基于核基因的蔷薇科系统重建及相关进化生物学研究

Rosaceae is a moderately large family of angiosperms, with about 90 genera and ~3000 species. It includes important fruit and ornamental species, such as peach, plum, apple, pear, strawberry, rose, cherry, and Spiraea. Rosaceae members include herbs, bushes, and trees and are important components of terrestrial ecosystems, providing foods and habitats for birds, mammals, insects and other animals and support the living environments for other plants such as ferns. In recent years, genomes of several Rosaceae species, such as peach, apply, pear and strawberry, have been sequenced, prompting more rapid advances in research of this family. Further studies in several areas in the family depends on clear phylogenetic relationships among Rosaceae members, yet current understanding contains quite many unresolved questions at the level of tribes, genera, and species. Previous work based morphological characters and organellar genes have not provided well-resolved hypothesis largely due to limited information provided by these approaches. In particular, relationships between subfamilies, between tribes, and between some genera are still uncertain. On the other hand, recent advances in sequencing technology have made it feasible to obtained a large number of nuclear gene sequences, thereby promoting angiosperm molecular phylogeny. The applicant of this project has built on the previous experience in molecular evolutionary studies of nuclear gene families and devoted much effort in recent years to investigate effective use of nuclear gene sequences to reconstruct angiosperm phylogeny, with encouraging results reported in recent publications. The aims of this project are to (1) identify nuclear genes for phylogenetic analysis; (2) to use nuclear genes to establish a phylogenetic framework at the levels for subfamily to genera, (3) and to use the new phylogenetic relationships as a foundation for molecular clock estimates, ancestral morphological character reconstruction, gene family evolution and other analyses. It is hoped that the completion of this project and its results will support many aspects of investigation with Rosaceae, from evolutionary biology to improvement of economically important species using gene information from model systems.

蔷薇科是被子植物中相对较大的科，包括约90个属和3000个种。常见的果树和观赏物种，如桃、李、梨、苹果、草莓、玫瑰、梅花、绣线菊等都属于蔷薇科。该科具有草本、灌木和乔木习性，是陆地生态系统的重要组成部分。 近年来桃、李、苹果、梨、草莓等基因组完成了测序，显著促进该科的相关研究。然而，之前基于有限的形态性状和细胞器基因所构建的蔷薇科系统发育关系树，还有很多地方尚不清晰，例如，亚科间、部分族和属间的关系还有待解决。当前新的测序技术为从未测序物种中获得基因序列提供了手段，大大促进了被子植物系统发育的重建。申请人有多年基因分子进化的基础，近年来致力于探索运用以核基因重建被子植物系统的可行性，建立了有效的方法并取得了一些初步成果。本项目拟利用核基因重建蔷薇科在亚科到属层次的系统关系，并进行分子钟、形态性状祖征重建、基因与基因组进化等方面的研究，进而促进蔷薇科进化生物学、比较基因组学等相关研究。

果实是被子植物的重要特征，通过保护和传播种子为被子植物的扩散做出贡献，并为人类和其他动物提供食物，具有许多形态类型和重要的生态与农业意义。蔷薇科植物有3000多种，其果实种类繁多，包括消费者喜爱的肉质桃子、苹果和草莓，以及干燥的瘦果，非常适合研究果实进化。为了解决蔷薇科果实进化等相关问题，我们收集了125个新的转录组和基因组数据集，并鉴定了数百个核基因，以重建一个高度解析的蔷薇科系统发育，我们发现所有亚科和族皆为高度支持的单系。分子钟分析表明，蔷薇科祖先的起源在101.6百万年前。系统基因组学分析为许多全基因组复制（WGD）提供了强有力的证据，支持了苹果族有一个WGD的假设，并揭示了该族肉质果实成员共享的另一个全基因组复制，桃族和其他类群的全基因组复制也得到了高度的支持。果实类型的祖先特征重建支持来自干果祖先的肉质果实的独立起源，包括来自五心皮的聚合蓇葖果的核果（如桃）和梨果（如苹果）的进化，以及来自聚合瘦果的聚合核果（覆盆子和黑莓）。我们最后提出，全基因组复制和古气候变化促进了蔷薇科的水果演化，这为理解果实进化提供了坚实的基础。