利用二代测序和BAC-FISH方法进行8个稻属AA-基因组节段重复的研究

Segmental duplications (SDs) have been recognized to play important roles in both gene and genome evolution in eukaryotes. However, this topic remains poorly studied in plants owing to the limitation of experimental and computational approaches. This project proposes to perform the first systematic and genome-wide analysis of SD events among eight Oryza AA genomes. BAC-FISH method will be first employed to experimentally estimate the unique and duplicated content in the Nipponbare genome. WGAC and NGS based WSSD methodologies will be followed to detect recently duplication sequences across these rice genomes. Combing the qPCR confirmation, dCGH will be used to present global comparisons of SD contents and then determine shared and lineage-specific duplications among these eight genomes. Finally, evolutionary rates of SDs will be estimated along different lineages to better understand the potential contribution of SDs to rice gene and genome evolution. This proposed study would enhance our understanding of the architecture and nature of SDs in rice genomes and build genome-wide fundamental database that is of greatly significance in studying segmental duplication and copy number variation in cultivated rice and wild relatives.

节段重复对真核生物基因和基因组进化具有十分重要的作用。由于受到实验以及计算手段的限制，目前在植物中的研究相对匮乏。本项目拟通过全基因组拼接比较、二代测序全基因组鸟枪法序列检测和数字比较基因杂交芯片的生物信息学分析，辅以BAC-FISH和定量PCR的实验验证，在全基因组尺度上开展稻属8个AA-基因组中节段重复事件的检测与分析；构建Nipponbare参考基因组中的唯一和重复参考区域数据，在全基因组水平上检测年轻节段重复事件，分析8个AA基因组的共享或分支特异的节段重复，估算AA基因组的节段重复发生速率，进而认识其变异和进化的规律。本项目的开展对促进栽培稻及其近缘种中节段重复和拷贝数目变异研究具有十分重要的意义。

节段重复对真核生物基因和基因组进化具有十分重要的作用。随着算法的进步和大量稻属完整基因组数据的发表，使得在稻属中系统研究节段重复成为可能。本项目通过全基因组拼接比较和二代测序全基因组鸟枪法序列检测，辅以定量PCR的实验验证，在全基因组尺度上开展稻属基因组中节段重复事件的检测与分析。WGAC分析粳稻日本晴基因组共获得8474对比对结果满足长度不小于１kb、相似性不小于90％的节段重复，总计30.06Mb的序列发生了节段重复，约占全基因的8.06%；利用SEDEF对稻属10个基因组进行了节段重复检测, 结果表明，稻属基因组中有29.55 ~ 95.15Mb不等的节段重复。三种栽培稻粳稻，籼稻，非洲栽培稻的节段重复分别1.5倍，2.6倍，2.4倍高于其野生近缘种普通野稻，一年生野稻和短舌野稻。稻属AA-BB组各基因组的节段重复都主要集中在7.84 ~ 8.94 Mya爆发，早于稻属AA-BB分化时间，有约8000~14000的基因收到节段重复的影响，增加了拷贝数目。WSSD分析结果显示平均每个稻属AA基因组有2.4%的SD (>20kb)覆盖，SD形成的新基因在与信号转导、细胞调控、生殖发育、核酸结合等功能类型中显著富集，尤其是对植物抗性具有重要影响，可能在物种的适应性进化中发挥了积极作用。基于上述数据我们构建了稻属基因组节段重复和拷贝数变异的数据库。本项目的开展对促进栽培稻及其近缘种中节段重复和拷贝数目变异研究具有十分重要的意义。