Roquet Cristina, Coissac Éric, Cruaud Corinne, Boleda Martí, Boyer Frédéric, Alberti Adriana, Gielly Ludovic, Taberlet Pierre, Thuiller Wilfried, Van Es Jérémie, Lavergne Sébastien
Laboratoire d'Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France.
Laboratoire d'Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France.
Ann Bot. 2016 Oct 1;118(5):885-896. doi: 10.1093/aob/mcw135.
Background and Aims Plant plastid genomes are highly conserved in size, gene content and structure; however, parasitic plants are a noticeable exception to this evolutionary stability. Although the evolution of parasites could help to better understand plastome evolution in general, complete plastomes of parasites have been sequenced only for some lineages so far. Here we contribute to filling this gap by providing and analysing the complete plastome sequence of Cytinus hypocistis, the first parasite sequenced for Malvales and a species suspected to have an extremely small genome. Methods We sequenced and assembled de novo the plastid genome of Cytinus hypocistis using a shotgun approach on genomic DNA. Phylogenomic analyses based on coding regions were performed on Malvidae. For each coding region present in Cytinus, we tested for relaxation or intensification of selective pressures in the Cytinus lineage compared with autotrophic Malvales. Key Results Cytinus hypocistis has an extremely divergent genome that is among the smallest sequenced to date (19·4 kb), with only 23 genes and no inverted repeat regions. Phylogenomic analysis confirmed the position of Cytinus within Malvales. All coding regions of Cytinus plastome presented very high substitution rates compared with non-parasitic Malvales. Conclusions Some regions were inferred to be under relaxed negative selection in Cytinus, suggesting that further plastome reduction is occurring due to relaxed purifying selection associated with the loss of photosynthetic activity. On the other hand, increased selection intensity and strong positive selection were detected for rpl22 in the Cytinus lineage, which might indicate an evolutionary role in the host-parasite arms race, a point that needs further research.
植物质体基因组在大小、基因含量和结构方面高度保守；然而，寄生植物是这种进化稳定性的一个显著例外。尽管寄生虫的进化总体上有助于更好地理解质体基因组的进化，但到目前为止，仅对一些谱系的寄生虫完整质体基因组进行了测序。在此，我们通过提供并分析 Cytinus hypocistis 的完整质体基因组序列来填补这一空白，Cytinus hypocistis 是锦葵目首个测序的寄生虫，也是一个被怀疑具有极小基因组的物种。方法：我们使用鸟枪法对 Cytinus hypocistis 的基因组 DNA 进行测序并从头组装其质体基因组。基于编码区对锦葵科进行了系统基因组分析。对于 Cytinus 中存在的每个编码区，我们测试了与自养锦葵目相比，Cytinus 谱系中选择压力的放松或增强情况。关键结果：Cytinus hypocistis 具有一个极其不同的基因组，是迄今为止测序的最小基因组之一（19.4 kb），仅含 23 个基因且无反向重复区域。系统基因组分析证实了 Cytinus 在锦葵目中的位置。与非寄生性锦葵目相比，Cytinus 质体基因组的所有编码区呈现出非常高的替换率。结论：推断 Cytinus 中的一些区域处于放松的负选择之下，这表明由于与光合活性丧失相关的纯化选择放松，质体基因组正在进一步缩小。另一方面，在 Cytinus 谱系中检测到 rpl22 的选择强度增加和强烈的正选择，这可能表明在宿主 - 寄生虫军备竞赛中具有进化作用，这一点需要进一步研究。
