Chloroplast genomes (cpDNA) in angiosperms are usually highly conserved. Although rearrangements have been observed in some lineages, such as Passiflora, the mechanisms that lead to rearrangements are still poorly elucidated. In the present study, we obtained 20 new chloroplast genomes (18 species from the genus Passiflora, and Dilkea retusa and Mitostemma brevifilis from the family Passifloraceae) in order to investigate cpDNA evolutionary history in this group. Passiflora cpDNAs vary in size considerably, with ∼50 kb between shortest and longest. Large inverted repeat (IR) expansions were identified, and at the extreme opposite, the loss of an IR was detected for the first time in Passiflora, a rare event in angiosperms. The loss of an IR region was detected in P. capsularis and P. costaricensis, a species in which occasional biparental chloroplast inheritance has previously been reported. A repertory of rearrangements, such as inversions and gene losses were detected, making Passiflora one of the few groups with complex chloroplast genome evolution. We also performed a phylogenomic study based on all the available cp genomes and our analysis implies that there is a need to reconsider the taxonomic classifications of some species in the group.

中文翻译：

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西番莲叶绿体基因组中的重排和反向重复区域的丢失。

被子植物中的叶绿体基因组 (cpDNA) 通常是高度保守的。尽管在一些谱系中观察到了重排，例如西番莲，但导致重排的机制仍不清楚。在本研究中，我们获得了 20 个新的叶绿体基因组（来自西番莲属的 18 个物种，以及来自西番莲科的Dilkea retusa和Mitostemma brevifilis），以研究该组的 cpDNA 进化历史。西番莲cpDNA 的大小差异很大，最短和最长之间约为 50 kb。发现了大的反向重复 (IR) 扩展，在极端相反的情况下，首次在西番莲中检测到 IR 的丢失，在被子植物中罕见的事件。在P. capsularis和P. costaricensis 中检测到 IR 区域的丢失，以前曾报道过这种物种偶尔会发生双亲叶绿体遗传。检测到一系列重排，例如倒位和基因丢失，使西番莲成为少数具有复杂叶绿体基因组进化的群体之一。我们还基于所有可用的 cp 基因组进行了系统发育研究，我们的分析表明需要重新考虑该组中某些物种的分类学分类。