferns). The ribosomal protein gene rps7 was under positive selection in Kandelia obovato, Rhizophora stylosa, Bruguiera sexangular and Rhizophora mangle, a monophyletic branch of clade fabids, while no evidence of positive selection was found in other mangrove lineages. Taken together, our data suggests that convergent evolutionary dynamics leaves no significant signal on the plastid genome of mangroves. The complete chloroplast genomes provided in this study shed light on the evolution of these important plastids and provides a valuable resource for further research efforts.

中文翻译：

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红树林质体基因组的谱系特异性进化

红树林是一个总称，是指生活在沿海地区，海洋和陆地之间的热带和亚热带地区的植物。所有的红树林都是从陆生植物演化而来的，从而提供了在遗传水平上评估趋同性以及谱系特定特征的机会。在这项研究中，我们比较了21种红树林物种的叶绿体基因组，涵盖了主要的系统发育进化枝。我们证明了叶绿体基因顺序，内容和基因组大小在红树林中基本上是保守的。唯一的例外是光系统I基因的失聚硅酸锌在老鼠簕和核糖体蛋白基因的反转rpl23在白骨germinans。红树林叶绿体的重复含量在不同物种之间有所不同，但在相同顺序的物种内却保持不变。序列多样性分析显示，在大多数系统进化进化枝中，除进化枝核心瘦孢子酸盐（蕨类）外，IR（反向重复）区域与SC（单拷贝）区域相比高度保守。核糖体蛋白基因rps7在Kandelia obovato，Rhizophora stylosa，Bruguiera sexangular和Rhizophora mangle中处于正选择状态，进化枝的单系分支很常见，而在其他红树林谱系中没有发现阳性选择的证据。两者合计，我们的数据表明，收敛的进化动力学在红树林的质体基因组上没有留下明显的信号。本研究提供的完整叶绿体基因组为这些重要质体的进化提供了线索，并为进一步的研究工作提供了宝贵的资源。