Evolution of Oryza chloroplast genomes promoted adaptation to diverse ecological habitats

First author: Li-Zhi Gao; Affiliations: CAS Kunming Institute of Botany (中科院昆明植物研究所): Kunming, China

Corresponding author: Li-Zhi Gao

The course, tempo and mode of chloroplast genome evolution remain largely unknown, resulting in limited knowledge about how plant plastome gene and genome evolve during the process of recent plant speciation. Here, we report the complete plastomes of 22 closely related Oryza species in chronologically ordered stages and generate the first precise map of genomic structural variation, to our knowledge. The occurrence rapidity was estimated on average to be ~7 insertions and ~15 deletions per Myr. Relatively fewer deletions than insertions result in an increased repeat density that causes the observed growth of Oryza chloroplast genome sizes. Genome-wide scanning identified 14 positively selected genes that are relevant to photosynthesis system, eight of which were found independently in shade-tolerant or sun-loving rice species. psaA seemed positively selected in both shade-tolerant and sun-loving rice species. The results show that adaptive evolution of chloroplast genes makes rice species adapt to diverse ecological habitats related to sunlight preferences.

目前，有关叶绿体基因组演化的速度和模式方面的知识仍然存在较大空白，导致我们对于最近的植物物种分化过程中植物质体基因和基因组是如何演化这一过程了解甚少。本文中，作者报道了22个按物种形成年代排序的近缘稻属物种的完整质体基因组序列，并得到了第一个稻属植物叶绿体基因组结构变异图谱。根据这些叶绿体基因组序列，作者估计了大概每一个百万年大概出现7个插入和15个删除事件。重复序列的删除远低于插入的频率，这导致叶绿体基因组上重复序列的增加，今而使得稻属物种叶绿体基因组的大小不断增加。作者通过全基因组范围上的扫描鉴定了14个受到正向选择的基因，这些基因与光合系统相关，其中八个与耐阴或喜阳水稻物种无关。psaA基因似乎在耐阴和喜阳的水稻物种中均受到了正向选择。本文的研究结果揭示了稻属物种叶绿体基因的适应性演化，标志着稻属物种在不同生态环境下与阳光偏好相关的适应。

通讯：高立志 (http://groups.kib.cas.cn/gbows/glz/)

个人简介：1987-1991年，云南大学，学士；1991-1994年，云南大学，硕士；1994-1997年，中科院植物研究所，博士。

研究方向：主要利用基因组学、生态学和生物信息学等方法手段，研究兴趣涵盖分子进化、理论群体遗传学、分子生态学和保护生物学等诸多领域的一些重要科学问题。

doi: https://doi.org/10.1038/s42003-019-0531-2

Journal: Communications Biology

Published date: July 26, 2019