Rearrangement and domestication as drivers of Rosaceae mitogenome plasticity.
Rearrangement and domestication as drivers of Rosaceae mitogenome plasticity.
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重排和驯化是蔷薇科线粒体基因组可塑性的驱动因素
DOI：
10.1186/s12915-022-01383-3
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发表时间：
2022-08-19
期刊：
影响因子：
5.4
通讯作者：
Wu, Jun
中科院分区：
文献类型：
--
作者：
Sun, Manyi;Zhang, Mingyue;Chen, Xuening;Liu, Yueyuan;Liu, Binbin;Li, Jiaming;Wang, Runze;Zhao, Kejiao;Wu, Jun
线粒体是植物细胞的重要组成部分，它的功能是为细胞产生必需的能量。然而，玫瑰科线粒体基因组（mitogenome）的进化和结构尚不清楚。在这项研究中，我们收集了34个蔷薇科有丝分裂基因组，并对这些有丝分裂基因组的基因组变异、重排率和选择信号变异进行了表征。对蔷薇科杏仁核亚科6属和蔷薇亚科5属进行比较分析发现，蔷薇亚科5属有丝分裂基因组中缺失3个蛋白编码基因。在38个蔷薇科有丝分裂基因组中发现了基因组大小与重复序列的正相关。具有高重组频率（bbb50 %）的20个重复提供了主要的有丝分裂基因组亚化学计量构象的证据。在11个属之间，以及梨属、苹果属、Prunus属和Fragaria属内部，鉴定了重排率的差异。基于种群数据，梨有丝分裂基因组的系统发育推断支持亚洲栽培梨的两个不同的母系。根据组装的基因组和群体数据，在选择性扫描中鉴定出pyrus特异性缺失（deld）。DEL-D序列片段最初产生后，它们可能通过同源重组和序列转移在杏仁核中经历了随后的加倍事件；之后，这种变异序列可能已经显著扩展到栽培群体，从而在驯化过程中提高了适应性。本研究分析了蔷薇科有丝分裂基因组在基因含量、基因组大小、重排率和驯化影响等方面的变化，并对其结构变异模式和系统发育关系进行了深入研究。在线版本包含补充材料，可在10.1186/s12915-022-01383-3获得。
The mitochondrion is an important cellular component in plants and that functions in producing vital energy for the cell. However, the evolution and structure of mitochondrial genomes (mitogenomes) remain unclear in the Rosaceae family. In this study, we assembled 34 Rosaceae mitogenomes and characterized genome variation, rearrangement rate, and selection signal variation within these mitogenomes. Comparative analysis of six genera from the Amygdaloideae and five from the Rosoideae subfamilies of Rosaceae revealed that three protein-coding genes were absent from the mitogenomes of five Rosoideae genera. Positive correlations between genome size and repeat content were identified in 38 Rosaceae mitogenomes. Twenty repeats with high recombination frequency (> 50%) provided evidence for predominant substoichiometric conformation of the mitogenomes. Variations in rearrangement rates were identified between eleven genera, and within the Pyrus, Malus, Prunus, and Fragaria genera. Based on population data, phylogenetic inferences from Pyrus mitogenomes supported two distinct maternal lineages of Asian cultivated pears. A Pyrus-specific deletion (DEL-D) in selective sweeps was identified based on the assembled genomes and population data. After the DEL-D sequence fragments originally arose, they may have experienced a subsequent doubling event via homologous recombination and sequence transfer in the Amygdaloideae; afterwards, this variant sequence may have significantly expanded to cultivated groups, thereby improving adaptation during the domestication process. This study characterizes the variations in gene content, genome size, rearrangement rate, and the impact of domestication in Rosaceae mitogenomes and provides insights into their structural variation patterns and phylogenetic relationships. The online version contains supplementary material available at 10.1186/s12915-022-01383-3.
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影响因子：
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作者：
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