基于基因组证据探讨古生代起源的卷柏科植物的系统发育与多样性分化

The cosmopolitan Selaginellaceae, with a single genus Selaginella, is one of the largest ancient lineages of lycophytes, and occupies a wide range of habitat regimes. This plant group contains arctic-alpine species, tropical rainforest species, subtropical woodland species, drought-adapted xerophytes, and some notorious resurrection species. The greatest extant species diversity occurs in primary tropical rainforests. Two scenarios are proposed as explanatory hypotheses for the current diversity origination: one is that the main elements of the group might have persisted in similar environments since the Late Paleozoic, the other one is the main ancient elements might be eliminated by multi extinction events since Permian, and the main diversity might originate along with the origin of Angiosperm in Cretaceous as recently revealed in Pteridophytes. To address this scientific question, a well resolved deep relationships of Selaginellaceae is necessary. However, the current multilocus phylogeny could not solve the basal relationships because of the remarkable substitution rate heterogeneity in the family, especially the extremely fast substitution rates in S. sanguinolenta clade and S. sinensis clade. Selaginella is now emerging as a model taxon in evolutionary botany, owing to its long evolutionary history, the key systematic position in vascular plants, and small genome size. Selaginella moellendorffii is the only species with the whole nuclear genome data published in Lycophytes and Pteridophytes, which provides excellent background for constructing the phylogeny using genome data. Phylogenomics based on the high-throughput sequencing and the related analytic algorithms open the avenue to resolve the deep relationship in Selaginellaceae. We will use Target Enrichment Sequencing based on nuclear genomic data of S. moellendorffii and the complete chloroplast genome data to reconstruct the deep phylogenetic relationships of Selaginellaceae, and further to investigate patterns and mechanisms of diversification within the family in the context of climatic and geological oscillations since the Late Paleozoic. Our study will not only gain better understanding of the evolutionary history of Selaginellaceae, but also yield new insights for the conservation and maintenance of the globe plant diversity.

卷柏科Selaginellaceae仅一属，隶属维管植物石松类。卷柏因起源古老、生境迥异及演化地位关键和基因组小等特点，成为进化研究的模式，是石松类和蕨类中唯一有全基因组数据的类群。系统发育证据揭示出现存蕨类植物的多样化发生在被子植物起源之后。现存卷柏的多样性是穿越多次大灭绝适应严酷的环境演化而来，还是在被子植物起源之后辐射分化？有分辨且稳定的系统发育框架是探讨该科学问题的关键。由于属内各分支的进化速率不一致，传统的分子标记因缺乏足够的信息无法解决基部关系，进化速率较快的红枝卷柏支和中华卷柏支的位置无法确定。高通量测序及系统发育基因组学的兴起为解决这一难题打开了通道。本立项将基于核与叶绿体的基因组数据建立卷柏科的系统发育框架；结合各支的习性、生境和丰富的化石记录，采用分子钟估算和多样化分析，重建其多样性的演化历史，探讨二叠纪以来生物大灭绝事件的影响，揭示现存卷柏多样性的形成机制。

卷柏科Selaginellaceae仅一属，隶属维管植物石松类。卷柏因起源古老、生境迥异、演化地位关键和基因组小等特点，成为进化研究的模式。由于其属内各分支的进化速率不一致，传统的分子标记无法解决其基部关系，进化速率较快的红枝卷柏支和中华卷柏支的位置无法确定，导致进化速率异质性的原因更是谜一样的存在。本研究基于转录组测序的核基因组数据与细胞器基因组数据建立了卷柏科稳定的系统发育框架，确定了该属下各疑难种类的系统学位置，深入揭示了细胞器基因进化速率异质性的驱动因素。综合基因流检测，物种网络分化式样和质体基因组系统发育关系，以及形态和染色体证据，本研究提出红枝卷柏群古杂交起源假说。对卷柏科质体和线粒体基因组特殊网状结构的深入解析，以及相关核基因家族的分析，首次在自然界揭示出核基因编码监控细胞器DNA复制重组修复的RRR系统中RecA1&3基因的缺失驱动了该早期登陆植物独特的细胞器基因组结构与序列等特征趋同演化和多样性演化，为理解陆地植物中细胞器特殊结构与序列变异提供了参照，拓展了人类在该领域的认识。