买麻藤类植物（Gnetophytes）基因组结构特征与进化调控研究

Exploring the genome structure and evolution will enhance our understandings on the divergent history and evolutionary pattern of extant seed plants. Previously, contrasting genome dynamics were observed between gymnosperms (represented by conifers & Ginkgo) and angiosperms basing on massively parallel revealing of genome diversity. However, recent reports on the similar genome dynamics between Amborella trichopod and Gnetum montanum suggested an exception to above prevailing sayings, which complement the nature of complexity of early seed plants genome evolution than ever. This further keep the ancestral genome features of seed plants in uncertain. To address this, by using of next-generation sequencing platform, we will skim the genomes of gnetophytes with more species included as well as two outgroup species from cycads and ferns, and analyse the data to broadly characterise repeats in those genomes. The reads will be mapped to the reference repeats assembly and compared patterns with small RNA distributions. The genes in RdDM who involved in epigenetic regulation and chromatin remodeling pathways would also be targeted to interrogate the signature of repeat transcription and regulation to test the hypothesis that different epigenetic processes underpin fundamental developmental and genomic differences between gymnosperms and angiosperms. Our efforts would shed new insights into the ancestral genome features of seed plants and derived ones to the subsequent divergent groups. The data could also be extremely valuable for other investigations in seed plant biology as a whole.

探索种子植物基因组的结构特征和进化，能够帮助我们了解现存类群分歧发展的历史，理解种子植物生命演化的终极方式。传统观点推断早期种子植物主要存在两种显著不同的基因组进化方式（以松柏类、银杏为代表的裸子植物和其他被子植物）。然而，近期买麻藤的基因组草图绘制并和无油樟比较分析后对这一观点提出了挑战，意味着这些古老类群基因组进化方式之间的联系比我们想象中更为复杂。本项目拟选择现存种子植物进化研究最具争议的类群——买麻藤类植物（gnetophytes）为主要研究对象，同时补充分析苏铁类和真蕨类代表物种。通过高通量测序技术分别从重复序列组成特征、甲基化水平、小RNA分布类型、RdDM调控通路分析等角度，综合深入揭示买麻藤类植物基因组的进化模型，并尝试对早期种子植物基因组分化和重复序列进化调控机制进行探讨，为我们研究各大分支类群基因组起源演化及多样性发展提供十分重要的理论依据和数据资源。

种子植物基因组演化尤其是裸子植物和被子植物两大支系的基因进化动力学研究是近年来学科热点问题之一。转座子（自主转座和非自主转座）的历史活跃度及在基因组中的积累和消亡对基因组大小起到重要贡献作用。同时，启动子区的转座子插入可能引起编码基因表达和功能修饰，进而加剧物种的多样性分化。现存的裸子植物支系明显经历了古辐射演化、大量灭绝事件、超长的形态停滞和近期局部多样化等复杂历史。本项目以买麻藤类植物为中心，重点调查了裸子植物重复序列消除机制，全基因组加倍分化历史，全基因组甲基化图谱绘制，重要功能基因家族进化等方面内容，系统研究买麻藤类及其他裸子植物基因组进化动力模型,提出早期种子植物祖先可能是存在一定的干扰基因组剧烈增大的机制，而松柏类的‘基因组瘫痪’模型可能仅仅局限于conifer类群内部，是一个后期特化的结果。同时深入解析了百岁兰功能基因组与适应性建立。极大拓展我们探讨植物基因组宏观和微观进化的视角，也为讨论裸子植物的兴衰演替提供了新的理论基础和数据资源。