植物线粒体基因组替代速率模式与机制研究

	植物线粒体基因组替代速率模式与机制研究; Study of the substitution rate pattern of plant mitochondrial genomes and the underlying mechanisms
	刘芳
导师	李德铢
摘要	Plant mitochondrial genome is notorious for its variable size, frequent insertions of foreign sequences, and complex structure due to rapid genomic rearrangements. These characteristics make it an ideal genetic system for studying the evolution of genomic complexity. How mitochondrial sequence divergence is still a mystery, especially the evolutionary features among different genes and different genomic regions. Plant mitochondrial genomes have typically low mutation rates, yet it has been found that the synonymous substitution rate in the mitochondrial genome varies by 1-3 orders of magnitude among different lineages. Due to the frequent arrangements, it’s generally difficult to perform genome-wide alignments for plant mitochondrial genomes, especially for non-coding regions, even among closely related species. Thus, it is necessary to investigate the patterns and mechanisms of mitochondrial genome sequence divergence and the relationship between sequence divergence and genomic complexity in plants (Ajugoideae and Frgaria) based on sampling at different evolutionary time scales. The main results of this study are as follows: 1. Generally, the synonymous substitution rate among different genes is quite stable within a genome. Strikingly, Ajuga reptans L. (Lamiaceae) mitochondrial genome showed unprecedented heterogeneity in the synonymous substitution rates among genes. However, the underlying mechanism of the extreme synonymous rate heterogeneity in the Ajuga mitochondrial genome is still unclear. To verify whether the synonymous substitution rate heterogeneity among different genes in the mitochondrial genome is universal, we performed depth sampling in Ajugoideae (diverged ～26 million-years ago). Our results showed that synonymous substitution rate heterogeneity did exist among different genes within a genome in the core species of Ajugoideae, and we also found differences in the timing and magnitude of rate acceleration for particular genes. The fast-evolved genes (dS>0.15) accelerated earlier, while almost all the RNA editing sites were lost. Moderately diverged genes accelerated later and retained relatively higher RNA editing frequency. Nearly all the fast-evolved genes were located in newly formed gene clusters, and the acceleration of synonymous substitution rates correlates with increased guanine–cytosine (GC) content at third codon positions. Therefore, based on all these results we inferred that retroprocessing, repair of ancestral gene clusters after breakage and GC-biased gene conversion may be the main evolutionary forces for the heterogeneity of substitution rates among genes in the mitochondrial genome. 2. The genic regions of mitochondrial genomes have an unusually high level of sequence conservation in plants, but the intergenic regions are hard to be aligned even among close relatives. This may be due to frequent genomic arrangements and/or fast sequence divergence in non-coding regions. Based on the above characteristics, whe
	2021-05
文献类型	学位论文
条目标识符	http://ir.kib.ac.cn/handle/151853/74633
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	刘芳. 植物线粒体基因组替代速率模式与机制研究, Study of the substitution rate pattern of plant mitochondrial genomes and the underlying mechanisms[D],2021.

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