普通野生稻全基因组序列图谱的完善、注释分析及数据库构建

Wild rice (Oryza rufipogon) is the most recent ancestral species of Asian cultivated rice (Oryza sativa), and has the nearest phylogenetic relationship with cultivated rice. Compared with the cultivated rice, it contains more genetic diversity. O. rufipogon is considered to be important genetic resource for the improvement of rice varieties, and it has many elite gene alleles which can be introduced to cultivated rice, such as those for drought and cold tolerance, disease resistance. Thus, a high quality genome sequence of O. rufipogon is urgently needed. With high-quality genome sequence and annotation information, researchers will be able to efficiently clone the key domestication genes, improve the cultivated rice varieties, generate new germplasm, and study the mechanism of the origin and domestication of Asian cultivated rice. All of these are of considerable significance to the rice breeding in China, wild rice germplasm research utilization and protection, as well as the national food security...In this study, we will improve and complete the assembly of the genome sequences of the wild rice O. rufipogon W1943. Large insertion mate pair sequences obtained by using second-generation high-throughput sequencing technology will help to build sequence scaffolds and pseudomolecues of O. rufipogon W1943. Then, we will carry on genome-wide annotation of the wild rice genome and comparative sequence analysis with other rice and other species. On this basis, a web-based database of O. rufipogon W1943 will be constructed, which will offer the genome sequence, gene annotation and comparative information and data sharing. Through this study, we will provide new ideas and common pipelines for the sequence assembly and genome annotation of rice genus or similar species, and will provide a platform for rice genetics and molecular breeding.

普通野生稻是与亚洲栽培稻亲缘关系最近的祖先种。与栽培稻相比，普通野生稻具有更高的遗传多样性，蕴藏着大量优异等位基因，如抗旱、耐冷、抗病等。一个高质量的普通野生稻基因组序列图谱，对于高效地进行水稻重要驯化基因的克隆、品种改良和种质创新以及研究栽培稻的起源与驯化机制都有重要的意义。本研究我们将对已经获得的普通野生稻基因组序列进一步拼接完善，利用第二代高通量测序技术获得基因组大插入片段的序列信息并参考已有的栽培稻基因组骨架，构建普通野生稻全基因组序列图谱。之后，我们将对野生稻全基因组进行基因注释和序列比较分析。在此基础上，我们将开发一个公共数据库平台，来提供相关的基因组序列、基因注释及序列比对信息，实现数据共享。本研究将为水稻及类似基因组的全基因组序列组装提供新的思路和通用流程，也可以为水稻的遗传学研究和分子辅助育种等提供一个很好的平台。

普通野生稻是与亚洲栽培稻亲缘关系最近的祖先种。与栽培稻相比，普通野生稻具有更高的遗传多样性，蕴藏着大量优异等位基因，如抗旱、耐冷、抗病等。一个高质量的普通野生稻基因组序列图谱，对于高效地进行水稻重要驯化基因的克隆、品种改良和种质创新以及研究栽培稻的起源与驯化机制都有重要的意义。本研究我们对已经获得的普通野生稻基因组序列进一步拼接完善，利用第二代高通量测序技术获得基因组大插入片段的序列信息并参考已有的栽培稻基因组骨架，构建普通野生稻全基因组序列图谱，得到序列重叠群的N50长度为40.6kb，序列框架图N50长度为219kb。我们还对野生稻全基因组进行基因注释和序列比较分析，在转录组数据的辅助下鉴定了31151个基因。在此基础上，我们开发了一个公共数据库平台，来提供相关的基因组序列、基因注释及序列比对信息，实现数据共享。此外，我们通过群体遗传学研究，发现非洲栽培稻和亚洲栽培稻虽然受到了完全独立的驯化选择，但是有18个的驯化位点却有重合而各自单倍体型却不一样，这表明它们有各自独立的驯化选择作用于相同的基因座位。同时非洲稻与亚洲稻存在着极低频的遗传渐渗。本研究将为水稻及类似基因组的全基因组序列组装提供新的思路和通用流程，也可以为水稻的遗传学研究和分子辅助育种等提供一个很好的平台。