禾本科新基因起源及其功能初探 ——以水稻和竹子为例

	禾本科新基因起源及其功能初探 ——以水稻和竹子为例; Study on the Origin and Function of New Genes in Poaceae—Taking Rice and Bamboo as Examples
	金桂花
导师	章成君
摘要	New genes refer to novel genetic loci that recently originated in the genome, are often species-specific or lineage specific. The emergence of new genes is one of the important factors of genome evolution and genetic differences between species. Since the discovery of the first new gene, the jingwei gene, the research of new genes has become a hotspot. Previous studies have revealed many origin mechanisms of new genes, such as gene duplication, retrotransposition, gene fusion or fission, and de novo, as well as revealed that some new genes play important roles in the development process, reproductive process, biological behavior, and brain development. Most of the research on the origin mechanism and function evolution of new genes focuses on animals, but less such studies in plants. Poaceae is one of the most diverse lineages of plants, with a lot of important cereals and other crops. Poaceae have already had rich genomic resources, which can provide a data base to study the origin and evolution of new genes at different evolutionary time scales. In the Poaceae, Oryza originated ~15 million years ago, and has sequenced 13 genomes. It is an ideal genus for studying the origin mechanism of new genes in a short timescale. Here, we investigated the origin of new genes in the model plant Oryza sativa ssp. japonica ‘Nipponbare’ genome using similarity and synteny analysis between Nipponbare with other 10 closely related Oryza species. We identified a total of 37 specific genes for Nipponbare genome, also called orphan genes, which showed short coding sequence lengths, elevated GC content, and absence of introns. Transposon-mediated and de novo origin are the main mechanisms for the genesis of Nipponbare orphan genes. Interestingly, half of (51%) these identified orphan genes originated by way of a distinctive mechanism that involved the generation of new coding sequences through independent and rapid divergence within the inserted transposable element. Additionally, 22% Nipponbare orphan genes originated from de novo mechanism. In the process of de novo origin, point mutations, insertion/deletion and obtaining the start codon are key mutations that transform ancestor non-coding sequences to coding sequences in Nipponbare. In order to explore whether the functional evolution after the origin of new genes is related to the specific phenotypes and traits of a species or lineage, we performed function researches of new genes on woody bamboos. Compared with other grasses in the Poaceae, woody bamboos have many unique morphological traits, such as highly lignified stems, the fast-growing shoots, and long vegetative growth periods. We sequenced the full-length transcriptome of Bonia amplexcaulis and Olyra latifolia (a herbaceous bamboos) through SMRT (Single Molecular Real-Time Sequence) technology, and obtained 107 598 and 73 457 non-redundant transcripts in B. amplexcaulis and O. latifolia, respectively. Based on the large evolutionary timescale, we downl
	2020-05
文献类型	学位论文
条目标识符	http://ir.kib.ac.cn/handle/151853/74140
专题	昆明植物所硕博研究生毕业学位论文
推荐引用方式 GB/T 7714	金桂花. 禾本科新基因起源及其功能初探 ——以水稻和竹子为例, Study on the Origin and Function of New Genes in Poaceae—Taking Rice and Bamboo as Examples[D],2020.

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