自养种子植物IR丢失类群叶绿体基因组进化研究

	自养种子植物IR丢失类群叶绿体基因组进化研究
	王子洵
导师	伊廷双
关键词	比较基因组学，IR丢失，叶绿体基因组，替换速率，结构变异 comparative genomics, plastid genome, inverted repeat (IR), structural variation, substitution rate
摘要	叶绿体是植物细胞的主要特征之一。大多数自养种子植物的叶绿体基因组具有高度保守的四分体结构，包含一个大单拷贝区 (LSC)，一个小单拷贝区 (SSC) 和两个反向重复区 (IRs)。IR丢失是一种非常罕见的现象，目前已有的研究仅在7个自养被子植物分支和2个自养裸子植物分支中发现了IR丢失的现象。在这项研究中，我们新测序了11个叶绿体基因组，并结合GenBank已公布的67个叶绿体基因组，选取所有已报道IR丢失分支的代表性叶绿体基因组及其近缘分支的正常结构的叶绿体基因组 (简称CRCIR) 进行比较基因组学的分析，以探索IR在维持的叶绿体结构和序列进化中的功能。我们发现，与其CRCIR相比，大多数IR丢失物种的叶绿体基因组经历了显著的结构重排、基因丢失和复制、新的小重复序列的积累和同义替换率的加快。然而，我们提出IR丢失不是以上变化的直接促进因素，而是核编码DNA修复基因功能丧失后，叶绿体基因组结构重排和分子进化的加剧的伴随事件。本研究首次综合性研究了种子植物IR丢失类群的叶绿体基因组结构变异和分子进化。本研究的主要结果总结如下： 1. IR丢失物种叶绿体基因组的基本特征豆科的IRLC (Inverted Repeat-Lacking Clade) 分支和Camoensia分支，8个牻牛儿苗科物种, 2个仙人掌科物种和柏类分支丢失了IRA；核果木分支, 2个西番莲科物种，1个棕榈科物种和松科丢失了IRB。所有IR丢失物种叶绿体基因组的长度都显著变短，长度在113,064 bp – 145,625 bp。除Tahina spectabilis外，本研究所有的IR丢失物种的叶绿体基因组具有不同程度的基因和内含子的丢失以及假基因化。丢失或假基因化的基因主要包括accD基因，infA基因，rpl基因，rps基因和ndh基因；内含子丢失主要发生在clpP基因、rps12基因和atpF基因。许多基因复制事件也发生在IR丢失物种中，主要包括8种tRNA基因和5种编码蛋白基因，其中trnI-GAU和trnA-UGC的发生复制的频率最高。 2. IR丢失物种叶绿体基因组的结构特征与其CRCIR相比，大多IR丢失物种具有数量更多和长度更长的散在重复序列，以及数量更少的串联重复序列。全基因组的比对分析显示，原始IR中六个核心基因 (rrn16、trnI-GAU、trnA-UGC、rrn23、rrn4.5和rrn5) 始终保持着相同的顺序和方向。大多数IR丢失物种的叶绿体基因组结构经历了更高程度的重排，IR丢失物种的重排距离为1–12，而其CRCIR的重排距离为0–3。约15%大倒位的两端存在散在重复序列，并且这种散在重复序列的长度与倒位的长度存在显著的正相关。对叶绿体微结构的分析显示，大多数IR丢失物种叶绿体基因组的插入/缺失 (InDels) 频率远大于其CRCIR，是其CRCIR的0.9–3.3倍。 3. IR丢失物种叶绿体基因组的序列进化特征在大多数IR丢失物种中，编码蛋白基因的同义替换速率普遍高于其CRCIR的同义替换速率，平均是其CRCIR的0.7–6.9倍。对蛋白编码基因进行功能分类后，11种功能不同的蛋白编码基因的同义替换速率平均是其CRCIR的0.2–12.0倍。在IR丢失物种中，IR区基因的同义替换率平均是其CRCIR的0.7–24.5倍；是SC区同类基因的0.2–10.8。选择压力的计算分析发现IR丢失的分支整体上处于纯化选择，与背景分支相比，除了棕榈科外，选择强度明显趋于放松，但11种功能不同的蛋白编码基因在9个分支中表现出不同的选择方向和强度。此外，大多数IR丢失物种叶绿体基因组单核苷酸变异 (SNVs) 速率远大于其CRCIR，是其CRCIR的0.7–3.5倍。最后，IR丢失物种全基因组的CG含量显著低于其CRCIR，而编码蛋白基因的GC含量和GC3含量则显著高于其CRCIR。; Plastid is one of the main distinguishing characteristics of the plant cell. The plastid genome (plastome) of most autotrophic seed plants possesses a highly conserved quadripartite structure containing a large single-copy (LSC) and a small single-copy (SSC) region separated by two copies of inverted repeat (IRs). However, the loss of a copy of inverted repeat (IR) is a very rare phenomenon. In this study, we newly sequenced 11 plastomes, along with 67 plastomes from GenBank representing and compering all reported nine IR-lacking lineages and those of their closely related IR-present relatives (CRCIR for short) to explore the function of IR in maintaining plastome structure and sequence evolution in a phylogenetic context. We found the plastomes of most IR-lacking lineages have experienced significant structure rearrangement, gene loss and duplication, accumulation of novel small repeats, and acceleration of synonymous substitution rates in IR-lacking lineages compared with those of their CRCIR. However, instead of a direct promoting factor, we proposed the IR loss should be an accompanying event with increased structure rearrangements and molecular evolution in IR-lacking plastomes following the loss of the function of nuclear-encoded DNA repair genes. We believe our study will contribute an essential effect for plastome structural variation and nucleocytoplasmic co-evolution. The main results of this study are summarized as follows: 1. Plastome Features of IR-lacking Species. The plastomes of the Inverted Repeat-Lacking Clade (IRLC) of Leguminosae, Camoensia of Leguminosae outside IRLC, eight species of Geraniaceae, two species of Cactaceae, the Cupressophyta clade have lost their IRA, while those of the Putranjivoids clade, two species of Passifloraceae, one species of Arecaceae, and Pinaceae have lost their IRB. Relative to those of their CRCIR, the plastome length of the IR-lacking species was much shorter, ranging from 113,064 bp to 145,625 bp. Except for Tahina spectabilis, the other IR-lacking lineages had different degrees of gene or intron loss. The gene loss/ pseudogenization main including accD、infA、rpl gene, rps gene, ndh gene; the gene intron loss including clpP、rps12, atpF. Many gene duplication events also occurred in the IR-lacking species, including eight tRNA genes and five coding-protein genes, among them, trnI-GAU and trnA-UGC have the highest duplication frequency. 2. Plastome Structural Features of IR-lacking Species We observed that most plastomes of IR-lacking species had richer dispersed repeats than those of their CRCIR in both length and quantity apparently but had significantly decreased tandem repeats than those of their CRCIR. Genome-wide comparative analysis showed that the original six genes (rrn16, trnI-GAU, trnA-UGC, rrn23, rrn4.5, and rrn5) in IR always maintained the same order and direction. Most IR-lacking species underwent higher rearrangement comparing those of their CRCIR. The rearrangement distance of IR
语种	中文
	2022-05
学位授予单位	中国科学院大学
文献类型	学位论文
条目标识符	http://ir.kib.ac.cn/handle/151853/75199
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	王子洵. 自养种子植物IR丢失类群叶绿体基因组进化研究[D]. 中国科学院大学,2022.

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