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| 颗粒野生稻与同源四倍体水稻的基因组变异与进化; Genome variation and evolution of Oryza granulata and the autotetraploid cultivated rice | |
| 施聪 | |
| Thesis Advisor | 高立志 |
| Abstract | Polyploidization and the accumulation of transposable elements are the two primary driving forces for the genome expansion, variation and evolution, but the underlying mechanisms remains largely unsolved. The genus Oryza includes more than 20 species with different genome sizes and ploidy levels, representing the largest number of sequenced species in flowering plants. It thus become an ideal study system to examine the basic questions in the the evolutionary biology. In this study, we sequenced, assembled and analyzed the Oryza granulata genome with high repetitive content andas well as high generation autotetraploid O. sativa. We fuether investigated the effects of transposable elements and whole genome duplication on plant genome variation and evolution. O． granulata occupies the basal position of the Oryza phylogeny, and possesses renowned traits that distinguish it from other Oryza species. Because of the large number of repetitive sequences, the genome size of O. granulata is about twice as large as that of cultivated rice. By using Illumina and Hi-C sequencing technologies, we completed the sequencing, assembly and annotation of the O. granulata genome. A total of 736.66 Mb genome sequences were assembled, of which 61.98% were repetitive sequences. Most intact LTR inserted during the last 5 Myr, while the earliest insertion event of the largest LTR family can be traced back to more than 20 Myr ago. This LTR retrotransposon family maintained retrotransposition activities during the evolutionary history, and its continuous large-scale amplification has contributed 28.13% to the genome size. The differential contraction and expansion of gene families related to the resistance and cell wall pathway, among different Oryza species, may provide genetic basis for the adaptability to different ecological habitats. Polyploidization can immediately double the C-value of a plant species, but its effect on genome size may expereince a very long evolutionary process. Through both flow cytometry and k-mer analyses, compared with its diploid parent, the genome size of this autotetraploid O. sativa did not change significantly after 48 selfing generations, but the heterozygosity of genome drastically increased. We assembled the diploid parent and autotetraploid O. sativa genomes. Through reads mapping analysis, we detected 15,786 SNPs, 8,257 indels and 7 SVs in autotetraploid, but failed to observe large-scale genomic variants affecting genome size. We found the correlation between the distribution of SNPs and Indels on the genome, but there is a negative correlation between the distribution and the allele frequency of variations. Several genes that may be greatly impacted by SNPs, were found to involve in chloroplast and photosynthesis, transcription and translation, which may play a role in the adaptation of autotetraploid O. sativa. In this study, we de novo sequenced, assembled and analyzed the O. granulata and high- generation autotetraploid rice. Our |
| 2020-08 | |
| Document Type | 学位论文 |
| Identifier | http://ir.kib.ac.cn/handle/151853/74171 |
| Collection | 昆明植物所硕博研究生毕业学位论文 |
| Recommended Citation GB/T 7714 | 施聪. 颗粒野生稻与同源四倍体水稻的基因组变异与进化, Genome variation and evolution of Oryza granulata and the autotetraploid cultivated rice[D],2020. |
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| File Name/Size | DocType | Version | Access | License | ||
| 施聪-博士毕业论文-施聪f76a7836（13080KB） | 学位论文 | 限制开放 | CC BY-NC-SA | Application Full Text | ||
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