基于叶绿体基因组的石竹目系统发育基因组学研究

Caryophyllales s.l. contains 37 families, over 800 genera, and about 11, 510 species. It is a large and attractive order in angiosperm. Many special plant groups, such as carnivorous plants, succulent plants, and C4 plants, are all included in it. A series of molecular phylogenetic studies involved Caryophyllales were conducted recently. As revealed in these studies, some families that had not been included in the traditional Caryophyllales s.s. were transferred into it, such as Droseraceae, Polygonaceae, Rhabdodendraceae. Additionally, some large families included in Caryophyllales s.s. were also disintegrated into many smaller families, such as Molluginaceae, Phytolaccaceae, Portulacaceae. To date, however, phylogenetic relationships among some families included in Caryophyllales s.l. are still unresolved and need to be clarified. The phylogenomic study based on chloroplast genomes is proved to be useful in clarifying some amphibolous phylogenetic relationships among angiosperm groups in recent years. In this study, a comprehensive phylogenomic study of Caryophyllales at the family level will be conducted based on the chloroplast genomic data of representatives within this order. For related genomic data, many of them have been obtained in previous study conducted by our research team and could be analyzed directly in this study, and other data for the supplementary representatives of Caryophyllales will be obtained through the next-generation sequencing technique. Results from this study would be important for people in understanding the evolutionary relationships within Caryophyllales more comprehensively and objectively.

石竹目是被子植物中一个既特殊又重要的分支，包含37科，超过800属，约11, 510种，众多食肉植物、多肉植物以及C4植物都包含在其中。近年来涉及石竹目科间系统发育关系的研究很多，其结果使得众多曾被认为与狭义石竹目关系较近或远的类群都被归入其中，狭义石竹目中原有的部分科也被不断拆分。到目前为止，该目之中众多科间系统关系依然不明，这在一定程度上阻碍了人们更加深刻、全面的理解石竹目类群的演化历史。系统发育学与基因组学相结合而产生的系统发育基因组学近年来逐渐兴起，尤其是基于叶绿体基因组的系统发育基因组学，为众多疑难类群系统关系的解决提供了极大帮助。本项目拟在前期工作的基础上，进一步完善对石竹目类群在科水平的取样，通过第二代测序技术（Illumina测序）对取样类群进行叶绿体全基因组测序，并试图从系统发育基因组学的角度来探讨石竹目科间的系统关系，以便更加客观、全面的揭示石竹目类群的演化历史。

石竹目是被子植物中一个起源古老的大分支，包含40科，约12,500种。该目类群几乎存在于所有陆生生境，并占据了众多特殊生境(如高山、干旱荒漠及盐碱地等)，也涉及了众多食肉植物、耐盐植物、多肉植物以及C4植物等特殊类群。然而该目系统发育关系（尤其深层节点）的解决一直以来被认为是一个难题，可能与其经历过快速辐射演化有关。本项目首次完成了对石竹目在科水平的全覆盖取样，并采用叶绿体系统发育基因组学手段获得了一棵系统关系得到高度解析的石竹目系统发育树，澄清了该目之中所存在的众多系统学问题；分化时间估算结果表明石竹目在白垩纪中期约114.4Ma分化出核心类群与非核心类群两个主要分支，并于白垩纪中期阿尔必阶至土伦阶时期（113.0-89.8Ma）与白垩纪/古新世边界附近时期（约66.0Ma）经历过两次明显的快速分化；分子进化分析结果表明该目叶绿体基因组结构变异与其分子进化速率异质性之间存在明显的正相关关系，而部分结构变异可能是某些分支的共衍征；此外，本项目基于广泛的类群取样与分子分化时间估算，进一步揭示出C4植物最早可能在始新世早期至中期就已经出现，这不仅将前人所认为的C4植物最早起源时间提前了至少1千万年，还进一步支持了关于C4植物起源演化与低浓度大气CO2条件之间关系的“碳饥饿假说”；以番杏科多肉类群为研究对象，并结合前人对其他多肉植物类群研究结果，揭示出位于被子植物系统树不同位置的多肉植物类群在中新世中期聚集式的快速物种分化可能是对同时期全球气候变化（如干旱条件的大范围出现）所作出的集体响应。本项目的开展深化了对石竹目类群起源与演化历史的理解，并为今后在该目之中开展分类学及进化生物学等相关领域的研究打下了坚持基础。